http://cni.su.domains/wiki/api.php?action=feedcontributions&feedformat=atom&user=LaimabCNI Wiki - User contributions [en]2026-10-30T09:49:51ZUser contributionsMediaWiki 1.45.3http://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59546Getting Started2026-10-29T23:43:43Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation date will be held on Thursday, November 19, 9:00 -10:30 AM.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the next new users session on Thursday, November 19, 2026, will be posted here soon ''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59545Getting Started2026-10-06T22:45:13Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation date will be held on Thursday, October 29, 9:00 -10:30 AM.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the next new users session on Thursday, October 29, 2026, is here - https://docs.google.com/forms/d/e/1FAIpQLSeRsJtbx9Wc_HlJlK6rYt8wDF_1sDOhQedW1oY-fpr8-3A20g/viewform?usp=header ''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59544Getting Started2026-10-01T22:01:20Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation date will be held on Thursday, October 29, 9:00 -10:30 AM.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the next new users session on Thursday, October 29, 2026, will be posted soon -''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59543Getting Started2026-09-09T00:05:23Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation date will be held on Thursday, October 1, 9:00 -10:30 AM.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the next new users session on Thursday, October 1, 2026, is here - https://docs.google.com/forms/d/e/1FAIpQLSfd6pXTvGqASyj7O_vSTTw6d9RTOCBMOJIAMv0AUA5keMypdg/viewform?usp=header .''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59542Getting Started2026-09-09T00:05:04Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation date will be held on Thursday, October 1, 9:00 -10:30 AM.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the next new users session on Thursday, October 1, 2026, is here https://docs.google.com/forms/d/e/1FAIpQLSfd6pXTvGqASyj7O_vSTTw6d9RTOCBMOJIAMv0AUA5keMypdg/viewform?usp=header .''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59541Getting Started2026-09-09T00:04:27Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation date will be held on Thursday, October 1, 9:00 -10:30 AM.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the next new users session on Thursday, October 1, 2026, is posted https://docs.google.com/forms/d/e/1FAIpQLSfd6pXTvGqASyj7O_vSTTw6d9RTOCBMOJIAMv0AUA5keMypdg/viewform?usp=header .''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59540Getting Started2026-09-04T01:44:52Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation date will be posted soon.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the next new users session will be posted soon.''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59539Getting Started2026-09-04T01:44:28Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation date will be posted soon.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the next new users session will be posted soon''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59538Getting Started2026-08-20T23:10:26Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday September 3, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the next new users session on Thursday September 3, 2026, is here - <br />
https://docs.google.com/forms/d/e/1FAIpQLSdG2ME1CLYof8mmk9FBpp2qhqrFqEqwlntAAxUgkzhpw4EWjA/viewform?usp=header''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59537Getting Started2026-08-14T00:13:58Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday September 3, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the next new users session on Thursday September 3, 2026, will be posted here soon''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59536Getting Started2026-08-14T00:11:36Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday August 13, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the next new users session on Thursday September 3, 2026, will be posted here soon''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59535Getting Started2026-08-06T22:39:29Z<p>Laimab: /* Billing Policies */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday August 13, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the Thursday August 13, 2026, is here - https://docs.google.com/forms/d/e/1FAIpQLSc61FTtavCkEBPacRiiVg7Q6STY6cu9VMHbSo8utaAsaCcHoQ/viewform?usp=header''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday.<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59534Getting Started2026-08-06T22:38:58Z<p>Laimab: /* Billing Policies */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday August 13, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the Thursday August 13, 2026, is here - https://docs.google.com/forms/d/e/1FAIpQLSc61FTtavCkEBPacRiiVg7Q6STY6cu9VMHbSo8utaAsaCcHoQ/viewform?usp=header''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 are:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59533Getting Started2026-08-06T22:38:20Z<p>Laimab: /* Billing Policies */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday August 13, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the Thursday August 13, 2026, is here - https://docs.google.com/forms/d/e/1FAIpQLSc61FTtavCkEBPacRiiVg7Q6STY6cu9VMHbSo8utaAsaCcHoQ/viewform?usp=header''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 will be:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday<br />
<br />
'''Rates for scanning effective September 1, 2026 - August 31, 2027 will be:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $550/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $448/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $448/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $126/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $126/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
Note: Holiday Weekends include the adjoining Sat/Sun when a Holiday falls on a Friday or Monday<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59532Getting Started2026-08-05T19:35:09Z<p>Laimab: /* Setting up a CNI account for research studies */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday August 13, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the Thursday August 13, 2026, is here - https://docs.google.com/forms/d/e/1FAIpQLSc61FTtavCkEBPacRiiVg7Q6STY6cu9VMHbSo8utaAsaCcHoQ/viewform?usp=header''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who would like to receive the invoice notice for this grant each month in addition to the project owner and the PI. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 will be:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59531Getting Started2026-08-05T19:31:14Z<p>Laimab: /* Setting up a CNI account for research studies */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday August 13, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the Thursday August 13, 2026, is here - https://docs.google.com/forms/d/e/1FAIpQLSc61FTtavCkEBPacRiiVg7Q6STY6cu9VMHbSo8utaAsaCcHoQ/viewform?usp=header''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> Project PI (Name, Email, SUNetID)<br />
<li> Project owner (Name, Email, SUNetID) Further information is here - https://cni.su.domains/new-cni-scheduling-policy/ <br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who will be receiving the invoice notice for this grant each month in addition to the project owner. The invoice contains the listing of all the bookings to the grant. This can be either the finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 will be:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59530Getting Started2026-08-05T19:24:19Z<p>Laimab: /* Setting up a CNI account for research studies */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday August 13, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the Thursday August 13, 2026, is here - https://docs.google.com/forms/d/e/1FAIpQLSc61FTtavCkEBPacRiiVg7Q6STY6cu9VMHbSo8utaAsaCcHoQ/viewform?usp=header''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person or persons, who will be receiving the invoice notice for this grant each month. The invoice contains the listing of all the bookings to the grant. This can be either the PI, finance manager for the grant, or any other designated person for these funds. With the current calendar system multiple people can receive the invoice.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 will be:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59529Getting Started2026-07-23T22:33:49Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday August 13, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the Thursday August 13, 2026, is here - https://docs.google.com/forms/d/e/1FAIpQLSc61FTtavCkEBPacRiiVg7Q6STY6cu9VMHbSo8utaAsaCcHoQ/viewform?usp=header''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person, who will be receiving the invoice notice for this grant each month. The invoice contains the listing of all the bookings to the grant. This can be either the PI, finance manager for the grant, or any other designated person for these funds. Please note that only one person can be set up in the system to receive the invoice. The invoice e-mail can, however, be forwarded to others to additionally to review if needed.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 will be:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59528Getting Started2026-07-16T23:08:18Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday August 13, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the Thursday August 13, 2026, will be posted shortly''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person, who will be receiving the invoice notice for this grant each month. The invoice contains the listing of all the bookings to the grant. This can be either the PI, finance manager for the grant, or any other designated person for these funds. Please note that only one person can be set up in the system to receive the invoice. The invoice e-mail can, however, be forwarded to others to additionally to review if needed.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 will be:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59527Getting Started2026-07-16T22:40:03Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
<br />
<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
<br />
=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
<br />
*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
<br />
*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
<br />
<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
<br />
''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
<br />
Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
<br />
<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
<br />
<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
<br />
===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday July 16, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
<br />
'''The registration form for the Thursday August 13, 2026, will be posted shortly''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
<br />
<br />
Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
<br />
===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
<br />
===Late night scan sessions approval policy===<br />
<br />
Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
<br />
== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
<br />
Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
<br />
== Setting up a CNI account for research studies ==<br />
<br />
To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person, who will be receiving the invoice notice for this grant each month. The invoice contains the listing of all the bookings to the grant. This can be either the PI, finance manager for the grant, or any other designated person for these funds. Please note that only one person can be set up in the system to receive the invoice. The invoice e-mail can, however, be forwarded to others to additionally to review if needed.<br />
</ul><br />
<br />
The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
<br />
== Scheduling Policies ==<br />
<br />
'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
<br />
We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
<br />
The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
<br />
The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
<br />
'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
<br />
If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
<br />
'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
<br />
Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
<br />
Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
<br />
Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
<br />
Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
<br />
'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
<br />
To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
<br />
We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
<br />
'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
<br />
Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
<br />
== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
<br />
'''Rates for scanning effective September 1, 2025 - August 31, 2026 will be:'''<br />
<br />
8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
<br />
6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
<br />
8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
<br />
8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
<br />
8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
<br />
EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
<br />
'''Cancellation Policies'''<br />
<br />
See above<br />
<br />
== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Getting_Started&diff=59526Getting Started2026-07-02T19:37:25Z<p>Laimab: /* CNI New User Orientation Session Registration Forms */</p>
<hr />
<div>The Stanford Center for Cognitive and Neurobiological Imaging ('''CNI''') research facility is designed to reflect the experimental needs of our human neuroimaging community. The core instrument is a research-dedicated 3T MRI scanner. To support the wide variety of human experimental methods from our community, the scanner is integrated with a range of experimental equipment. This includes MR compatible visual displays, audio presentation equipment, and an MR-compatible EEG system. There is an MRI simulator to provide subjects, particularly children, with training. Several testing rooms are available in the suite to help people who are collecting surveys, using TMS, or obtaining behavioral measures. See the [[MR Hardware]] page for more details.<br />
<br />
If you would like an introductory tour of the facility please email [mailto:laimab@stanford.edu Laima Baltusis] or call her office phone (5-8382).<br />
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<br />
== User Access/Onboarding & Training ==<br />
<br />
The Stanford Center for Cognitive and Neurobiological Imaging (CNI) Committee uses the internationally accepted recommendations from the American College of Radiology in establishing the general rules pertaining to safe operation of research MRI facilities.<br />
<br />
All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.<br />
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=== Access/Onboarding ===<br />
<br />
As of September 2025 new CNI users must complete the following three step onboarding process.<br />
*'''Step 1. ''' The first step of the on-boarding process is to complete the Canvas course: CNI User Training, Link here - (https://canvas.stanford.edu/enroll/DLBL8L) The CNI Canvas course must be completed prior to attending the in-person orientation outlined in the Step 2 below. <br />
:The Canvas course consists of high level summary of important information related to working at an MRI facility. There is a quiz at the end of each module that needs to be completed before proceeding to the next module. There will be a code provided in the final Canvas module that is required to register for the in-person orientation session.<br />
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*'''Step 2. ''' A tour of the facility, and key safety and operations policies will be reviewed at an in-person orientation session. These sessions are typically held every four weeks on Thursdays at 9-10:30AM. ''' The Registration link for the next scheduled session is found in "CNI New User Orientation Session Registration Forms" section below.'''<br />
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*'''Step 3. ''' The final step for on-boarding is completion of a post orientation session assignment. A link to this assignment will be emailed following the in-person session to those who have attended the in-person session. New users are allowed approximately one week to complete this assignment. After completing the assignment, user badges will be added to the CNI access list. Users are contacted during this process only if there is an issue with adding their Stanford badge. Once a user’s badge is added to the CNI access list they will be able to use the Lenel card readers located at all CNI doors and at entrances of Building 420, which are locked during off hours.<br />
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<br />
New users will also be automatically added to the cni-mrusers@lists.stanford.edu mailing list as well as the Stanford CNI Slack workspace. These are the mailing list and communication channels used by CNI to send technology and administrative updates to CNI users. The mailing list can be subscribed to or unsubscribed to as needed at the Stanford mailman website https://uit.stanford.edu/service/mailinglists/tools , and Slack channel can be administered through the Slack application or website interface https://uit.stanford.edu/service/slack .<br />
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''In Summary:'' Access to CNI is a privilege. It is important for users to maintain a healthy respect for the instrumentation as failure to do so can lead to injury, possibly life-threatening. Users also need to be good citizens and be respectful of others. Finally, users must be able to effectively instruct and manage their research participants, particularly those new to MRI technology.<br />
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Any questions regarding the on-boarding process should be directed to the CNI facility manager, Laima Baltusis (email: laimab@stanford.edu) <br />
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<br />
Access status to CNI is organized into three categories:<br />
<ul><br />
<li> '''Level 1: Safety Trained User'''. Level 1 investigators may enter the magnet room to assist with scans. Level 1 investigators must have passed Safety training . They cannot schedule or operate the scanner. They must work with Level 2 and 3 investigators. </li><br><br />
<li> '''Level 2: Apprentice Operator'''. Level 2 operators may enter the Magnet room to assist setting up the equipment, instructing and positioning volunteer subjects. A Level 2 investigator may only operate the MRI scanner under the supervision of Level 3 personnel.</li><br><br />
<li> '''Level 3: Operator'''. Level 3 operators may run the MRI Scanner when CNI staff members are not present and they may supervise Level 1 and Level 2 personnel. Level 3 investigators must have accumulated experience at Level 2, and then have passed a hands-on certification test administered by the CNI Facility Manager. As Level 3 users are mentors and teachers to Level 1 and Level 2 users, the certification exam has been created to demonstrate the ability of the new Level 3 user to instruct other users in correctly setting up and positioning volunteers, setting up and using scanning protocols relevant to their area of research, archiving data. and leaving the scanner ready for the next users. Level 3 operators are given full privileges to the facility and can enter the facility at any time </li><br />
</ul><br />
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<br />
'''Note - Users who complete the onboarding process described above are classified as Level 2 users. For those users interested in a promotion to a Level 3 user status, please contact the CNI Facilty Manager via email to make arrangements for a Level 3 certification session.'''<br />
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===CNI New User Orientation Session Registration Forms===<br />
New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI. <br />
<br />
'''The next CNI new user orientation will be on Thursday July 16, 2026, 9:00AM to 10:30AM at CNI.''' CNI is located in the basement of the Psychology Department, 450 Jane Stanford Way, Building 420, Rooms 61-76. <br />
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'''The registration form for the Thursday July 16, 2026, session is here - https://docs.google.com/forms/d/e/1FAIpQLScjKy-2eej71borYd2XiPJJEyT2_Gt5VZO6o8zvFyY8jOvLww/viewform?usp=header ''' Please notate the date and time of this orientation session in your calendars as upon registering for this session there is no additional confirmation e-mail sent out. Please arrive on time and ring the door bell when you arrive for the orientation session at CNI.<br />
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Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions.<br />
(1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo<br />
(2) https://www.youtube.com/watch?v=vIQaGt_fkkw<br />
The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.<br />
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===CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing===<br />
For those groups that are doing Urine-based testing approved in their Stanford IRB the following steps must be completed to be CLIA Certificate of Waiver compliant [https://www.cdc.gov/lab-quality/php/waived-tests/index.html]<br />
#The PI's must complete the verification form [https://forms.gle/QGV4CjYg7jnDKZ1h9], which stipulates the following - I am completing this form to verify that my team and I will be performing CLIA-waived urine test at the CNI facility for our IRB protocols. All current and new study personnel will be trained by me to perform urine testing according to the [[Media:CNI_SOPP.pdf|CNI Standard Operating Procedures (SOP)]]. I am responsible for the adherence to the CNI SOP. My team will be providing all necessary materials and supplies needed to the performance of the urine testing. If there is a urine spill during the testing procedures I will be responsible for any cleaning fees that might occur because of the urine spill.<br />
#All team members of the group must read the [[Media:CNI_-_Urine_Test_-_SOP.pdf | SOP for urine testing at CNI]]<br />
#All team members of the group must take the quiz for urine testing after reviewing the SOP document [https://forms.gle/6xcwrt3ptszxynmE7]<br />
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===Late night scan sessions approval policy===<br />
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Research groups scanning at night between 10PM and 7AM must meet with the CNI Facility Manager prior to booking time for such sessions. The Facility Manager will discuss the logistics of their late night sessions and address all the important safety issues during these scans. Meeting topics will include discussion of the experience level of the scanning team, backup support for technical issues during the scan sessions, and participant support before and after the scan session.<br />
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== IRB Approval for Project ==<br />
Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval. <br />
* General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at [http://humansubjects.stanford.edu Human Subjects Research web sites]. <br />
* There are also detailed [[IRB | instructions for modifying existing IRB protocols]]. <br />
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Researchers must provide a copy (pdf) of the IRB approval to the CNI Facility Mananger. Researchers should also provide a copy of all IRB renewal letters as needed during the project duration. The PI for the project must make sure that the protocols list all personnel who will be conducting the MRI research.<br />
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== Setting up a CNI account for research studies ==<br />
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To start a research study requires setting up a funded grant that will be charged for the scans in the CNI scheduler. To setup a project, Please e-mail the following information to the CNI Facility Manager [mailto:laimab@stanford.edu].<br />
<br />
<ul><br />
<li> Full project title (ex. Neural Basis of Visual Pattern Appearance)<br />
<li> Funding source (ex. NIH, NSF)<br />
<li> PTA assigned to this project<br />
<li> Grant (PTA) Expiration Date<br />
<li> IRB approval letter<br />
<li> Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).<br />
<li> A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.<br />
<li> Name, e-mail, and SUnetID of the person, who will be receiving the invoice notice for this grant each month. The invoice contains the listing of all the bookings to the grant. This can be either the PI, finance manager for the grant, or any other designated person for these funds. Please note that only one person can be set up in the system to receive the invoice. The invoice e-mail can, however, be forwarded to others to additionally to review if needed.<br />
</ul><br />
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The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.<br />
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== Scheduling Policies ==<br />
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'''Overview:''' All scanner time is booked via the [https://stanford-cni.calpendo.com CNI on-line scheduling system]. Only researchers who have completed Level 2 training can make bookings.<br />
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We ask users to all commit together to only scheduling scan time when they actually have a confirmed need. Our experience is that the user demand as evidenced in actual paid-for scan time is that only about 50% of regular daytime hours is used on average and it is even less than that for off-peak hours. <br />
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The scheduler software does not enforce an as-needed scheduling approach. Rather, we have cancellation policies in place that charge for late cancellations as well as the possibility of restricting advance booking access for users that have an excessive number of cancellations.<br />
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The scanner can be booked in increments of 30-minute slots beginning on the hour or 30 minutes into the hour. When booking time, please avoid leaving single 30-minute slots idle between your time and any immediate neighbors. <br />
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'''Tiered Advance Booking Policy:''' Certain time periods in the calendar are reserved (blocked out for booking) based on the amount of time ahead. In brief,<br />
* '''Short Term''' - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.<br />
* '''Mid Term''' - Monday, Friday, Sunday (whole days except for Friday 2PM-6PM for Short Term reservation) are reserved for Mid Term bookings and will be available 8 weeks in advance.<br />
* '''Long Term''' - Tuesday, Wednesday, Thursday, Saturday (whole days except for Tuesday 8AM-12PM for Short Term reservation) are reserved for Long Term bookings and will be available 16 weeks in advance.<br />
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If you have exceptional study requirements that require booking further in advance than the 16-week period, please email your request together with some justification to the CNI facility manager. We will review and accommodate as possible. <br />
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'''Protocol Development Policy:''' The CNI provides PIs the option to book a small amount of uncharged scan time under “Protocol Development”. The purpose of this scan time is to establish and test protocol settings and to ensure any stimulus presentation and scan synchronization are working. The protocol development time used by a PI, or their research assistants should be on the order or 2-5 hours with a maximum of 10 hours for each new grant. Please note that research studies frequently benefit by using protocol development time occasionally throughout the lifetime of a grant--such as when evaluating a new software implementation of a stimulus task--and so PIs are encouraged to husband their protocol development time carefully. <br />
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Under no circumstances are data acquired during protocol development to be used as research product. Accounting rules require that research data must be derived from time charged against a funded grant. <br />
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Protocol development time should be used for establishing specific parameters and validating workflow for already developed technologies. It should in general not be used for technology development, or any other purpose that would be deemed very investigational in nature. In rare cases, a researcher may wish to take advantage of technology new to CNI but otherwise proven on other GE MRI systems. In these instances, PIs should consult with CNI staff if more protocol development time will be permitted. <br />
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Protocol development time has lower scheduling priority than funded research time. As such, users may not book protocol development time more than 48 hours in advance during daytime hours (8am-6pm), and no more than 5 days in advance for off-peak hours. Users who have received CNI Innovation Grants or Seed Funding are not to use protocol development time for their development. ALL scan time for the innovation grant purposes is to be booked under the Seed Funding grant. <br />
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Available protocol development hours can be tracked with the "Run Reports" tool in the CNI scheduler to prevent overspending grants. The "Run Reports" tool is located at the top of the CNI scheduler page in the "Select an Action" drop-down menu next to the date field. Please contact the CNI Facility Manager if you need help in using this tool.<br />
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'''Late Cancellation Policy:''' The late cancellation deadline is 2 weeks before the scheduled time. A late cancellation fee (10% of the cancelled time) will be charged unless the cancelled time is (a) replaced by a funded study or (b) a CNI study (scan time reserved by CNI staff). Principal Investigators should note that cancellation fees may not be allowed against some sponsored projects depending on the sponsor's restrictions in which case the PI should make sure cancellations fees are booked against an unrestricted account.<br />
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To promote lab accountability we exclude all subject-related justifications: subject no-show, subject illness, inability to be scanned (e.g. size, claustrophobia) for waiving the 10% late cancellation fee. This will result in some late cancellation charges for which the PI had no control, but we expect these occurrences to be relatively infrequent. We hope that by charging individual labs rather than by distributing the costs amongst all labs, we will increase user accountability. <br />
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We will not charge cancellation fees, nor count as cancellation time should a scan be cancelled due to CNI service center hardware or software malfunction. In such events, the CNI facility manager should promptly be notified of the malfunction if not already aware. Please note this does not include the malfunction or unavailability of any non-standard hardware, software or materials. <br />
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'''Cancellation limits:''' Booking and cancellation statistics will be compiled each billing cycle (calendar month) for each PI. If a PI group member cancels a funded study, no matter whether it is a late or early cancellation, any slot that eventually goes without being replaced by another funded or CNI study will add to the total cancellation time allotted to that PI. If the total canceled time in a billing cycle is more than 20% of the funded time used by that PI, the CNI will review the situation with the PI and adjust future bookings and limit advance booking access if needed. <br />
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Our intent is to discourage overbooking slots before having a confirmed need. For example, we wish to discourage booking time for a Monday from 9-11am several months in advance and then cancelling this slot only to book a time 2-½ weeks in advance for an open slot Monday 1-3pm. Adjusting the funding source of a slot is not considered a cancellation.<br />
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== Billing Policies ==<br />
Scanner time is compiled from the web-based scheduling system and charged on a monthly basis. The CNI Facility Manager sends e-mail invoices (either to the PI or other designated staff) and usage summaries (to those who have booked time during the month) at the beginning of each month containing all the hours scanned for the previous month and the PTA's used. All users must verify that the information is correct and send a request for changes by the date indicated in the invoice or usage summary cover letter, whichever has been received. If the CNI Facility Manager has not heard back from a researcher by the designated date, the charges will be considered correct and the grants (PTA's) will be charged by the end of the month. Information about cancellations for that month will be included in a separate invoice.<br />
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'''Rates for scanning effective September 1, 2025 - August 31, 2026 will be:'''<br />
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8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour<br />
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6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour<br />
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8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour<br />
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8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour<br />
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8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour<br />
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EEG usage has no charge currently (see CNI staff for more info)<br />
<br />
<br />
Our five-year-budget plan currently includes an annual 3% raise in hourly scan rates beginning September 1 each fiscal year. We emphasize that this is a plan. Rate adjustments will continue to be reviewed by the Advisory Board and the Research Administration Policy and Compliance staff, and will need to stay within Service Center guidelines.<br />
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'''Cancellation Policies'''<br />
<br />
See above<br />
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== User Etiquette ==<br />
<br />
<strong>Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:</strong><br />
<br />
&nbsp;<br />
<ol><br />
<li><b>Please show up for scan time that you have booked, and start and stop your scan session on time.</b><br />
<ul><br />
<li>If your scan is running late please contact the CNI staff to determine the best course of action. Given how busy the scanner is, any overtime may impact the next group.</li><br />
<li>Please cancel any time that you will not be able to utilize as soon as possible, so that other researchers can use that time. Please also do not forget to cancel any mock scanner or testing rooms bookings, so that other users can have access to those rooms. </li><br />
<li>Please book your scans with valid grants.</li><br />
<li>Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>After your scan please return all supplies and equipment to where they should be so that the MRI suite is ready for the next scanning group to use.</b><br />
<ul><br />
<li>Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.</li><br />
<li>Be careful not to misplace or throw away smaller but important items such as memory foam pads, MRI lenses, and tape dispensers. Keep track of these as you use them and put them away in their labelled boxes.</li><br />
<li>The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.</li><br />
<li>Do not put MRI lenses into the wrong storage slots. This delays the next group trying to fit a participant with the correct set of lenses. If you are starting to run short on time someone from CNI can help you to finish putting things away.</li><br />
<li>If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.</li><br />
</ul><br />
</li><br />
<br><br />
<li><b>Do not leave trash, empty coffee cups, water bottles and empty food containers in the control room or reception area for the next users or for CNI staff to clean up.</b><br />
<ul><br />
<li>After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.</li><br />
<li>Food consumption is discouraged at CNI. We have eradicated past pest problems (silver fish, cockroaches) with various remedies and would like to continue to be pest free.</li><br />
<li>If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.</li><br />
<li>Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.</li><br />
<li>Ink stains, coffee stains, and food stains on furniture, counters and floors are difficult to clean. If an accident occurs please let staff know as possible.</li><br />
</ul><br />
</li><br />
</ol><br />
<br />
<br />
<br />
To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form [https://forms.gle/upDcti3PxeKQZNbq6 Etiquette Form].</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59525Spectro2026-06-26T01:57:00Z<p>Laimab: /* 1.4.1 High Order Shimming for MRSI */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
=='''1.2 Spectroscopy Literature'''==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
<br />
==='''1.3.1 Current CNI spectroscopy sequences'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser prototocol examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
=='''1.4 Tools for Spectroscopy Data Acquisitions'''==<br />
<br />
<br />
==='''1.4.1 High Order Shimming for MRSI'''===<br />
<br />
<br />
High Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming workflow procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
==='''1.4.3 Extracting voxel prescription information retrospectively'''===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
=='''1.5 Processing of sLASER SVS and MRSI data'''==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
=='''1.6 Legacy and Other Spectroscopy Sequences'''==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
=='''1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences'''==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= '''2. Miscellaneous Historical Information''' =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59524Spectro2026-06-26T01:56:37Z<p>Laimab: /* 1.4.1 High Order shimming for MRSI */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
=='''1.2 Spectroscopy Literature'''==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
<br />
==='''1.3.1 Current CNI spectroscopy sequences'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser prototocol examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
=='''1.4 Tools for Spectroscopy Data Acquisitions'''==<br />
<br />
<br />
==='''1.4.1 High Order Shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming workflow procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
==='''1.4.3 Extracting voxel prescription information retrospectively'''===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
=='''1.5 Processing of sLASER SVS and MRSI data'''==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
=='''1.6 Legacy and Other Spectroscopy Sequences'''==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
=='''1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences'''==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= '''2. Miscellaneous Historical Information''' =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59523Spectro2026-06-26T01:55:28Z<p>Laimab: /* 1.3.2 sLaser Prototocol examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI) */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
=='''1.2 Spectroscopy Literature'''==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
<br />
==='''1.3.1 Current CNI spectroscopy sequences'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser prototocol examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
=='''1.4 Tools for Spectroscopy Data Acquisitions'''==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming workflow procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
==='''1.4.3 Extracting voxel prescription information retrospectively'''===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
=='''1.5 Processing of sLASER SVS and MRSI data'''==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
=='''1.6 Legacy and Other Spectroscopy Sequences'''==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
=='''1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences'''==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= '''2. Miscellaneous Historical Information''' =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59522Spectro2026-06-26T01:53:25Z<p>Laimab: /* 1.4.1 High Order shimming for MRSI */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
=='''1.2 Spectroscopy Literature'''==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
<br />
==='''1.3.1 Current CNI spectroscopy sequences'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
=='''1.4 Tools for Spectroscopy Data Acquisitions'''==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming workflow procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
==='''1.4.3 Extracting voxel prescription information retrospectively'''===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
=='''1.5 Processing of sLASER SVS and MRSI data'''==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
=='''1.6 Legacy and Other Spectroscopy Sequences'''==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
=='''1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences'''==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= '''2. Miscellaneous Historical Information''' =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59521Spectro2026-06-26T01:52:11Z<p>Laimab: /* 1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI) */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
=='''1.2 Spectroscopy Literature'''==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
<br />
==='''1.3.1 Current CNI spectroscopy sequences'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
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[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
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[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
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[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
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[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
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[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
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==='''1.3.2 sLaser Prototocol examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
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An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
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{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
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==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
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===='''1.3.3.1 T1'''====<br />
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Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
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[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
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===='''1.3.3.2 Single Voxel'''====<br />
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An example of single voxel of the ACC region<br />
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After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
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[[File:SVS-GE-Table-2.png|none|1000px]]<br />
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Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
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[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
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Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
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[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
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Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
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[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
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Advanced tab coronal and sagittal views only (Figure 4)<br />
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[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
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===='''1.3.3.3 2D MRSI'''====<br />
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Example of Right Subcortical MRSI<br />
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After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
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[[File:MRSI-GE-Table.png|none|1000px]]<br />
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Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
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Details tab with coronal and sagittal views only (Figure 6)<br />
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[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
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Advanced tab coronal and sagittal views only (Figure 7)<br />
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[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
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Advanced tab coronal and sagittal views only (Figure 8)<br />
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[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
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=='''1.4 Tools for Spectroscopy Data Acquisitions'''==<br />
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==='''1.4.1 High Order shimming for MRSI'''===<br />
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Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
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Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
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==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
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(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
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(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
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(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
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(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
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==='''1.4.3 Extracting voxel prescription information retrospectively'''===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
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To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
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=='''1.5 Processing of sLASER SVS and MRSI data'''==<br />
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Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
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[[File:Wiki-FlowChart.png|none|1000px]]<br />
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2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
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3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
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MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
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Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
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=='''1.6 Legacy and Other Spectroscopy Sequences'''==<br />
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Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
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{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
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References<br />
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[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
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[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
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[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
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[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
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[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
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[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
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[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
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=='''1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences'''==<br />
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CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
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[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
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'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
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{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
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|}<br />
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'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
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If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
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MEGA-PRESS results will continue to be in the analyses tab.'''<br />
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[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
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{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
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References from the Gannet web site include:<br />
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Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
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Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
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Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
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The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
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An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
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Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
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|}<br />
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{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
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= '''2. Miscellaneous Historical Information''' =<br />
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[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59520Spectro2026-06-26T01:51:45Z<p>Laimab: /* 1.3.1 Current CNI spectroscopy protocols */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
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=='''1.1 Overview'''==<br />
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'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
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'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
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Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
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Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
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Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
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Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
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Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
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Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
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Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
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=='''1.2 Spectroscopy Literature'''==<br />
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==='''1.2.1 Websites'''===<br />
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'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
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To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
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==='''1.2.2 Books'''===<br />
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[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
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'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
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The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
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==='''1.2.3 Papers'''===<br />
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'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
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'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
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"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
<br />
==='''1.3.1 Current CNI spectroscopy sequences'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
=='''1.4 Tools for Spectroscopy Data Acquisitions'''==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
==='''1.4.3 Extracting voxel prescription information retrospectively'''===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
=='''1.5 Processing of sLASER SVS and MRSI data'''==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
=='''1.6 Legacy and Other Spectroscopy Sequences'''==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
=='''1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences'''==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= '''2. Miscellaneous Historical Information''' =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59519Spectro2026-06-26T01:48:36Z<p>Laimab: /* 1.4.3 Extracting voxel prescription information retrospectively */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
=='''1.2 Spectroscopy Literature'''==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
=='''1.4 Tools for Spectroscopy Data Acquisitions'''==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
==='''1.4.3 Extracting voxel prescription information retrospectively'''===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
=='''1.5 Processing of sLASER SVS and MRSI data'''==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
=='''1.6 Legacy and Other Spectroscopy Sequences'''==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
=='''1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences'''==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= '''2. Miscellaneous Historical Information''' =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59518Spectro2026-06-26T01:46:21Z<p>Laimab: /* 2. Miscellaneous Historical Information */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
=='''1.2 Spectroscopy Literature'''==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
=='''1.4 Tools for Spectroscopy Data Acquisitions'''==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
=='''1.5 Processing of sLASER SVS and MRSI data'''==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
=='''1.6 Legacy and Other Spectroscopy Sequences'''==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
=='''1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences'''==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= '''2. Miscellaneous Historical Information''' =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59517Spectro2026-06-26T01:45:41Z<p>Laimab: /* 1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
=='''1.2 Spectroscopy Literature'''==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
=='''1.4 Tools for Spectroscopy Data Acquisitions'''==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
=='''1.5 Processing of sLASER SVS and MRSI data'''==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
=='''1.6 Legacy and Other Spectroscopy Sequences'''==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
=='''1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences'''==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= 2. Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59516Spectro2026-06-26T01:45:19Z<p>Laimab: /* 1.6 Legacy and Other Spectroscopy Sequences */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
=='''1.2 Spectroscopy Literature'''==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
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=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
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==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
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'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
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[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
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[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
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[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
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[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
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[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
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[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
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==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
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An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
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{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
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==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
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===='''1.3.3.1 T1'''====<br />
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Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
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[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
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===='''1.3.3.2 Single Voxel'''====<br />
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An example of single voxel of the ACC region<br />
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After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
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[[File:SVS-GE-Table-2.png|none|1000px]]<br />
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Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
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[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
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Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
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[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
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Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
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[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
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Advanced tab coronal and sagittal views only (Figure 4)<br />
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[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
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===='''1.3.3.3 2D MRSI'''====<br />
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Example of Right Subcortical MRSI<br />
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After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
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[[File:MRSI-GE-Table.png|none|1000px]]<br />
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Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
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Details tab with coronal and sagittal views only (Figure 6)<br />
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[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
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Advanced tab coronal and sagittal views only (Figure 7)<br />
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[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
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Advanced tab coronal and sagittal views only (Figure 8)<br />
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[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
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=='''1.4 Tools for Spectroscopy Data Acquisitions'''==<br />
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==='''1.4.1 High Order shimming for MRSI'''===<br />
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Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
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Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
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==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
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(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
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(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
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(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
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(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
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===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
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To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
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=='''1.5 Processing of sLASER SVS and MRSI data'''==<br />
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Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
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[[File:Wiki-FlowChart.png|none|1000px]]<br />
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2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
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3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
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MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
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Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
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=='''1.6 Legacy and Other Spectroscopy Sequences'''==<br />
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Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
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{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
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References<br />
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[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
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[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
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[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
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[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
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[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
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[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
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[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
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==1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
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CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
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[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
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'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
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{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
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|}<br />
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'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
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If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
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MEGA-PRESS results will continue to be in the analyses tab.'''<br />
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[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
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{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
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References from the Gannet web site include:<br />
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Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
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Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
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Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
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The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
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An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
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Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
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{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
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= 2. Miscellaneous Historical Information =<br />
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[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59515Spectro2026-06-26T01:44:53Z<p>Laimab: /* 1.5 Processing of sLASER SVS and MRSI data */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
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=='''1.1 Overview'''==<br />
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'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
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'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
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Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
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Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
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Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
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Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
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=='''1.2 Spectroscopy Literature'''==<br />
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==='''1.2.1 Websites'''===<br />
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'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
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==='''1.2.2 Books'''===<br />
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[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
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The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
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==='''1.2.3 Papers'''===<br />
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'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
=='''1.4 Tools for Spectroscopy Data Acquisitions'''==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
=='''1.5 Processing of sLASER SVS and MRSI data'''==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==1.6 Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= 2. Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59514Spectro2026-06-26T01:44:06Z<p>Laimab: /* 1.4 Tools for Spectroscopy Data Acquisitions */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
=='''1.2 Spectroscopy Literature'''==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
=='''1.4 Tools for Spectroscopy Data Acquisitions'''==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==1.5 Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==1.6 Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= 2. Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59513Spectro2026-06-26T01:42:57Z<p>Laimab: /* 1.3 Spectroscopy Data Acquisition Methods at CNI */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
=='''1.2 Spectroscopy Literature'''==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
=='''1.3 Spectroscopy Data Acquisition Methods at CNI'''==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==1.4 Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==1.5 Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==1.6 Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= 2. Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59512Spectro2026-06-26T01:42:21Z<p>Laimab: /* 1.2 Spectroscopy Literature */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
=='''1.2 Spectroscopy Literature'''==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==1.4 Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==1.5 Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==1.6 Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= 2. Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59511Spectro2026-06-26T01:41:48Z<p>Laimab: /* 1.1 Overview */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
=='''1.1 Overview'''==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
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[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
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[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
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==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
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<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
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==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
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===='''1.3.3.1 T1'''====<br />
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Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
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<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
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===='''1.3.3.2 Single Voxel'''====<br />
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An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
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<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
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Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
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[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
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Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
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[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
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Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
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[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
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Advanced tab coronal and sagittal views only (Figure 4)<br />
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[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
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===='''1.3.3.3 2D MRSI'''====<br />
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Example of Right Subcortical MRSI<br />
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After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
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<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
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Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
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Details tab with coronal and sagittal views only (Figure 6)<br />
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[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
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Advanced tab coronal and sagittal views only (Figure 7)<br />
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[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
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Advanced tab coronal and sagittal views only (Figure 8)<br />
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[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
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==1.4 Tools for Spectroscopy Data Acquisitions==<br />
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==='''1.4.1 High Order shimming for MRSI'''===<br />
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<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
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Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
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==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
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(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
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(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
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(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
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===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
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To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
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==1.5 Processing of sLASER SVS and MRSI data==<br />
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Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
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<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
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2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
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3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
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Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
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==1.6 Legacy and Other Spectroscopy Sequences==<br />
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Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
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<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
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[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
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[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
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[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
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[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
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==1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
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<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
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[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
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'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
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{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
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'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
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If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
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[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
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<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
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References from the Gannet web site include:<br />
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Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
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Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
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The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
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An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= 2. Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59510Spectro2026-06-26T01:41:22Z<p>Laimab: /* 1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI */</p>
<hr />
<div>='''1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI'''=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==1.4 Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==1.5 Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==1.6 Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= 2. Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59509Spectro2026-06-26T01:39:53Z<p>Laimab: /* Miscellaneous Historical Information */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==1.4 Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==1.5 Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==1.6 Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= 2. Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59508Spectro2026-06-26T01:39:30Z<p>Laimab: /* Spectroscopy Data Processing Tools at CNI for legacy sequences */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==1.4 Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==1.5 Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==1.6 Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==1.7 Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59507Spectro2026-06-26T01:38:25Z<p>Laimab: /* Legacy and Other Spectroscopy Sequences */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==1.4 Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==1.5 Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==1.6 Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59506Spectro2026-06-26T01:38:04Z<p>Laimab: /* Processing of sLASER SVS and MRSI data */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==1.4 Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==1.5 Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59505Spectro2026-06-26T01:37:44Z<p>Laimab: /* Extracting voxel prescription information retrospectively */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==1.4 Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===1.4.3 Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59504Spectro2026-06-26T01:37:05Z<p>Laimab: /* Prescribing a rotated voxel */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==1.4 Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''1.4.2 Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59503Spectro2026-06-26T01:36:40Z<p>Laimab: /* High Order shimming for MRSI */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==1.4 Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''1.4.1 High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59502Spectro2026-06-26T01:36:18Z<p>Laimab: /* Tools for Spectroscopy Data Acquisitions */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==1.4 Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59501Spectro2026-06-26T01:35:09Z<p>Laimab: /* 2D MRSI */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''1.3.3.3 2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59500Spectro2026-06-26T01:34:39Z<p>Laimab: /* Single Voxel */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''1.3.3.2 Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
===='''2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59499Spectro2026-06-26T01:34:15Z<p>Laimab: /* T1 */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''1.3.3.1 T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
===='''Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
<br />
<br />
<br />
===='''2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59498Spectro2026-06-26T01:33:41Z<p>Laimab: /* Screen shots of parameters and CV's for a typical spectroscopy protocol */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''1.3.3 Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
<br />
<br />
<br />
<br />
===='''Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
<br />
<br />
<br />
===='''2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
<br />
<br />
<br />
'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
<br />
|}<br />
<br />
'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
<br />
If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
<br />
MEGA-PRESS results will continue to be in the analyses tab.'''<br />
<br />
<br />
[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
<br />
References from the Gannet web site include:<br />
<br />
Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
<br />
Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
<br />
The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
<br />
An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
<br />
Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
<br />
|}<br />
<br />
{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
<br />
= Miscellaneous Historical Information =<br />
<br />
[[Historical Information]]</div>Laimabhttp://cni.su.domains/wiki/index.php?title=Spectro&diff=59497Spectro2026-06-26T01:32:40Z<p>Laimab: /* sLaser Prototocol Examples for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI) */</p>
<hr />
<div>=1. MRS in Neurosciences: In-vivo spectroscopy methods and applications at CNI=<br />
<br />
==1.1 Overview==<br />
<br />
'''Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The interest of measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements continues to grow. CNI continues to support the research of its user community by providing state-of-the art data acquisition and state-of-the-art data management and analysis capabilities for in-vivo spectroscopy. Through collaborative efforts the special interest spectroscopy group at CNI has enabled education, participated in experimental design, and guided analyses and interpretation of results.'''<br />
<br />
'''Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities as recommended by the at-large MRS community. Through collaborative efforts, the special interest spectroscopy group at CNI has enabled education and participated in experimental design, guided analyses, and interpretation of results.''' <br />
<br />
Link to most recent spectroscopy blog post is here - https://cni.su.domains/recent-advances-in-in-vivo-spectroscopy-at-cni/<br />
<br />
<br />
Examples of studies at the CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as addiction, pain, depression, and various forms of dementia. Collaborative studies performed at CNI include:<br />
<br />
Method applications (DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654),<br />
<br />
New method developments (Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47),<br />
<br />
Participation in multi-site spectroscopy studies (Hui et al. Frequency drift in MR spectroscopy at 3T, NeuroImage 241(2021) 118430),<br />
<br />
Voxel placement method development (James H. Bishop, Andrew Geoly, Naushaba Khan, Claudia Tischler, Ruben Krueger, Poorvi Keshava, Heer Amin, Laima Baltusis, Hua Wu, David Spiegel, Nolan Williams, Matthew D. Sacchet Real-Time Semi-Automated and Automated Voxel Placement using fMRI Targets for Repeated Acquisition Magnetic Resonance Spectroscopy, Journal of Neuroscience Methods 392 (2023) 109853).<br />
<br />
Data analysis and validation methods (Hurd RE, Gu M, Okamura K, Shibata M, Ono Y, Haidar M, Riemer RK, Hanley FL, Spielman DM. Detection of elevated succinate in brain during circulatory arrest in a piglet model: A 3T 1H MR spectroscopy study. Magnetic Resonance in Medicine 93(5) 1874 (2025))<br />
<br />
Focal 2D MRSI: a robust alternative method for metabolite measurement in challenging deep gray matter brain structures, Donna E. Murray, Meng Gu, Laima Baltusis, Hua Wu, Ralph E. Hurd, Troy A. Murray, Saché M. Coury, Daniel M. Spielman, - to be published -<br />
<br />
==1.2 Spectroscopy Literature==<br />
<br />
<br />
==='''1.2.1 Websites'''===<br />
<br />
'''An excellent spectroscopy resource website is https://mrshub.org/ '''<br />
'''The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).'''<br />
<br />
To analyze the data from MEGA-PRESS experiments Gannet can be used. It is a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here http://www.gabamrs.com/<br />
<br />
==='''1.2.2 Books'''===<br />
<br />
[http://onlinelibrary.wiley.com/book/10.1002/9780470512968;jsessionid=5537E205EAAA89060F0EE654DB7CAD21.f02t01 In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library]<br />
<br />
'''The recently updated 3rd edition: [https://onlinelibrary.wiley.com/doi/book/10.1002/9781119382461 In Vivo NMR Spectroscopy, 3rd Edition, Author: Robin de Graaf, Wiley Online Library]'''<br />
<br />
The 2014 book [http://www.sciencedirect.com/science/book/9780124016880 Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications]<br />
<br />
==='''1.2.3 Papers'''===<br />
<br />
'''A very comprehensive collection of MRS papers have been published in 2021 in a special issue of NMR in Biomedicine - Advanced methodology for in vivo magnetic resonance spectroscopy - https://doi.org/10.1002/nbm.4504''' <br />
<br />
'''Key points abstracted from the Editorial page of this special issue are summarized here and the most relevant papers to the CNI spectroscopy tools are in bold type:'''<br />
<br />
"For this Special Issue, these 13 topics of advanced methodology in clinical and pre-clinical MRS have been reviewed by multi-institutional groups of authors, and a consensus overview of the most relevant facts and recommendations has been assembled for each of them. They now appear along with proffered review papers from single or smaller groups of authors and proffered research papers with a broad range of topics covering latest research results."<br />
<br />
"The consensus articles that lay out the current state of the art and present recommendations for use in terms of several aspects of advanced MRS were written by teams of prime experts in these fields, where the teams had been instructed to self-organize under consideration of the width of the field and respecting geographic and gender aspects. However, limiting the number of authors to a size that allows productive interchange, it was not possible to include all potential expert authors as based on their publication records. Thus, it was decided for many of the papers to include a larger group of experts as a collaborator group to receive input from and to cross-check and support the experts' recommendations. None of these papers that include “experts' consensus recommendations” in their titles are to be considered as typical white papers where traditionally detailed advice on exact measurement protocols and parameters is given. This had not been our intention because the topics covered are of an advanced nature and hence inherently still touch many work-in-progress frontiers. Furthermore, all topics covered still present challenges in terms of identifying overall optimal methods as approved by the community as a whole. In contrast, the recommendations in these papers were arrived at as a consensus opinion among the specific group of experts without claiming validity for the whole community, and also with the possibility to vary the weight of advice from hints to more strongly encouraged recommendations."<br />
<br />
"The experts' consensus papers are targeted primarily at two types of readers: on one hand, the non-MRS-specialized MR physicist or high-end user (eg a clinician or neuroscientist) commissioned with the task of implementing state-of-the-art MRS methods for a specific research or clinical target that go beyond the vendor-provided MRS techniques; on the other hand, MRS specialists who try to grasp the background and current advances in topics with which they are not intimately familiar and to provide starting points to them when they consider incorporating them in their research or technical developments."<br />
<br />
The 13 topics for the experts' consensus recommendation papers include two general papers followed by articles on specific topics in advanced MRS grouped in three fields of research.<br />
<br />
'''*Two papers on the general background of methodology and publishing in MRS.'''<br />
<br />
'''**Terminology and concepts in MRS Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: background and experts' consensus recommendations. NMR Biomed. 2020;e4347. https://doi.org/10.1002/nbm.4347 The first article of the special issue has the broad scope of presenting the basic framework of concepts and terminology in the field of in vivo MRS, which will hopefully help to standardize the language used and thus prevent misunderstandings in future publications in the field. It also contains suggestions for the use of abbreviations and provides references to the origin of concepts, methods and common abbreviations that at times appear without reference.''' <br />
<br />
'''**Reporting standards Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations. NMR Biomed. 2021;e4484. https://doi.org/10.1002/nbm.4484 The second paper of a more general scope is concerned with minimal reporting guidelines for papers that include MRS data, whether published in MR literature or even more so in clinical journals. It has been a common experience for many of the experienced MRS methods experts to find essential details about employed MRS methods missing from published papers or in manuscripts submitted for review. Hence, Lin et al have assembled a list of items that the authors, who are all experienced referees, suggest should be covered in the methods section of future papers including MRS results. For ease of use, the paper also contains a checklist that could be submitted along with a manuscript as supplemental material or as a way to check that all vital information is provided in the methods section.'''<br />
<br />
'''Checklist''' from https://doi.org/10.1002/nbm.4484<br />
<br />
MRI system description<br />
<br />
a. Field strength, eg 1.5 T, 3 T, 7 T, 9.4 T<br />
<br />
b. Manufacturer, eg General Electric, Philips, Siemens, Toshiba<br />
<br />
c. Model, eg General Electric Signa HD/X/T/de, Optima MR450/MR450W, Discovery MR750/MR750W, Signa Premier; Siemens Biograph mMR,Magnetom, Aera, Espree, Prisma, Skyra, Trio, Verio, Magnetom 7 T, Terra; Phillips Ingenia 1.5 T S, 3 T X/S, Elition 3 T X/S, Ambition 1.5 T X/S, Achieva 1.5 T/3 T. Software version, eg Siemens VB17A, VD19, VE11C; General Electric 12x-24x; Phillips Release 5, 5.1 (R1-3), 5.6, 6<br />
<br />
d. RF coils used (nuclei, number of channels, type, body part), eg 1H, 31P, 13C, 31P-1H; type, eg head/neck, torso, knee; if not manufacturer, design, eg<br />
butterfly, quadrature etc<br />
<br />
e. Additional hardware, eg shim inserts, dielectric pads<br />
<br />
<br />
Acquisition parameters in full<br />
<br />
i. Pulse sequence, eg spin-echo, point resolved spectroscopy (PRESS), stimulated echo acquisition mode (STEAM), semi-LASER, etc.<br />
<br />
ii. Location of volume(s) of interest (VOI(s)), eg posterior cingulate gyrus, M. tibialis anterior, internal capsule of prostate, etc. A figure that displays the VOI on anatomic images is recommended.<br />
<br />
iii. Nominal VOI size [cm3, mm3], eg 40 × 40 × 10 mm3.<br />
<br />
iv. Repetition time (TR), echo time (TE) [ms, s]; if STEAM, mixing time (TM).<br />
<br />
v. Total number of excitations per spectrum.<br />
<br />
vi. Additional sequence parameters, eg<br />
<br />
i. Spectral width [Hz, kHz] and number of data points<br />
<br />
ii. Frequency offset (if any)<br />
<br />
iii. If magnetic resonance spectroscopic imaging (MRSI): specification of two-dimensional (2D) or three-dimensional (3D) spatial mapping, field of view (FOV), matrix size, acceleration factor, sampling/reconstruction method (eg parallel imaging, compressed sensing, spatial spectral encoding, etc), nominal and effective (ie final) voxel volumes, flip angles for fast MRSI<br />
<br />
iv. For multidimensional acquisitions, number of encodings in the second spectral dimension<br />
<br />
v. For editing methods, editing pulse information including pulse shape, bandwidth and offset frequency<br />
<br />
vi. For multinuclear sequences: details of decoupling or polarization transfer sequences and related parameters.<br />
<br />
<br />
<br />
f. Water suppression method (and any other suppression methods used, eg lipid suppression, outer volume suppression).<br />
<br />
g. Shimming method, reference peak used for assessing shim performance, and thresholds for “acceptance of shim” chosen.<br />
<br />
h. Triggering method, if used (respiratory, peripheral, cardiac triggering, including device used and delays).<br />
<br />
i. Frequency and motion correction methods, if used (prospective or retrospective, external tracker or navigator method).<br />
<br />
<br />
Spectral quantification methods and parameters<br />
<br />
a. Software package used to reconstruct and analyze the MRS data including MR manufacture software (eg General Electric PROBE, Siemens Syngo, or Phillips SpectroView) and/or third-party software packages (eg LCModel, jMRUI, TARQUIN, SIVIC, INSPECTOR, FID-A, BrainSpec, MIDAS, GANNET)<br />
<br />
b. Deviations in processing steps from quoted reference or product defaults<br />
<br />
c. Quantitative output measures<br />
<br />
d. Quantification references and assumptions, model fitting assumptions<br />
<br />
<br />
Quality assurance. Studies must include the following<br />
<br />
a. Reported variables (SNR, linewidth, and description of how they were obtained)<br />
<br />
b. Data exclusion criteria<br />
<br />
c. Other quality measures from fitting software are also recommended (eg standard deviation (SD), Cramér-Rao lower bound (CRLB)), and/or the<br />
robustness of the measures gained (repeatability measures if known)<br />
<br />
d. Figure showing representative spectra<br />
<br />
<br />
<br />
'''*Four papers dealing with commonly used MRS acquisition sequences and processing methods.''' <br />
<br />
'''**Advanced single-voxel MRS Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2020;e4236. https://doi.org/10.1002/nbm.4236''' <br />
<br />
'''**Advanced neuro-MRSI Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2020;e4309. https://doi.org/10.1002/nbm.4309'''<br />
<br />
'''**Spectral editing Choi IY, Andronesi OC, Barker P, et al. Spectral editing in 1H magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4411. https://doi.org/10.1002/nbm.4411'''<br />
<br />
'''**Processing and quantification Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4257. https://doi.org/10.1002/nbm.4257'''<br />
<br />
<br />
*Three papers related to MRS techniques that are critical to ensure the quality of data.<br />
<br />
**Water and lipid suppression Tkac I, Deelchand D, Dreher W, et al. Water and lipid suppression techniques for advanced 1H MRS and MRSI of the human brain: experts' consensus recommendations. NMR Biomed. 2020;e4459. https://doi.org/10.1002/nbm.4459 <br />
<br />
**B0 shimming Juchem C, Cudalbu C, de Graaf RA, et al. B0 shimming for in vivo magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2020;e4350. https://doi.org/10.1002/nbm.4350<br />
<br />
**Motion correction Andronesi OC, Bhattacharyya PK, Bogner W, et al. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2020;e4364. https://doi.org/10.1002/nbm.4364<br />
<br />
<br />
*Four papers appertaining to special targets of MRS studies.<br />
<br />
** Macromolecular signals and ways to accommodate them in1H MR brain spectra Cudalbu C, Behar KL, Bhattacharyya PK, et al. Contribution of macromolecules to brain 1H MR spectra: experts' consensus recommendations. NMR Biomed. 2020;e4393. https://doi.org/10.1002/nbm.4393 <br />
<br />
**1H MRS of skeletal muscle Krssak M, Lindeboom L, Schrauwen-Hinderling V, et al. Proton magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4266. https://doi.org/10.1002/nbm.4266<br />
<br />
**31P MRS of skeletal muscle Meyerspeer M, Boesch C, Cameron D, et al. 31P magnetic resonance spectroscopy in skeletal muscle: experts' consensus recommendations. NMR Biomed. 2020;e4246. https://doi.org/10.1002/nbm.4246<br />
<br />
**Specifics for MRS methods in preclinical applications Lanz B, Abaei A, Braissant O, et al. Magnetic resonance spectroscopy in the rodent brain: experts' consensus recommendations. NMR Biomed. 2020;e4325. https://doi.org/10.1002/nbm.4325<br />
<br />
<br />
<br />
*This special issue also includes authoritative reviews of the current state of <br />
<br />
**fast MRSI methodology Bogner W, Otazo R, Henning A. Accelerated MR spectroscopic imaging—a review of current and emerging techniques. NMR Biomed. 2020;e4314. https://doi.org/10.1002/nbm.4314 <br />
<br />
**hyperpolarized 13C MRI and MRS Crane JC, Gordon JW, Chen H-Y, et al. Hyperpolarized 13C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2020;e4280. https://doi.org/10.1002/nbm.4280<br />
<br />
**functional MRS in rodents Just N. Proton functional magnetic resonance spectroscopy in rodents. NMR Biomed. 2020;e4254. https://doi.org/10.1002/nbm.4254<br />
<br />
<br />
*Fifteen proferred original research contributions complete this special issue. They cover latest research results in terms of novel advanced MRS methodology or its application. The methodology addresses issues in<br />
<br />
'''**standardization - Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2019;e4218. https://doi.org/10.1002/nbm.4218'''<br />
<br />
**diffusion MRS Lundell H, Ingo C, Dyrby TB, Ronen I. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR Biomed. 2020;e4304. https://doi.org/10.1002/nbm.4304 Hanstock C, Beaulieu C. Rapid acquisition diffusion MR spectroscopy of metabolites in human brain. NMR Biomed. 2020;e4270. https://doi.org/10.1002/nbm.4270 Genovese G, Marjańska M, Auerbach EJ, et al. In vivo diffusion-weighted MRS using semi-LASER in the human brain at 3 T: methodological aspects and clinical feasibility. NMR Biomed. 2020;e4206. https://doi.org/10.1002/nbm.4206<br />
<br />
**editing Deelchand DK, Marjańska M, Henry P-G, Terpstra M. MEGA-PRESS of GABA+: influences of acquisition parameters. NMR Biomed. 2019;e4199. https://doi.org/10.1002/nbm.4199 Ma RE, Murdoch JB, Bogner W, Andronesi O, Dydak U. Atlas-based GABA mapping with 3D MEGA-MRSI: cross-correlation to single-voxel MRS. NMR Biomed. 2020;e4275. https://doi.org/10.1002/nbm.4275 Bell T, Boudes ES, Loo RS, et al. In vivo Glx and Glu measurements from GABA-edited MRS at 3 T. NMR Biomed. 2020;e4245. https://doi.org/10.1002/nbm.4245<br />
<br />
**novel acquisition techniques Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR Biomed. 2019;e4196. https://doi.org/10.1002/nbm.4196 Posse S, Sa De La Rocque Guimaraes B, Hutchins-Delgado T, et al. On the acquisition of the water signal during water suppression: high-speed MR spectroscopic imaging with water referencing and concurrent functional MRI. NMR Biomed. 2020;e4261. https://doi.org/10.1002/nbm.4261<br />
<br />
**processing techniques Francischello R, Geppi M, Flori A, Vasini EM, Sykora S, Menichetti L. Application of low-rank approximation using truncated singular value decomposition for noise reduction in hyperpolarized 13C NMR spectroscopy. NMR Biomed. 2020;e4285. https://doi.org/10.1002/nbm.4285 Marjańska M, Terpstra M. Influence of fitting approaches in LCModel on MRS quantification focusing on age-specific macromolecules and the spline baseline. NMR Biomed. 2019;e4197. https://doi.org/10.1002/nbm.4197 Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR Biomed. 2019;e4129. https://doi.org/10.1002/nbm.4129<br />
<br />
**reported applications probe the feasibility of novel uses of advanced MRS methods van Houtum Q, Mohamed Hoesein FAA, Verhoeff JJC, et al. Feasibility of 31P spectroscopic imaging at 7 T in lung carcinoma patients. NMR Biomed. 2019;e4204. https://doi.org/10.1002/nbm.4204 Rioux JA, Hewlett M, Davis C, et al. Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing. NMR Biomed. 2019;e4241. https://doi.org/10.1002/nbm.4241 Peeters TH, van Uden MJ, Rijpma A, Scheenen TWJ, Heerschap A. 3D 31P MR spectroscopic imaging of the human brain at 3 T with a 31P receive array: an assessment of 1H decoupling, T1 relaxation times, 1H-31P nuclear Overhauser effects and NAD+. NMR Biomed. 2019;e4169. https://doi.org/10.1002/nbm.4169<br />
<br />
<br />
<br />
<br />
Several new publications here on advanced editing techniques - http://www.gabamrs.com/<br />
<br />
<br />
''Voxel placement publication''<br />
<br />
[https://doi.org/10.1002/mrm.27203 AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy] Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203<br />
<br />
<br />
''New open-source processing package currently under evaluation -'' <br />
<br />
[https://doi.org/10.1016/j.jneumeth.2020.108827 Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data] Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods<br />
Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827 <br />
<br />
<br />
''Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques''<br />
<br />
[https://doi.org/10.1002/nbm.4314 Accelerated MR spectroscopic imaging—a review of current and emerging techniques] Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314<br />
<br />
==1.3 Spectroscopy Data Acquisition Methods at CNI==<br />
<br />
==='''1.3.1 Current CNI spectroscopy protocols'''===<br />
<br />
'''For all spectroscopy research projects CNI actively follows the recommended best practices from the ISMRM (International Society for Magnetic Resonance in Medicine) Spectroscopy Study Group and recently published experts’ consensus recommendations (1,2,3,4,5,6) . Currently the semi-LASER sequence is the ISMRM consensus method, particularly for multi-site 3T MRS studies(5). We have, therefore, transitioned studies at CNI from previously recommended sequences (PRESS, as example) to the sLASER sequence (a GE product sequence) for both short TE single voxel and new focal 2D MRSI studies.'''<br />
<br />
[1] Choi I., Kreis R. Advanced methodology for in vivo magnetic resonance spectroscopy, NMR in Biomedicine, 2021;34:e4504<br />
<br />
[2] Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton MRS of the brain: review and recommendations. Magn Reson Med. 2019;82:527-550<br />
<br />
[3] Maudsley AA, Andronesi OC, Barker PB, et al. Advanced magnetic resonance spectroscopic neuroimaging: experts' consensus recommendations. NMR Biomed. 2021;34:e4309<br />
<br />
[4] Oz G, Deelchand DK, Wijnen JP, et al. Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: experts' consensus recommendations. NMR Biomed. 2021;34:e4236<br />
<br />
[5] Deelchand DK, Berrington A, Noeske R, et al. Across-vendor standardization of semi-LASER for single-voxel MRS at 3T. NMR Biomed. 2021;34:e4218.<br />
<br />
[6] Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR Biomed. 2021;34:e4257.<br />
<br />
==='''1.3.2 sLaser Prototocol Examples on CNI scanner for single voxel spectroscopy (SVS) and focal MR spectroscopic imaging (focal-MRSI)'''===<br />
<br />
<br />
<br />
An example spectroscopy protocol (CNI-spectro-2025) is located in the CNI "Other" tab on the CNI 3T UHP scanner with examples of the sLaser sequence for both single voxel and 2D focal MRSI applications. The table of the typical sequences and accompanying screen shots is shown below.<br />
<br />
<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Description and General Information<br />
|-<br />
|Localizer<br />
|<br />
|-<br />
|T1<br />
|High Resolution T1 with automatic reformatting for sagittal, coronal, and axial views for voxel placement.<br />
|-<br />
|HOS (High Order Shimming)<br />
|The high order shimming sequence is performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage<br />
|-<br />
|Voxel Placement<br />
|Sequence for rotated voxel placement (details described in separate section further below)<br />
|-<br />
|sLASER<br />
|This sequence is now a GE product sequence (PROBE-sl) and is consistent with the ISMRM Experts' consensus recommendations for this sequence. MRS and MRSI at 3T or higher have technical challenges such as achieving a uniform B1 field or a specific flip angle. The use of the semi-localized by adiabatic selective refocusing (sLASER) sequence can address these issues. The major advantage of the sLASER approach is reduced chemical shift displacement error. This is especially important for volume excited MRSI, avoiding spatial regions with biased metabolite ratios and J-evolution differences. <br />
|}<br />
<br />
==='''Screen shots of parameters and CV's for a typical spectroscopy protocol'''===<br />
<br />
<br />
<br />
<br />
===='''T1'''====<br />
<br />
Anatomical Scan Parameters: A T1-weighted structural scan was acquired using a 3D fast gradient-echo (GRE) BRAin VOlume (BRAVO) sequence: TE = 3.2 ms, TR = 7.83 ms, field of view = 256 × 256 mm, voxel size = 1 x 1 x 1 mm, number of slices = 172, slice orientation = sagittal, FA = 11 deg, receiver bandwidth = 27.78 kHz, acquisition time = 4 min and 4 sec. The Single voxel (SVS) and MRSI Volumes of Interest were prescribed on the T1-weighted scans.<br />
<br />
<br />
[[File:Testcsi52_scoutRight_T1_beforeRx.png|none|1000px]]<br />
<br />
<br />
<br />
<br />
<br />
===='''Single Voxel'''====<br />
<br />
An example of single voxel of the ACC region<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing a voxel on the axial image will allow for voxel size adjustment in the details tab in the "length" parameters (example of 16 X 20 X 20 shown in Figures below). Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 1-4 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:SVS-GE-Table-2.png|none|1000px]]<br />
<br />
Figure 1. sLASER voxel prescription with coronal, sagital and axial reference views <br />
<br />
[[File:Testcsi52_ACC_rx_size_position.png|none|1000px]]<br />
<br />
Figure 2. Click on the right arrow to reveal details tab showing additional information including TE and NEX<br />
<br />
[[File:Testcsi52_ACC_details_useThisOne.png|none|1000px]]<br />
<br />
Figure 3. Selection of the Advanced tab to reveal advanced control water suppression and spectral sampling conditions<br />
<br />
[[File:Testcsi52_ACC_Advanced_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 4)<br />
<br />
[[File:Testcsi52_ACC_Advanced_2of2.png|none|1000px]]<br />
<br />
<br />
<br />
<br />
===='''2D MRSI'''====<br />
<br />
Example of Right Subcortical MRSI<br />
<br />
After reformatting the T1 images to obtain high resolution images in the coronal, sagittal, and axial views, placing an MRSI slab on the axial image will allow for size adjustment in the details tab in the "length" parameters and is done prior to changing the sequence from a single voxel acquisition mode to the MRSI acquisition mode. Key parameters used in the sLaser sequence are outlined in the table below and referenced to figures 5-8 further below following parameter reporting guidance - Lin A, Andronesi O, Bogner W, et al. Minimum reporting standards for in vivo magnetic resonance spectroscopy (MRSinMRS): experts' consensus recommendations.<br />
<br />
<br />
<br />
[[File:MRSI-GE-Table.png|none|1000px]]<br />
<br />
<br />
Details tab with coronal, sagittal, and axial views (Figure 5)<br />
[[File:Testcsi52_R_Subcort_location.png|none|1000px]]<br />
<br />
Details tab with coronal and sagittal views only (Figure 6)<br />
<br />
[[File:Testcsi52_R_Subcort_details.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 7)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_1of2.png|none|1000px]]<br />
<br />
Advanced tab coronal and sagittal views only (Figure 8)<br />
<br />
[[File:Testcsi52_R_Subcort_Adv_2of2.png|none|1000px]]<br />
<br />
==Tools for Spectroscopy Data Acquisitions==<br />
<br />
<br />
==='''High Order shimming for MRSI'''===<br />
<br />
<br />
Higher Order Shimming (HOS): A General Electric (GE) higher order shimming sequence of the VOI box was performed prior to 2D MRSI data collection to improve spectral data quality. The GE works in progress (WIP) experimental patch incorporates an improved ratio of matrix size to spatial coverage, 64 x 64 matrix to 128 x 128 matrix.<br />
<br />
Shimming - Placement of MRSI Volume of Interest on T1 images followed by standard shimming procedures in the following figures<br />
[[File:Testcsi52_HOSpatch_Details.png|none|1000px]]<br />
Shimming-1<br />
[[File:Testcsi52_HOSpatch_msg_linkedTo_Rsubcort.png|none|1000px]]<br />
Shimming-2<br />
[[File:Testcsi52_HOS_ROIselection.png|none|1000px]]<br />
Shimming-3<br />
[[File:Testcsi52_HOSpatch_ROIselection_calcShim.png|none|1000px]]<br />
Shimming-4<br />
[[File:Testcsi52_HOSpatch_sameSeries.png|none|1000px]]<br />
Shimming-5<br />
[[File:Testcsi52_HOSpatch_calcShim_2.png|none|1000px]]<br />
Shimming-6<br />
<br />
==='''Prescribing a rotated voxel'''===<br />
At the moment GE’s DV26 and higher software platforms release doesn’t support voxel rotation for spectroscopy sequences. A workaround however is available:<br />
<br />
(1) After the 3-plane reconstruction of the T1w images, setup a 3D imaging scan. We saved a template of this 3D scan in the protocol “CNI Example Spectroscopy” and named it as “Voxel prescription”. Add this sequence to your protocol and put it before the MRS scan.<br />
[[File:Spectro_add_sequence.png|none|1000px]]<br />
<br />
(2) Setup the voxel prescription scan. The Scan Plane is set to “Oblique”, FOV and Locs per Slab are set as close to the voxel size of the spectro scan as possible. Prescribe the 3D box, place it to the desired location and rotate to the right angle. Because the box is usually bigger than the voxel size you want to prescribe, the coverage you see in this step is not accurate. It’s crucial to get the correct orientation of the box. Save Rx.<br />
[[File:Spectro_voxel_prescription.png|none|1000px]]<br />
<br />
(3) Setup the MRS scan. Copy Rx from the voxel prescription scan. By default the Mode Filter in the Copy Rx is set to “MRS”, you need to change it to “All” or “3D” in order to see the voxel prescription scan in the Copy Rx list. Select it and accept.<br />
[[File:Spectro_copy_rx.png|none|1000px]]<br />
<br />
(4) Adjust voxel location and size. You can move the box around and change its size on the graphic interface, or set its coordinates and size by setting the Center and Length in X, Y, Z. If you want to adjust the orientation of the voxel, you need to go back to the 3D voxel prescription scan, and repeat step 2-4 again. After you finish setting up the MRS scan, Save Rx and proceed with scanning.<br />
[[File:Spectro_voxel_size.png|none|1000px]]<br />
<br />
===Extracting voxel prescription information retrospectively===<br />
The prescription information of the voxel of an MRS scan is saved in the header of the raw data (p-file). Specifically, the x, y, z dimensions of the voxel are stored in header fields rdb_hdr_image.user8, rdb_hdr_image.user9, rdb_hdr_image.user10; the x, y, z locations of the center of the voxel are stored in header fields rdb_hdr_image.user11, rdb_hdr_image.user12, rdb_hdr_image.user13, in RAS coordinates (e.g. if the voxel is at L26.0 then rdb_hdr_image.user11 will record -26.0). The unit is mm. <br />
<br />
To look for this information on [https://cni.flywheel.io Flywheel], open the information window of the p-file, and search for op_user_8, op_user_9, op_user_10, etc.<br />
<br />
==Processing of sLASER SVS and MRSI data==<br />
<br />
Specific customized steps to process the 2D focal MRSI data were developed and are shown with a listing of additional data processing details below. An analogous custom data processing pipeline is used for single voxel data processing.<br />
<br />
<br />
<br />
<br />
[[File:Wiki-FlowChart.png|none|1000px]]<br />
<br />
<br />
2D focal MRSI sLASER Data Processing and Reconstruction: To suppress leakage of the artifact signals from voxels outside of the excited volume, a 2D version of the spatial Fermi filter was applied to the k-space data before Fourier transformation. Coil combination was then performed voxel by voxel using a summed square of the magnitude of the first data point in the FID. The spectral grid was extrapolated to 32 x 32 grid.<br />
<br />
3D T1 weighted Processing: Structural data were processed with the open source package FreeSurfer tool(36) version 7.3.2 for automated whole brain tissue segmentation of Gray Matter (GM) and White Matter (WM) as well as Cerebrospinal Fluid (CSF). Using X atlas, brain regions from the 3D T1 weighted image are parcellated, masked and labeled. Visual quality control procedures were performed including assessing motion artifacts, checking segmentation accuracy and confirming there were no processing errors.<br />
<br />
MRSI Mask: An in-house MATLAB script created a multi-value (non-binary) mask of the MRSI Volume of Interest that was registered to the 3D T1 weighted MRI anatomical scan. The location of the MRSI mask and regions within the mask were quality checked for accuracy against screenshots of the MRSI Volume of Interest taken during data acquisition.<br />
<br />
Gray Matter/ White Matter/ Cerebrospinal Fluid (GM/WM/CSF) Segmentation (Separate GM/WM/CSF): After the 3D T1w structural processing and MRSI Mask steps are completed, the outputs from these steps are fed into two in-house data processing scripts in order to compute and separate voxels based on tissue percentages of GM/WM/CSF for each voxel in the Volume of Interest and to identify (label) brain regions in the MRSI Mask (achieved with two in-house data processing scripts). This was done to identify and correct for potential influences on metabolite estimates from different tissue amounts in each voxel using percentage of gray matter as a covariant (GM/(GM+WM)).<br />
<br />
==Legacy and Other Spectroscopy Sequences==<br />
<br />
Legacy and other spectroscopy sequences used at CNI include methods both for edited GABA (gamma-Aminobutyric acid) specific data acquisition (MEGA-PRESS [1] and IM-SPECIAL [3]), and for multi-metabolite data acquisition (Optimized-PRESS [4], [5], [6]). Many sequences are linked to automatic processing pipelines in CNI's data management system, Flywheel, as referenced in the table below.<br />
<br />
<br />
{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS [1]<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|Gannet [2]<br />
|-<br />
|IM-SPECIAL [3]<br />
|GABA, Glu(Glutamate), Glx(Glutamate, Glutamine)<br />
|Sequence specific Matlab code<br />
|-<br />
|Optimized-PRESS [4], [5], [6]<br />
|All metabolites<br />
|LCModel fitting [7]<br />
|}<br />
<br />
<br />
References<br />
<br />
[1] Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R (1998) Simultaneous in vivo spectral editing and water suppression, NMR Biomed. 11:266–272 https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-1492%28199810%2911%3A6%3C266%3A%3AAID-NBM530%3E3.0.CO%3B2-J <br />
<br />
[2] Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
<br />
[3] Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691<br />
<br />
[4] Webb PG, Sailasuta N, Kohler SJ, Raidy T, Moats RA, Hurd R (1994) Automated single voxel proton MRS: technical development and multisite verification, Magnetic Resonance in Medicine 31(4):365-373 https://doi.org/10.1002/mrm.1910310404<br />
<br />
[5] Bodenhausen G, Freeman R, Turner DL (1977) Suppression of artifacts in two dimensional J spectroscopy, Journal of Magnetic Resonance Imaging 27:511-514 https://doi.org/10.1016/0022-2364(77)90016-6 <br />
<br />
[6] Tran TK, Vigneron DB, Sailasuta N, Tropp J, Le Roux P, Kurhanewicz J, Nelson S, Hurd R (2000) Very selective suppression pulses for clinical MRSI studies of brain and prostate cancer, Magnetic Resonance in Medicine 43(1):23-33. https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291522-2594%28200001%2943%3A1%3C23%3A%3AAID-MRM4%3E3.0.CO%3B2-E<br />
<br />
[7] Provencher SW (2001) Automatic quantitation of localized in vivo1H spectra with LCModel, NMR in Biomedicine 14(4):260-264 https://doi.org/10.1002/nbm.698<br />
<br />
==Spectroscopy Data Processing Tools at CNI for legacy sequences==<br />
<br />
<br />
<br />
CNI currently uses Flywheel as its data base management system. A critical feature of this data base management is the ability to share computational methods within the system. The CNI now provides a combination of data repository and integrated open source processing tools such as Gannet [2] and LCModel [7]. This combination of tools supports scientific transparency for both data and computational sharing. Spectroscopy analysis methods such as LCModel can be containerized as a gear in Flywheel for automated processing and data visualization.<br />
<br />
<br />
[[Image:Flywheel_Fig.jpg|1200px|thumb|center|Flywheel]]<br />
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'''Each of the spectroscopy sequences is linked to a Flywheel gear for automatic data processing'''<br />
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{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
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|Optimmized_PRESS<br />
|All metabolites<br />
|Sequence specific Matlab code, LCModel fitting - Flywheel processing gear placeholder information here: LCMODEL_r_dlpfc_nfl_[BASIS_SET=02_01_19,FIXED_NAA=0]_(2021-05-13)<br />
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|}<br />
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'''For users using the CNI Optimized PRESS "nfl" sequence with LCModel data analysis - <br />
Users who are in groups that are not themselves Flywheel "Lab" customers will need to download their results from the session tab now (not the analyses tab as was done before and shown in the figure below)<br />
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If you are using Google Chrome as the browser to download the processed data, then you will need to add the extension .zip to the downloaded file name. This operation does not not need to be done if using Safari or Firefox browsers.<br />
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MEGA-PRESS results will continue to be in the analyses tab.'''<br />
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[[Image:Screen Shot LCModel Session.png|1200px|thumb|center|LCModel Results]]<br />
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{| class="wikitable"<br />
|-<br />
! Spectroscopy Sequence<br />
! Measured Metabolites<br />
! Analysis Methods<br />
|-<br />
|MEGA-PRESS<br />
|GABA+, Glx(Glutamate, Glutmine)<br />
|To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data http://www.gabamrs.com/. Currently the latest version 3.1 is Docker containerized. This needs to be manually run, but this analysis method will soon be changed to a Flywheel gear for automatic analysis and storage of results (see location of data analysis results section below).<br />
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References from the Gannet web site include:<br />
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Richard A.E. Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter B. Barker, and C. John Evans (2014) Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid–Edited MR Spectroscopy Spectra, Journal of Magnetic Resonance Imaging 40:1445–1452 https://doi.org/10.1002/jmri.24478<br />
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Paul G.Mullins David J.McGonigle Ruth L.O'Gorman Nicolaas A.J.Puts RishmaVidyasagar C. JohnEvans Cardiff Symposium on MRS of GABA Richard A.E.Edden Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA https://doi.org/10.1016/j.neuroimage.2012.12.004<br />
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Ashley D. Harris, Muhammad G. Saleh, Richard A.E. Edden Edited 1H magnetic resonance spectroscopy in vivo: Methods and metabolites https://doi.org/10.1002/mrm.26619<br />
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The Gannet manual can be downloaded here - http://www.gabamrs.com/downloads<br />
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An example of the use of voxel segmentation is described here - DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332, <br />
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Analysis results of MEGA-PRESS with Gannet is shown in Figure 1 (Gannet Fit), Figure 2 (Gannet Output), Figure 3 (Gannet CoRegister), and Figure 4 (Gannet Segment) for the ACC brain region.<br />
|-<br />
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|}<br />
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{|<br />
|[[File:Figure 1.png|400px|thumb|left|Gannet Figure 1 ]]<br />
|[[File:Figure2.png|400px|thumb|left|Gannet Figure 2 ]]<br />
|[[File:Figure3.png|400px|thumb|left|Gannet Figure 3 ]] <br />
|[[File:Figure4.png|400px|thumb|left|Gannet Figure 4 ]]<br />
|}<br />
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= Miscellaneous Historical Information =<br />
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[[Historical Information]]</div>Laimab