Getting Started

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.

If you would like an introductory tour of the facility please email Laima Baltusis or call her office phone (5-8382).

User Access/Onboarding & Training

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.

All researchers using the CNI MRI facility must complete the CNI onboarding process outlined below.

Access/Onboarding

As of September 2025 new CNI users must complete the following three step onboarding process.

• 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.

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.

• 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.

• 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.

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 .

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.

Any questions regarding the on-boarding process should be directed to the CNI facility manager.

Access status to CNI is organized into three categories:

• 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.


• 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.


• 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

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.

CNI New User Orientation Session Registration Forms

New user in-person CNI orientation sessions are held on Thursdays 9:00AM to 10:30AM at CNI.

The next CNI new user orientation will be on January 15, 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.

The registration form for the January 15, 2026 session is here https://docs.google.com/forms/d/e/1FAIpQLSePRU7CAa8KNJiB9dEC5F_K3UFZFBUdDTx6Q9xDtUJaUFp0wA/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.

Youtube videos of magnet projectiles. These videos will be discussed during the CNI new user orientation sessions. (1) https://www.youtube.com/watch?reload=9&v=plvIEf7JsKo (2) https://www.youtube.com/watch?v=vIQaGt_fkkw The links to these videos will be emailed to attendees in the post orientation session assignment following the in-person session.

CNI Standard Operating Procedures and Registration Forms for CLIA-Waived, Point of Care, Urine-Based Testing

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 [1]

1. The PI's must complete the verification form [2], 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 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.
2. All team members of the group must read the SOP for urine testing at CNI
3. All team members of the group must take the quiz for urine testing after reviewing the SOP document [3]

Late night scan sessions approval policy

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.

IRB Approval for Project

Before using the MR scanner, a research group must have IRB approval for the project. Scanning at CNI is not allowed without IRB approval.

• General information about the procedures and policies related to obtaining IRB approval for research projects conducted at Stanford University is at Human Subjects Research web sites.
• There are also detailed instructions for modifying existing IRB protocols.

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.

Setting up a CNI account for research studies

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 [4].

• Full project title (ex. Neural Basis of Visual Pattern Appearance)
• Funding source (ex. NIH, NSF)
• PTA assigned to this project
• Grant (PTA) Expiration Date
• IRB approval letter
• Abbreviated project title: one or two word description. (This is the grant name that will be seen in the CNI scheduler).
• A list of researchers (names, e-mails, and SUNetID's) who will be booking scanning time with this grant.
• 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.

The CNI Facility Manager will contact the PI (or whoever initiated the account setup request) via email once the account has been set up.

Scheduling MRI Scanner Time

All scanner time is booked via the CNI on-line scheduling system.

Only researchers who have completed Level 2 training can make bookings.

Scheduling Policy

Overview: 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.

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.

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.

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,

• Short Term - Tuesday 8AM-12PM and Friday 2PM-6PM are reserved for Short Term bookings and will be available 2 weeks in advance.
• 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.
• 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Billing Policies

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.

Rates for scanning effective September 1, 2025 - August 31, 2026 will be:

8:00AM to 6:00PM weekdays (Monday-Friday) - $534/hour

6:00PM to 8:00PM weekdays (Monday-Friday) - $435/hour

8:00AM to 8:00PM weekends (Saturday-Sunday) - $435/hour

8:00AM to 8:00PM Holidays, Holiday Weekends, Winter Shutdown - $122/hour

8:00PM to 8:00AM any day (Monday-Sunday) - $122/hour

EEG usage has no charge currently (see CNI staff for more info)

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.

Cancellation Policies

See above

User Etiquette

Please help us to continue to maintain a safe and productive environment for everyone at CNI by noting following:

 

1. Please show up for scan time that you have booked, and start and stop your scan session on time.
   • 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.
   • 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.
   • Please book your scans with valid grants.
   • Please e-mail IRB approval letters for new and extended studies to the CNI Facility Manager Laima Baltusis (laimab@stanford.edu)


2. 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.
   • Every item has its place. Do not leave supplies, equipment, or furniture in arbitrary locations. This causes delays in scanning for the next groups.
   • 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.
   • The hampers are for linens only. Do not put trash, used ear plugs, used scrubs, or memory foam pads into these containers.
   • 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.
   • If you have plugged in or reconfigured anything to a non-standard configuration, please make sure that you have returned everything to standard configurations.


3. 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.
   • After making coffee or tea please make sure that the kitchenette area is clean. Please wipe up any sugar or creamer spills.
   • 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.
   • If it is necessary to consume food, all empty food containers must be taken outside to the recycle/trash bins in the outside courtyards.
   • Some participants can be messy. As a courtesy to following groups, it is important to tidy up after them.
   • 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.

To maintain a safe and welcoming environment at CNI please also review and sign the CNI User etiquette form Etiquette Form.