Adam Kerr

CNI User Meeting - 2024.12.06

Thanks to all who made it to our recent CNI User Meeting. We’ve attached the presentation slides.  If you have any questions on the slide material, please feel free to ask any of the CNI team. Thanks! The CNI Team 2024.12.06 CNI Town HallDownload

CNI User Meeting - 2022.10.14

Thanks to all who made it to our recent CNI User Meeting in person or on Zoom. We’ve attached the presentation slides and Zoom recording here.  If you have any questions on the slide material, please feel free to ask any of the CNI team. Thanks! The CNI Team Slides: 2022.10.14.CNI User Meeting PDF Zoom Recording: 2022.10.14.CNI… Read more CNI User Meeting - 2022.10.14

New Nova 32-Channel Coil

Summary CNI’s original Nova 32-channel coil went out of service earlier this year.  After multiple discussions with Nova, it appears that the original coil cannot be fixed.  We are fortunate that our friends at GE generously lent us a Nova coil that we have been using since the end of January. We purchased and have received a… Read more New Nova 32-Channel Coil

New Holiday Weekend and Closure Rates

The CNI advisory board has approved a small modification to our scanner scheduling and fee structure. The modification will not affect most users.  We describe the reason for the adjustment and its implementation in this message. Reason:  The scheduling modification is designed to allow users to reserve longer periods of time for complex scientific experiments… Read more New Holiday Weekend and Closure Rates

Updated Anatomical T1 Data on Flywheel

Background Earlier this year we learned that some anatomical T1 data were collected with GE’s GradWarp processing disabled.  GradWarp is GE’s method for correcting spatial image distortions that are introduced by physical gradient fields not being perfectly linear.  In practice, these gradient fields are nearly linear over a normal head volume but deviate at the edge of the field of view (FOV).… Read more Updated Anatomical T1 Data on Flywheel

New Masking Guidelines

New Masking Guidelines CNI will begin following the new masking guidelines established by the University as of today.  These guidelines are that Wearing masks is optional Wearing masks is recommended for all individuals regardless of vaccination status. This decision is based on several factors.  First, the air flow throughout the CNI is good.  Second, the… Read more New Masking Guidelines

CNI User Meeting (10/15/2021)

Thanks to all of the CNI users who participated in our User Meeting earlier this month. We’ve attached the presentation slides and Zoom recording here.  If you have any questions on the slide material, please feel free to ask any of the CNI team. Thanks! The CNI Team Slides: 2021.10.15 CNI User Meeting Zoom Recording: 2021.10.15… Read more CNI User Meeting (10/15/2021)

Updated SOP for Scanning After October 1st

Beginning October 1st, 2021 we will resume nearly normal operations.  Users will no longer include a 1/2-hour COVID Mitigation block between scans, do a full cleaning at the beginning of their scan, but instead perform it only at the end of their scan as described in the revised  SOP (see CNI Wiki).  The higher density scheduling parallels the changes… Read more Updated SOP for Scanning After October 1st

Extending COVID Mitigation Procedures Through September

Delay in New CNI Guidelines Previously we announced a return to back-to-back scanning as of September 1st.  Now, in consideration of this new wave (Delta) of COVID disease, and after consultation with Stanford health experts, we have decided that it will be CNI policy to maintain the COVID mitigation procedures through September.  This is not a University imposed requirement. After reviewing… Read more Extending COVID Mitigation Procedures Through September

Scan Data Acquired From August 19--23

Post Scanner Upgrade Problem The CNI UHP scanner received a minor system upgrade on Tue. Aug 17 — Wed. Aug. 18.  The updates were to support two new multipurpose flexible AIR coil receive arrays.  You can read more about these coils here. After the upgrade, GE confirmed the system met the “in spec” requirements that are normally used… Read more Scan Data Acquired From August 19--23

Scan Data Acquired From August 2--11

Discovery of Coherent Noise Source On August 9th, we were making very sensitive noise measurements during testing of an investigational 64-channel receive array.  We observed some artifacts in the noise covariance matrix when testing the array. We originally attributed the noise to an issue in the device under test. However, after repeating the test while turning off all power… Read more Scan Data Acquired From August 2--11

New CNI Guidelines

Scanning After Aug 2nd: New mask and distancing guidelines Beginning Monday, Aug. 2, CNI will follow Stanford’s updated guidelines for mask-wearing and physical distancing with one addendum.  The new guidelines do not require fully vaccinated individuals to wear a mask indoors; but, individuals who are not fully vaccinated are required to continue wearing a mask when indoor.… Read more New CNI Guidelines

Adoption of Stage 3 Guidelines

As many of you will have seen, the University just announced the start of  Stage 3 of Research Recovery.  I am sure we all look forward to reducing the COVID mitigation burden, while still maintaining high health and safety standards. The University’s announcement leaves open several practical questions about managing shared research facilities like ours. As you understand, researchers… Read more Adoption of Stage 3 Guidelines

Maintaining Access to the CNI for all our Users

As the CNI becomes increasingly busy, we are asking for your help. Please schedule your scans as efficiently as possible.  We require only a single 30-minute COVID mitigation block between scans; please avoid having back-to-back COVID mitigation blocks, or 1/2-hour orphans between COVID mitigation blocks. We ask that you only schedule times for confirmed participants who are… Read more Maintaining Access to the CNI for all our Users

UHP Upgrade Update

Unfortunately, we’ve run into a number of issues with the system upgrade that has delayed the process considerably.  The issues are summarized below. We regret the inconvenience. Failed scan room power supply: The upgrade installed some new hardware (connecting cables) into the scanner suite.  Upon powering up, the GE service engineers were unable to get the system to… Read more UHP Upgrade Update

Update on Physiological Data Association in Flywheel

Dear CNI Users, In August we wrote to you regarding a problem we found within the CNI Flywheel instance (cni.flywheel.io). In some cases the physiological data (respiratory and cardiac waveforms) from the scanner were not matched to the correct acquisition in Flywheel, or were not uploaded at all. We have determined that such failures occurred most… Read more Update on Physiological Data Association in Flywheel

New Human Subjects Research Guidelines

Introduction This note summaries significant developments in the University Human Subject Research Guidelines.  We specifically address how these changes will impact the CNI Standard Operating Procedures (SOP). The University’s updated guidelines dramatically increase the permitted research activity at the CNI.  In anticipation of increased activity, we are modifying our SOP to increase access to well-ventilated spaces for… Read more New Human Subjects Research Guidelines

New CNI SOP with Increased Occupancy Limits

We have good news to report. There have been a number of recent developments in Stanford’s Research Recovery process, several of which will benefit CNI users. The first is the increase in density restrictions for laboratory space which will now allow up to 3 people to be present in the CNI scan room or control room.  These new… Read more New CNI SOP with Increased Occupancy Limits

Normal Protocol Development Policy Resumes Oct. 1, 2020

We are glad that many groups start to come back and use the CNI services.  We are seeing that the transition from the MR 750 to the UHP is going smoothly, and there are only a few adjustments needed to get different people back scanning again. We have noted that the calendar is starting to fill up… Read more Normal Protocol Development Policy Resumes Oct. 1, 2020

Hyperband Transition

Executive Summary The GE product Hyperband BOLD and diffusion sequences are a result of close collaboration between GE scientists and engineers with the CNI staff.  The CNI SMS implementation, which we called the “MUX” research sequence, served as a resource and a benchmark for the GE Hyperband product.  Over the last several months Adam and… Read more Hyperband Transition

Updated CNI SOP

Updated CNI SOP We updated the CNI SOP for COVID-19 mitigation on our CNI wiki.  The update adds some details regarding EEG  and EEG/fMRI studies. We now have approval to have multiple groups using the CNI at the same time.  Please note that density requirements still need to be followed except for very short periods (< 15… Read more Updated CNI SOP

Slack and Volunteers

Remember to Sign Up for CNI Slack Workplace CNI has created a Slack workplace (https://stanford-cni.slack.com) to help expand intrauser communication and sharing of information.  If you haven’t used Slack before, please checkout these resources (https://uit.stanford.edu/service/slack/resources). Volunteer Recruiting With the expansion of the volunteer recruitment pool (see post from July 14), PIs are now allowed to recruit from… Read more Slack and Volunteers

Expanded Subject Recruiting Pool

Subject Pool Expanded to Include Any Stanford Affiliate Already on Main Campus Please note that as of tomorrow, July 15,  Stanford has expanded the allowable human subject recruiting pool for researchers using CNI to anyone already approved to be on the main campus.  The complete text from the Research Recovery Handbook reads as follows. IRB-approved, in-person,… Read more Expanded Subject Recruiting Pool

Reopening the CNI - Update and FAQ (part 4)

Partial Opening Update This is a brief update on our post of June 6 (Reopening the CNI – partial opening (part 3)).  Please review that blog post in conjunction with the material here. The CNI COVID-19 Mitigation SOP  has been revised (June 16, 2020) to make it very clear that the human subjects research (HSR) stages… Read more Reopening the CNI - Update and FAQ (part 4)

2020.03.15 CNI and COVID-19

The University response to the COVID-19 continues to evolve.  We will use these blog posts as well as additional communication mechanisms that we are setting up to stay in touch with you.  Here is a summary of the current situation. Overview The CNI remains open, but Hua and Michael will be working remotely.  They can… Read more 2020.03.15 CNI and COVID-19

COVID Response / Cancellations

Hello CNI Users, In response to recommendations from the CDC, Stanford Infection Control, and also in consistency with Lucas Center procedures, we have listed a few steps that will help prevent the spread of the COVID-19 virus from contacts at CNI. Please ask all volunteers and participants, before they arrive at CNI, if they have… Read more COVID Response / Cancellations

CNI User Meeting Slides (3/6/2020)

Thanks to all of the CNI users who participated in our User Meeting on Friday. We’ve attached the presentation slides here.  If you have any questions on the slide material, please feel free to ask any of the CNI team. Thanks! The CNI Team 2020.03.06 Town Hall.pdf

CNI Users' Meeting Tomorrow – Friday, March 6, 10:30 to 11:30AM

The CNI users’ meeting will be held tomorrow, Friday, March 6, 10:30 to 11:30AM in the new Wu Tsai Neurosciences Building Room E153. We will be sharing the meeting on Zoom — please see the details at the bottom of this message.  As per Stanford’s recommendations (https://healthalerts.stanford.edu) we are encouraging users to take advantage of Zoom to avoid… Read more CNI Users' Meeting Tomorrow – Friday, March 6, 10:30 to 11:30AM

Required IRB Protocol Modifications for CNI (important)

Dear CNI Users: The new UHP system being installed at CNI is an investigational device.  IRB protocols listing CNI as a resource facility need to be modified to include the description of this new system, note that the system is an investigational device, and modify consent forms appropriately. We have a letter from GE qualifying the safety standards… Read more Required IRB Protocol Modifications for CNI (important)

CNI New Hourly Scan Rates

Service center charges are closely monitored and approved by Stanford’s Research Administration Policy and Compliance (RAPC) staff.  The principles of rate setting are mainly that the service center does not make or lose much money in any given year.  The CNI charges are also reviewed by our Advisory Board.  Our expenses include the staff salaries, scanner maintenance,… Read more CNI New Hourly Scan Rates

CNI User Meeting 2018.12.07

Thanks to all of the CNI users who participated in our Round Table Discussions and the User Meeting in the last couple weeks. I’ve attached the presentation slides here.  If you have any questions on the slide material, please feel free to ask any of the CNI team. Thanks! The CNI Team 2018.12.07_CNI_UsersMeeting_Final

Upgrade Plan for DV26

Executive summary We will be upgrading the GE software and computational infrastructure in late September (from DV25 to DV26). The reasons and implications for your projects are explained below in detail. To migrate the CNI sequences to this new environment, the CNI development team needs time on the scanner (we estimate about 12 hours).  As… Read more Upgrade Plan for DV26

Optimizing image quality: Fieldmaps and shimming

Acquiring a high quality fieldmap of the mean magnetic field is crucial to obtaining a good measurement.  Making sure you set the parameters so that this field map is obtained as part of your protocol is something we help you with.  There are cases, including new sequences, where this can require some extra attention. The… Read more Optimizing image quality: Fieldmaps and shimming