Center for Cognitive and Neurobiological Imaging

CNI Scheduling Change

The CNI continues to experience unprecedented demand for scan time.  After consulting users regarding our proposed scheduling change we have decided to make the following adjustments that we hope will work better for most people.  We expect there will be ongoing iteration of the scheduling policy, and we ask for patience from users as we refine it in response to unforeseen issues.

This scheduling policy will go into effect this Tuesday, April 23 at 9:00am and will incur a 2-3 hour disruption to access to the CNI scheduler.  Schedule access will also be changed to use Calpendo, a system currently in use by the Lucas Center.  All existing reservations, grants and user accounts will be transferred into Calpendo.

The key features of the new scheduling policy are as follows:

• Calendar access will open for booking in 3 tranches (see Fig. 1)
  • Certain days/times will be made available for long-term access opening 16 weeks in advance
  • Certain days/times will be made available for medium-term access opening 8 weeks in advance
  • Certain days/times will be made available for short-term access opening 2 weeks in advance
• Scan time quotas will be applied on a per-project basis, and per-PI basis
• There will be two types of quotas
  • Daily:  The maximum amount of time that can be booked on a business day (6am-6pm)
  • Weekly:  The maximum amount of time booked in a given week
  • Quotas will not apply to time during weekends, holidays or outside of 6am-6pm
• Quota limits will vary depending on the access time.  Per-project limits are:
  • 8 – 16 weeks out: daily – 3h / weekly – 7h
  • 2 – 8 weeks out: daily – 6h / weekly – 10h
  • 0 – 2 weeks out: no quota limits
• Quota limits across all projects for a PI are 1.5x the per-project limits
• Time slots open for booking at 9am the respective period in advance — e.g on a Wednesday at 9am, the entire day on Wednesday 8 weeks in the future will open for booking.  Similarly, the short-term slots on Tuesday and Friday will open at 9am on the Tuesday and Friday 2 weeks in advance.
• In the first week of using the Calpendo system, long-term access will only be open 9 weeks in advance. On Monday, April 29, at 9am, we will extend the long-term access to the full 16 weeks. This will give users some time to get used to the new Calpendo system.

Other features of the CNI scheduling policy will remain unchanged.  This includes the requirement that schedulers must have specific subjects in mind when booking slots, the restrictions on protocol development time, and the cancellation fee rules.

Very rare exceptions to this scheduling policy will be considered on request but are not guaranteed to be granted.

The Calpendo scheduling system provides substantially more features that will be of use to our community.  The system is very intuitive, but users will find it helpful to consult the linked Calpendo Quick Start PDF that describes it in more detail.

CNI Scheduling Proposal

The CNI is experiencing unprecedented demand for scan time. In addition, user needs are becoming more varied and with a number of labs asking to reserve time outside of the current scheduling window (8 weeks).

There is no perfect solution apart from acquiring more scanners and offering our users more time.  We are doing our best on that front, but that will take some time.  In the near term, we are considering changes to the current scheduling policy that we hope will work better for most people.

The key features of the new scheduling policy we are considering are as follows:

• Calendar access will open for booking in 3 tranches (see Fig. 1) 
  • Certain days/times will be made available for long-term access opening 16 weeks in advance
  • Certain days/times will be made available for medium-term access opening 8 weeks in advance
  • Certain days/times will be made available for short-term access opening 2 weeks in advance
• Scan time quotas will be applied on a per-project basis
• There will be two types of quotas
  • Daily:  The maximum amount of time that can be booked on a business day (6am-6pm)
  • Weekly:  The maximum amount of time booked in a given week
  • Quotas will not apply to time during weekends, holidays or outside of 6am-6pm
• Quota limits will vary depending on the access time
  • 8 – 16 weeks out: daily – 3h / weekly – 6h
  • 2 – 8 weeks out: daily – 6h / weekly – 9h
  • 0 – 2 weeks out: no quota limits

Other features of the CNI scheduling policy will remain unchanged.  This includes the requirement that schedulers must have specific subjects in mind when booking slots, the restrictions on protocol development time, and the cancellation fee rules.

Very rare exceptions to this scheduling policy will be considered on request but are not guaranteed to be granted.

Please remember that our goal is to better meet user needs and ensure equitable access.  This scheduling policy is not yet in place, rather it is a policy we are proposing.  Below, we list various times when we will meet with users to discuss and evaluate the proposal.

Scheduling Proposal Discussions

We invite all groups to join a Zoom discussion of this proposal on the following dates/times:

• Monday, Nov. 20 12-1pm
• Monday, Nov. 27 12-1pm
• Tuesday, Nov. 28 12-1pm

Zoom links are being sent separately through the cni-mrusers@lists.stanford.edu mailing list, and the CNI Slack channel.  You are also welcome to send email feedback on this policy to Adam and Laima but Zoom attendance is preferred for interactive discussion.

Scheduler Implementation

The new scheduler will be implemented in Calpendo.  Further information will be sent out regarding the Calpendo system in advance of the switch.

The CNI Team

This week’s topics are reminders about important practices of time management, neatness, and supply usage we follow to make our facility run smoothly. Our facility is extremely busy so it is important to adhere to these best practices for the facility to work efficiently and well for all users. We thank you for that and look forward to continuing this culture.

1. Time management.  We depend on our community to be respectful of the schedule.

• Good practice is to stop your scan before the end of your scheduled time so that your participant can get changed and collect all their personal items in a timely way.
• Make sure that MRI scanner and console is ready for the next group.  This includes
  • ending the exam so that the GE scanning computer is ready for the next users,
  • closing all the data viewers on the GE scanning computer,
  • wiping down with Lysol wipes highly touched surfaces such as the squeeze ball, pulse-oximetry attachment, button boxes, etc.,
  • wiping down and putting away all the memory foam pad and neck supports in their storage boxes in the magnet room,
  • cleaning off any tape residue on the squeeze ball with a Lysol wipe, please do not leave sticky messes on the attached black hose – clean it off with a Lysol wipe,
  • unplugging and putting away button boxes used during your scanning session,
  • detaching the web camera and/or the IR source from the coil
  • if you used the MRI safe lenses, please clean them and put them back into their correct mini drawers. Please check to make sure that your participant is not leaving CNI and taking MRI safe glasses with them.
  • If you break something or find something that is broken please let CNI staff know as soon as possible, so that it can be replaced with a backup.

2.  Neatness.  This really has a big effect.  The reminders below are examples of mistakes over the last few months.  Please help. Like visiting wilderness areas — please leave no trace of your presence.

• Do not leave used coffee cups, empty water bottles, used earplugs, used socks, and used paper bags, used Lysol wipes, used sanitary covers, used pieces of tape, and other trash in the magnet room, in the control room, in the mock scanner room, in the testing room, and in the rest rooms.
• Also do not leave personal items such as jackets, hair ties, bobby pins, baby clothes, jewelry.
• Please supervise your participants so that they know where used scrubs, used socks, used earplugs and used paper bags go when a scanning session has been completed. This is particularly important whcn scanning adolescents as they tend to leave things in strange places.  But it is always important.
• Please put used linens and used scrubs into their bins, do not drape them over the sides.
• Do not put trash into the used linens bins. Put trash into the labelled trash bins.
• Enjoying food and drink at CNI is a privilege. We can only continue to allow this if everyone is fastidious about cleaning up any residue. Please wipe down tables and chairs. Vacuum the floor if there are food crumbs with the portable vacuum cleaner located in the control room. Take any leftover food or food stained packages to the garbage containers outside — they will otherwise attract ants and other critters if left inside. If we can’t keep the place clean, we will be forced to ban food and drink.  We don’t want to do that!

3.  Supplies.  You may be surprised to learn that the CNI operates on a very lean budget, and you may be further surprised to learn that a large fraction of it goes to supplies.  To help us keep our rates low, please:

• Do not take pens, paper, gloves, masks, Lysol wipes away for your own use.
• Scrubs are for participants only. Do not take them away for personal use in other locations.
• Do not take computer chargers located by the GE console. If they are not there this causes great stress to users.
• Do not take computer adapters. There is a good collection of various types and users do depend on them being there for their scanning session.

We are always open to suggestions for any improvements to our operations and happy to help users anytime.

Thanks,

The CNI Team

Each year, the CNI team welcomes back many users. We also look forward to meeting new users who have a wide variety of experience in research environments.  Over the next few weeks we will be posting messages to remind those of you who are returning, and inform those of you who are new to the CNI, about our community’s culture and priorities.

1. Safety

The safety of both participants and researchers is the highest prority at CNI.

• We use the internationally accepted recommendations from the American College of Radiology as guidelines to establish our safety rules. All new users are required to learn about these procedures by completing the on-boarding process.
• We strongly encourage experienced members of research groups to mentor new research group members, particularly with respect to MRI safety related procedures and practices. Teaching is a good way to remember and to help others.

2. Managing Research Participants

It is important that all research participants have a safe and positive experience while they are the CNI.  Our good will in the community depends on this.  Research participants include both the person being scanned and any accompanying family members or supporters.

• Please make sure that participants have been thoroughly screened for contraindications prior to their scanning session. It is not an acceptable situation to ask for last minute advice about a potential contraindication from CNi staff as the participant is about to enter the magnet room. It is the responsibility of PI’s to establish rigorous participant screening procedures for their research studies. CNI staff are always available for consultation.
• Please make sure that you have your Stanford ID with you arrive at CNI for your scanning session. Depending on activities at CNI we may or may not be available to let you into the facility, thereby potentially delaying your scan.
• Please make sure that participants arrive at CNI either with you, the researcher, or that you are already at CNI to greet your participant. Please do not create situations where a participant arrives unaccompanied at CNI and says “I have a scan today” and no other instructions.
• Research participants must be chaperoned at all times when they are CNI. If accompanying family members cannot be in the control room during a scan, then they must be in a reserved area in CNI (such as the CNI lobby, testing room, or mock scanner room). Please check on these people periodically and treat them courteously.
• While friendly smiles and answering simple questions is appreciated, please communicate instructions only to your own research participants. If a participant from another study groups ask questions, then it is mandatory that a member of that group answer those.
• If you find an unaccompanied research participant in a CNI area that you have reserved, please find a researcher from the participant’s group and have them tell the participant where to go.

3. Sign up for CNI Slack Workspace

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).

We are always open to suggestions for any improvements to our operations and happy to help users anytime. 

Thanks, 

The CNI Team

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 User Meeting MP4

At the beginning of each year, the CNI welcomes back many users, and we are glad to meet new users.  It is also a good time to remind everyone to please help us maintain a safe and productive environment at CNI.

Over the years, our community has worked together helping one another to follow the best practices.  This message is a reminder about important practices we follow to make our facility work well.

1. Shared spaces.  CNI has many shared spaces that you can reserve using the CNI calendar.

• Please be respectful of other users by being aware which areas have been reserved. A reserved space, even the CNI lobby, can be used only by the group that has reserved the space, or if  you are granted explicit permission by the group that reserved the space.
• Please note that the front rest room is shared by all staff and visitors.  If you use it as a changing space for your subject, or for urine collection it is your repsonsibility to leave it pristine for the next person.  Do not use it to store clothes or samples.

2. Managing research participants.  It is important that all research participants have a safe and positive experience while they are the CNI.  Our  good will in the community depends on this.  Research participants includes both the person being scanned and any accompanying family members or supporters.

• Research participants must be chaperoned at times when they are CNI. If accompanying family members cannot be in the control room during a scan, then they must be in a reserved area in CNI (such as the CNI lobby, testing room, or mock scanner room). Please check on these people periodically and treat them courteously.
• While friendly smiles and answering simple questions is appreciated, please communicate instructions only to your own research participants. If a participant from another study groups ask questions, then it is mandatory that a member of that group answer.
• If you find an unaccompanied research participant in a CNI area that you have reserved, please find a researcher from the participant’s group and have them tell the participant where to go.

3. Time management.  We depend on our community to be respectful of the schedule.

• Good practice is to stop your scan before the end of your scheduled time so that your participant can get changed and collect all their personal items in a timely way.
• Make sure that MRI scanner and console is ready for the next group.  This includes
  • ending the exam so that the GE scanning computer is ready for the next users,
  • closing all the data viewers on the GE scanning computer,
  • wiping down with Lysol wipes highly touched surfaces such as the squeeze ball, pulse oximetry attachment, button boxes, etc.,
  • wiping down and putting away all the memory foam pad and neck supports in their storage boxes in the magnet room, cleaning off any tape residue on the squeeze ball with a Lysol wipe,
  • unplugging and putting away button boxes used during your scanning session, and
  • detaching the web camera and/or the IR source from the coil
  • if you used the MRI safe lenses, please clean them and put them back into their correct mini drawers.

4.  Neatness.  This really has a big effect.  The reminders below are examples of mistakes over the last few months.  Please help. Like visiting wilderness areas — please leave no trace of your presence.

• Do not leave used coffee cups, empty water bottles, used earplugs, used socks, and used paper bags, used Lysol wipes, used sanitary covers, used pieces of tape, and other trash in the magnet room, in the control room, in the mock scanner room, in the testing room, and in the rest rooms.
• Also do not leave personal items such as jackets, hair ties, bobby pins.
• Supervise your participants so that they know where used scrubs, used socks, used earplugs and used paper bags go when a scanning session has been completed. This is particularly important whcn scanning adolescents as they tend to leave things in strange places.  But it is always important.
• Enjoying food and drink at CNI is a privilege. We can only continue to allow this if everyone is fastidious about cleaning up any residue. Please wipe down tables and chairs. Vacuum the floor if there are food crumbs with the portable vacuum cleaner located in the control room. Take any leftover food or food stained packages to the garbage containers outside — they will otherwise attract ants and other critters if left inside. If we can’t keep the place clean, we will be forced to ban food and drink.  We don’t want to do that!

5.  Supplies.  You may be surprised to learn that the CNI operates on a very lean budget, and you may be further surprised to learn that a large fraction of it goes to supplies.  To help us keep our rates low, please:

• Do not take pens, paper, gloves, masks, Lysol wipes away for your own use.

Thanks,

The CNI Team

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 new Nova 32-channel coil (the same model as currently in use).  We conducted a number of tests validating that its performance matches our borrowed Nova coil.  The results described here show a slight performance improvement (see below) for CNI’s new Nova coil compared to the one we borrowed.  We have put this coil into operation effective as of today.  GE’s Nova coil  is being returned to them with many thanks.

SNR Comparison Between the two Nova Coils

To compare the signal quality on the two coils, we acquired a multislice 2DFT sequence using a phantom.  We then repeated the acquisitions with the RF flip angle set to 0 in order to acquire pure noise images. The SNR maps for an optimal coil combining (Roemer PB, et al. The NMR phased array. Magn Reson Med. 1990 Nov;16(2):192-225.) are shown for representative slices are c0mpared in Fig. 1a.  The sensitivity shading and SNR maps are comparable between coils across all slices covering the volume.

The noise covariance arrays for the 32-channel data (Fig. 1b) with the new CNI Nova coil are somewhat more concentrated on the diagonal – a good thing meaning better coil independence.  The signal-to-noise ratio (SNR) histograms from the voxels inside the phantom are also comparable (Fig 1c). The CNI Nova coil is slightly higher (histogram shifted to the right), but by an amount that is irrelevant compared to the impact of the physiological noise that will be present when scanning a brain. 

We also compared the integrated signal and noise power across the whole volume for each of the coil channels (Figure 2).  The signal power follows the same trend across coils (individual elements are in the same positions and so we expect similar distribution of maxima and minima).  The noise power values can also be impacted by local loading of the array by the phantom which leads to the similar higher distribution on the channels 17-32 which correspond to the lower (posterior) half of the array.   We do not see any individual coil signal drops in the new CNI Nova coil, and that’s a good thing.

Finally, the temporal SNR of an axial BOLD EPI time series are very similar (Figure 3).  The images on the left are tSNR maps and the graph on the right is the tSNR histogram from voxels in all 42 slices, covering the whole spherical phantom.  There are no meaningful differences – especially compared to the additional physiological noise present in any real brain scan.

New Nova Coil Base

We’ve chosen to use the new base that came with our coil. The new base has better handles for transporting the coil, as well as cable management hooks.  We’ve taken this opportunity to also abandon the bite bar posts and have not transferred them from the old base.  The double mirror and Loc-line connectors for the webcam / IR illuminator / etc. were transferred.

Summary

We installed the newly purchased Nova coil.  Its performance is very similar to the borrowed Nova coil we have been using.  Thank you to GE!  And to everyone else – please carry on as you were.  We at the CNI are feeling grateful to our friends and glad to have this episode in our rear view mirror.
The CNI Team

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 involving, for example, post-mortem scans or equipment development scans (new coils).  It has been hard to accommodate this research during the normal periods of operation.  Based on historical usage patterns, we can make the instrument available for such projects on long holiday weekends without disrupting other users.

Policy: On the official University 3-day weekends in 2022 (Labor Day) and 2023 (Martin Luther King Day, Presidents’ Day, and Memorial Day) and extended closures (Thanksgiving and Winter Closure in 2022), we will allow investigators to book extended periods of time.  We will charge all of the scan hours on these long weekends and closures at the night time rate ($111, this coming fiscal year).  Here is a link to the University Holiday schedule.

All investigators interested in using these periods for very long scan blocks should reach out to CNI staff in advance of our normal 8-week scheduling window.  Please note that the intent of the change is not to enable a large consecutive block of time to scan multiple subjects, but rather to enable special types of research activities that require very long acquisitions.

The CNI advisory board will review this policy in advance of the FY24 period (September 1, 2023-August 31, 2024) to determine if it will continue.

Thank you,

The CNI Team

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).

GradWarp was unintentionally disabled in the cni_efgre3d sequence during a software update on 10/21/2021.  The method was re-enabled during another update on 2/14/2022. Disabling GradWarp had a significant effect only on scans that were acquired with a rectangular (not square) FOV.  The reason is that GE combines the image resampling that corrects for the rectangular FOV together with the GradWarp processing.  Thus,  rectangular FOV scans were reconstructed incorrectly assuming equal FOVs in both X & Y.  For example,  in a case where the yFOV is only 80% of the xFOV, the final reconstruction will be stretched by 25% in the Y direction.  This is easily detected.

Processing

We have been in contact with all groups that acquired data with rectangular FOVs, and we worked with them to identify and fix the problem. We just completed rolling out a correction that implements the GradWarp processing retrospectively to all the relevant data on Flywheel.

We also applied the GradWarp correction to data acquired with a square FOV (most anatomical data is acquired this way). In this case the correction is quite small (the gradients are close to linear over the head).  The typical displacement for a pixel at the edge of the brain will be 1 mm or less  This is shown in the images below where white gridlines are pictured in gradient space (which appear as a perfect grid spaced every 10 pixels) while the pink gridlines are as they appear after GradWarp is applied.  In this case the underlying brain image was acquired at a resolution 0f 0.9 x 0.9 mm. The GradWarp spatial correction depends on the position — positions further from the gradient isocenter have larger deviations from linear and the GradWarp corrections are larger.

Identifying Updated Data

In a recent update, Flywheel added version control to user data.  This is described by Flywheel in their online document: File Versioning. We used this feature when correcting the DICOM and NIfTI for anatomical T1 data.  Specifically, you will see a number “2″ next to the filename (see below).  When you view, download or operate on the Flywheel data, by default you will be provided the GradWarp corrected data (version 2).  You can restore the original data at any time by clicking on the version control number “2″.  A popup window will appear and you can restore version “1″ as the default (note that this will create a new version “3″ of the file).

In addition, Projects with acquisitions containing uncorrected anatomical T1 data (not GradWarp corrected) have a CSV file attached to the project level. The files are named using the following convention: 

    cni-gradwarp_<group_name>_<project_name>.csv

This file contains information describing the acquisitions with uncorrected and subsequently fixed T1 data. The csv file contains the following information for each corrected scan: Group|Project|Subject|Session|Acquisition|AcquisitionId. This information can be used to help you find data that was corrected.

We have implemented a new Flywheel tool, the GE Physio File Converter Gear. It is designed to help users read and summarize the physiological recordings from the GE scanner. This tool may be helpful to you for cases in which you collect PPG and respiratory respiratory data.

In those cases, there will be a file in your acquisition called something like

“24558_4_1_physio.gephysio.zip”

You can use Flywheel to run the Analysis Gear (“CNI GE Physio File Converter”) on your data.

The Gear will synchronize the recorded data to the associated fMRI acquisition. It filters the recorded raw data, finds the peaks in the waveform using the bandpass filter, saves out the waveform as a graph, and summarizes the waveform with various simple statistics.

The output of the Analysis Gear looks like this (click on the Analysis tab to find it):

It includes both tabular and graphical data files that you can view or download. Here is a plot of a portion of the time series of the heart beat signal.

Hua Wu implemented the Gear, which is based on code developed by Dora Hermes (see also https://github.com/vistalab/BrainBeat). We found it useful, in particular for pulling out signals in cases when the pulse oximeter was not well positioned on the subject’s finger and the physiological recordings are noisy.

Onward,
The CNI Team

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 overlap between different groups is minimal.  Third, we know that our community is cautious, and respectful of one another.

Our community has been very supportive during the darkest moments of this pandemic.  We ask you to continue respecting each individual’s choice in this matter, and we will continue to work with you to be safe in all matters regarding behavior at the CNI.

Ongoing COVID Mitigation

We will continue to provide regular and MRI-safe masks, hand sanitizer and gloves at the front entry for those who would like to use them.  Regular disinfection of any pads that are used or frequently touched surfaces is still required.  When time is available, we also encourage you to wipe down the scanner bore.  Scrubs and disposable socks for scan subjects are still required.  The CNI COVID screening form will still need to be completed until we have an update from the Stanford Reseach Recovery group.  We also highly encourage you to run on the MRI bore fan whenever a subject exits the scanner.  Thorough ventilation is healthy.  Always.

Groups scanning vulnerable subjects such as unvaccinated (COVID-19) children may continue through the end of March to book a 1/2-hour COVID mitigation block in advance of their scan to allow for more air exchange.  Beginning April this will not be offered and we ask investigators to please reschedule their scans back-to-back wherever possible to avoid inefficient scanner use.

Thanks for your help in keeping everyone safe!

The CNI Team

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 CNI User Meeting MP4

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 at the Lucas Center, and our changes have been approved in consultation with Stanford EHS.  The one exception is for groups scanning vulnerable subjects (such as unvaccinated children under twelve)  who may continue to book a 1/2-hour COVID-19 Mitigation block in advance of their scan.

Going forward, please be considerate of  other users.

• Book scans with either no gap, or a one-hour gap or larger between successive sessions.
• Stay on time during your scan session.  Scan operators and subjects should leave the scan control room by or before the end of your session.

Thanks for your help in keeping everyone safe!

The CNI Team

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 the current schedule, it is our impression that keeping the current mitigations will not be a substantial burden on the CNI users for the month of September. To maintain the mitigation procedures we modified the current scan schedule to add COVID mitigation 1/2-hour blocks wherever possible in September.  Please schedule any new scans accounting for the 30 minute mitigation blocks.

We will be in contact with groups that need to adjust their schedules to accommodate the 1/2-hour gap between subjects.  Please do not cancel scans and make changes yourself — we will do this so no cancellation fees will be triggered.

Please remember that as always:  you should be complete with all scanning and have exited your subject by the end of your normal scan slot.  The only thing that should be happening during the COVID mitigation block is additional cleaning, and should only take 5-10 minutes — the major intent of this block is to allow for air exchange in the room.

Scanning After October 1st

Assuming the current COVID wave subsides, we will resume more normal operations beginning October 1st.  After that date users will no longer be asked to  include a 1/2 hour COVID Mitigation block between scans.  At that time,  we will also remove the enhanced cleaning procedure requirement, though we will still ask scan operators to wipe down surfaces the subject touches (squeeze ball, inside of the receive array, ear pads) within the normal scan reservation period.

When we return to normal, please be considerate of  other users: Book scans with either no gap, or a one-hour gap or larger between successive sessions.

Remember — you will need to pay attention and stay on time during your scan session.  Scan operators and subjects should leave the scan control room by or before the end of your session.

Thanks for your help in keeping everyone safe!

The CNI Team

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 to confirm a system is ready for return to clinical service.  In addition, we ran our system stability QA that is important for fMRI scans and this also passed.

Unfortunately, Monday we discovered that certain MRI sequences now have substantial artifacts.  We resolved the issue Monday, with help from GE service and GE Headquarter’s Engineering ,by redoing the eddy current calibration procedures.  We determined that the original calibration files were corrupted during the upgrade.  We’re now on the alert for any further possible damage to these files, and GE is working to determine how their installation procedure corrupted these critical calibration files.

The sequences that are affected are few — so far, we’ve seen BRAVO T1-weighted scans, MR spectroscopy scans, and the Hyperband DTI scans being impacted.  If you used these sequences in this date range, please check to see if your data are corrupted.  In addition, we ask all users who collected data in the days after August 17th to check their data to make sure we have identifed all the problematic sequences.

The artifacts are not subtle.  Example images showing the artifacts we’ve seen are shown below.  We have not seen any problems with the fMRI sequences, either the stock EPI or Hyperband acquisitions.  So just visualizing your data with the Flywheel viewer should be enough.

If you do identify any unusable data, please contact Laima Baltusis regarding your scan and she will be able to arrange for no charge.  Sorry for the inconvenience!

The CNI Team

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 to accessory devices in the scan suite (TV, Eyelink, Biopac, Webcam, Lights, and Medlux table lights) we found an effect related to the room lights (Fig. 1).   The noise covariance matrices in Fig. 1b show correlations between channels when the room lights were turned on  – indicative that there is a coherent noise source related to the room lights.

This artifact may not appear in reconstructed MRI data.  The reasons is that a typical reconstruction performs noise whitening, effectively weighting down the contribution from channels with large noise power. This results in SNR maps (Fig. 1a) and an SNR histogram (Fig. 1c) that vary only slightly between the two conditions of room lights being on or off.  So the noise is there, but the reconstruction algorithms may remove the effect.

Based on this testing, we believe the noise was introduced from a bulb that went bad.  On the evening of August 11th, we replaced all the large bulbs in the scanner room and repeated our tests (Fig. 2).  The SNR maps and noise covariance matrices now show identical behaviour, irrespective of the condition of the room lights being on or off.  So, that’s good.   We further analyzed the last year’s worth of image quality data, which is all stored on Flywheel, and determined the onset of the problem was sometime on August 2nd, 2021 and it was resolved when the light bulbs were changed on the August 11th, 2021.

What does this mean to you?

Please check data you acquired between August 2nd and 11th.  Our  tests don’t show a significant SNR variation in the reconstructed images, but some reconstruction methods may fail to suppress the higher noise. If you find unusable data, please contact Laima Baltusis and she will arrange for replacement scan time to reacquire the data.

What is CNI doing to stop this problem from occurring in the future?

A number of events that can cause coherent noise to appear on MRI data: degradation in the room shielding, a failure in any electrical accessories in the room, or a failure in the MRI scanner hardware itself.  We acquire QA data once a week, but in this case we didn’t check it right away. We have now implemented a simple software app to monitor the Flywheel QA project week by week and show the results.  The data are consistently at a high SNR for more than a year, so this seems to have been a single case.

Over time we will continue to refine the types of QA data that we acquire in order to be sensitive to a larger variety of issues, and we will be quicker to read the QA data.  We also have regularly scheduled GE service maintenance that checks the system for issues such as these as well as many more.

You are the best steward of your data.

Prof. Nolan Williams’ group is to be congratulated for independently discovering a change in data quality on some of their scans and reaching out to CNI. Their messages to us were important. While we are improving our QA processes, we cannot promise to detect all possible sources of bad data.  We urge everyone to regularly check their data as soon as possible after acquisition for any change in quality or behavior — you can help the entire CNI community by making an early discovery of a data problem.

Thanks, and stay safe,

The CNI Team

Funding opportunity -

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.  Also, physical distancing will no longer be required.

The CNI specific addendum is that scan participants must wear a mask in the scanner. We adopt this requirement to be consistent with healthcare requirements and in recognition of the increasing (but still small) presence of COVID positive individuals in the our community.

We are asking Human Subjects to approve a modified screening form that includes a question regarding vaccinated status.

We will post new signage reminding unvaccinated individuals to wear a mask.  We will continue to require scan operators to follow the enhanced cleaning procedures before and after each scan session through the end of August.  And we ask you to be considerate of people who decide that they wish to wear a mask.

Scanning After September 1st

Beginning September 1st, users will no longer be asked to  include a 1/2 hour COVID Mitigation block between scans.  At that time,  we will also remove the enhanced cleaning procedure requirement, though we will still ask scan operators to wipe down surfaces the subject touches (squeeze ball, inside of the receive array, ear pads) within the normal scan reservation period.

As we return to normal, please be considerate of  other users: Book scans with either no gap, or a one-hour gap or larger between successive sessions.

Remember — you will need to pay attention and stay on time during your scan session.  Scan operators and subjects should leave the scan control room by or before the end of your session.

Reminders

A few reminders as research density at CNI continues to increase:

1. Protocol Development time is restricted — it can only be booked during regular time within 48 hours, and during off hours within 5 days.  If you need to book Protocol Development time outside of those bounds, please ask Laima in advance for permission.
2. Cancellation fees are in effect.  Please be sure to only schedule time when you have a confirmed subject, and cancel as early as possible so that other users may have an opportunity to use the scanner.

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 and community human subjects are present at the CNI.  Some are vaccinated or have a recent negative COVID test, and  others not.  We have been asked to consider the situation – balancing risks and benefits – to establish the new rules.

We are in discussions at the CNI and with the Lucas team to fill in details of a new plan (SOP) for  Stage 3.  For the coming week, we will continue following the current guidelines and CNI SOP.  This means uniform mask wearing and disinfection processes will continue for all groups.  During this week, in consultation with many of our users and other centers, we will update the SOP and send you the new plan.  We wish we could have been ready for Monday, but there are a few too many issues to consider.

Thanks for your patience.

The CNI Team

As the CNI becomes increasingly busy, we are asking for your help.

1. 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.
2. We ask that you only schedule times for confirmed participants who are appropriately screened.  To encourage this behavior, the CNI will be reinstating the cancellation policy described on our Wiki.  Specifically, scans after May 31st  must be cancelled at least 2 weeks in advance.  If the canceled time is not rebooked for another funded study or a CNI study, there will be a 10% cancellation fee.  To reduce the chances of a no-show, and avoid cancellation fees, we encourage everyone to remind participants in advance about their appointments.

Thanks, and stay safe!

The CNI Team

An urgent plea

Like most of you, the CNI team is eager to see the challenges of the pandemic recede.  As we approach the pandemic’s end (hopefully), it is  important that we continue to closely follow the COVID Mitigation procedures at the CNI.  We must help one another to get across the finish line strong – slip ups now will delay recovery.

We are particularly attentive just now because of comments from the national leadership coupled with Stanford’s decision to allow juniors and seniors to fly from around the country back to Stanford.  The risk that new people on campus wil be carrying the virus increased this week.  Our vigilance at CNI, and adherence to the CNI SOP, must increase.

To keep CNI a safe and productive environment please note the following

1. While many RAs are vaccinated, or may feel comfortable with colleagues in their pod, Stanford still requires us to observe ALL COVID-19 protocols including social distancing and masking and the mitigation procedures in the CNI SOP.

2. Please inform us promptly if you see something that does not meet the SOP requirements. We will act to fix any problems we know about, and we need your help to learn about such problems.  Please remember, we will not penalize people.  We will fix the problem pleasantly!

3. As part of the CNI SOP, we require a full 30 minutes for COVID-19 mitigation between scans. Groups MUST complete their responsibilities in 15-minutes to allow for redundant cleaning by the follow-on group.

We appreciate that everyone is worn down by the pandemic.  Please:  Do not relax your vigilance at this time.  Finish strong. A life or serious illness may be on the line.

An SOP reminder

Here are the Overview of Daily Workflow and Cleaning Procedures for Each Station from the CNI SOP.

Key parts of the SOP text are copied here for your convenience.

I. Overview of Daily Workflow
1. The CNI facility will operate with lower user presence in order to meet County and University guidelines. Researcher and subject access will be restricted to the main entrance.

2. Each morning the Stanford University Janitorial service will clean CNI, paying special attention to disinfecting commonly touched surfaces.

3. On the day of their scan, researchers must have confirmed they meet Stanford’s requirements for employees coming into work prior to arriving at CNI. This will be facilitated by the use of the Stanford HealthCheck Form https://healthcheck.stanford.edu/ .

4. For each scan, researchers will arrive 15 to 30 minutes in advance of their subject.

5. Social Distancing: As much as possible researchers will practice social distancing, maintaining 6 feet of separation between each other and research subjects. This is especially important when interacting with individuals that are not yet masked.

6. On arrival researchers will use hand sanitizer, put on gloves in preparation of cleaning, and a mask (or leave on an existing one at their discretion). Researchers will also confirm with the contactless thermometer that their temperatures are not above 100 degrees.

7. Researchers will then proceed to each of the areas they will use for their subject and follow the cleaning procedures outlined in the sections below for each station. Note only a single occupant is allowed at a time in any of the restrooms and the small testing room.

8. After cleaning, one or more researchers will greet their subject. Please note that University guidelines for external (non-Stanford affiliate) participants require they be met in an outdoor location.

a. The researcher will offer hand sanitizer to their subject and give them a procedural mask. Note: scan participants must be provided an MRI Safe mask. This is a regular mask from which the CNI staff has stripped the metal ribbon. The metal ribbon is mildly
ferromagnetic–not enough to cause a projectile hazard, but it will create substantial image artifacts! An accompanying guardian should be provided a regular disposable mask.
b. Researchers will confirm the answers for the subject that will have been collected during pre-screening on the CNI screening form. A single additional visitor, such as a parent or guardian, will be allowed only if necessary to accompany a participant. This visitor must also be screened with the CNI screening form.
c. A contactless temperature measurement of the subject and any visitor will be taken.
d. If the subject (or visitor) presents with a temperature over 100 degrees or has any COVID19 symptoms, researchers will not scan the subject and escort them from CNI premises while maintaining social distance. Researchers should then cancel their scan booking in the CNI scan scheduler and are then free to leave.
e. Assuming no contraindications, signatures will be collected on the screening forms and they will be deposited into the collecting box.
f. The participant will then be instructed to change into disposable scrubs in the changing area/bathroom. A disposable bag will be provided for their clothes and belongings.
g. Any accompanying guardian may accompany the subject to the changing room but must otherwise remain in the waiting area.

9. The researchers will then fill out the MRI screening and consent forms, perform any necessary tests or acclimatization, and then scan the subject. Hand sanitizer will be available at each station and researchers will instruct the subject to frequently clean their hands when moving from one station to another. The sink area in the MRI control room will always be available for additional hand washing and glove changing. Maintain social distancing as much as possible.

10. During the scan, there will be one primary “scan room” researcher. This researcher will be provided with a personal face shield by CNI that they will keep and reuse for all studies. They will be the sole researcher to be present in the scan room with the research subject assisting with preparation of the subject for scanning, scanner entry and egress. Note: Scan participants must wear their MRI-safe masks throughout the entire study.

11. Glove use: Gloves are to be worn whenever interacting with the subject in the scan room, and we recommend they also be used during cleaning. Gloves should not be worn when exiting the CNI. Gloves may be worn in the control room and waiting area, but frequent hand washing or sanitizing is an acceptable alternative and will help preserve our supply of gloves.

12. After completion of the scan, the researchers will instruct the subject to return to the changing room to change back into their clothes. Used gloves, masks and other trash can be disposed of in the normal trash container. ONLY in the event of items being visibly contaminated with bodily fluid do they need to need to be disposed of in the biohazard container.

13. Researchers will escort the participant out of the facility.

14. Researchers will then perform the cleaning procedures at each of the stations they or their subject have utilized.

15. Researchers should reserve in advance any of the stations they will be using on the CNI calendar to ensure no overlap between groups (Scan room, Testing Room, Mock Scanner, Conference Room, CNI Lobby, and Room 050).

II. Cleaning procedures for Each Station
Super Sani-Cloths are intended to be the primary instrument used to disinfect all stations. Please note the EPA recommends a 2-minute contact time for the active ingredient to kill SARS-Cov2 — this means you need to make sure the surfaces are moist enough not to dry out within that period. Please use your best judgment of making sure you refresh your Sani-Cloth as needed, but please also try to use them as efficiently as possible — they are a precious resource! As Sani-Cloths are currently in short supply, we also will be using Sani-Prime Germicidal spray (2-minute contact) and paper towels as well as Clorox Disinfecting wipes (0.5-minute contact). Please note that you should spray your towel first and then wipe, rather than spray the surface as this can cause some aerosolization of any surface virions.

Please also note that ALL supplies are ONLY for the internal use at CNI. Under no circumstances should researchers remove supplies from CNI for their lab or personal use outside CNI.

Station 2: Mock scanner Room
1. Use Sani-Cloth wipes to clean hard surface areas around the table cushion, all over the head coil.
2. Use the Swiffer mop with Swiffer Dry Sweeper Pads soaked with Sani-Prime spray to wipe down the bore area.
3. Place clean linens on the table cushion and the base of the head coil. Remove and place used linens in the hamper located in the mock scanner room.

Station 3:  Changing Area and Bathroom
1. Use Sani-Cloth wipes to clean door handles, faucets.
2. Use Sani-Cloth wipes to clean the bench.
3. Dispose of any used temporary clothing bag.

Station 4: Scanner Control Room
1. Use Sani-Cloth wipes to clean the console keyboard and mouse, surrounding desk surfaces, microphone buttons and control surfaces of the video switch, serial trigger box, FORP and stereo. Also wipe down chair arms.
2. If after the scan, wipe down any other areas you have touched including MRI safe glass frames, lens storage door, etc.

Station 5: Scan Room
1. All following steps to be complete before and after each subject.
2. Clean the MRI table with Sani-Cloth wipes.
3. Use Swiffer pole and Swiffer Dry Sweeper Pads soaked with Sani-Prime spray to clean the MR bore from entry up to the interior air vent. Please leave the scanner fan OFF while disinfecting, and then turn ON after 3 minutes in order to air out the scanner bore. You can subsequently adjust the fan for subject comfort as needed during the scan session.
4. Clean all used pads and positioners with Sani-Cloth wipes. Notify Laima if any are torn or fraying.
5. Clean any coil used inside and out with Sani-Cloth wipes.
6. Clean all ancillary equipment that was used such as bellows, plethysmograph, earmuffs with Sani-Cloth wipes.
7. Clean all common surfaces such as door handles and scanner buttons.

Station 6:Testing Room
1. Use Sani-Cloth wipes to wipe down the table surface and chair arms.
2. If using any supplies from the filing cabinet, be sure to wipe down both the supply container and any handles that were touched.

Station 7: Bathroom
1. Use Sani-Cloth wipes to clean door handles, faucets.

Station 9: Conference Room
1. Use Sani-Cloth wipes to clean door handles, conference table, chair arms.
2. Be sure to keep the conference windows open (there is a block limiting opening to 6” or less) whenever present.

Station 10: Room 050
1. Use Sani-Cloth wipes to clean areas that have been touched such as door handles, conference table, chair arms, etc..
2. We advise keeping the windows open when in use (there is a block limiting opening to 6” or less) whenever present.
3. Users can access Room 050 by exiting through the exterior door immediately outside CNI’s main entrance. However, users must return to CNI via the main entrance of Psychology. This will require users to walk up the exterior stairs and around to the front of Building 420.

We are glad to see more users returning to scan at CNI. We would like to share two important updates.

(1) Addition of Classroom 050 as a resource for CNI users

We are pleased to report that CNI users have been recently granted access to another room (Classroom 050).  The room is just outside CNI between Building 420 and the Math Building.

Key points regarding the usage of Room 050:

1. CNI users must have a department-approved SOP that would cover their intended use for Classroom 050.  Their department-SOP should also be updated to include the latest CNI SOP if it is not simply being referenced. 
2. Use of Classroom 050 is strictly for use in conjunction with a CNI scan — it is not to be used as an independent resource area. Users should reserve Classroom 050 on the CNI scheduling system as they do with other CNI rooms.
3. The maximum occupancy of Classroom 050 is 4 persons.
4. Cleaning requirements are identical to other areas in CNI including using disinfecting wipes to clean areas that have been touched such as door handles, conference table, chair arms prior to and after using this room.
5. We advise keeping the windows open when in use for additional ventilation.
6. IMPORTANT – Entry access to Building 420 is only via the Psychology main entrance facing the oval.  Users who take advantage of 050 must be prepared to walk up the exterior stairs and around to the front of Building 420 when wishing to re-enter CNI.  We recognize this may be an  inconvenience but it is required to meet county guidelines.

For access to Room 050 please contact the CNI staff.

This information is in the updated CNI SOP pointed to on the CNI Wiki Getting Started page.

(2) All CNI users must be registered in ORMS

All Stanford employees or students coming to Stanford campus (or CNI) must be registered in the Stanford On-Site Role Management System (ORMS).   It is the responsibility of PIs to contact their departmental manager to make sure their staff or students are registered.  New CNI users will not be granted badge access to CNI or Building 420 until they are registered in ORMS.

As a reminder, new CNI users must complete all of the following steps:

1. Complete CNI new user orientation session on Zoom.  Session times and registration forms are posted on the CNI Wiki Getting Started page.
2. Review the CNI Standard Operating Procedure (SOP). The CNI SOP covers procedures for participant screenings, enhanced cleaning procedures and other general required behavior during a research session as well as Stanford’s recommendations for employee screening as to whether they can come in to work. Please also review the CNI SOP Slideshow illustrating the main processes of the CNI SOP.
3. Complete the CNI COVID mitigation quiz/verification form
4. Complete the EHS training (STARS course code EHS-2470-WEB) on COVID19 information

We look forward to seeing you at the CNI!

The CNI Team

Stanford’s winter shutdown will be the three weeks from Saturday, December 12, through Sunday, January 3. Qualified CNI users wishing to scan during this period are welcome to book time for their studies as needed. A change in county guidelines such as a new shelter-in-place order may affect whether the CNI can remain open, or what types of in-person human subject research are still permissible, so please be sure to check our blog for updates prior to scanning.  

For everyone’s health and safety, please note the following guidelines for scanning during this shutdown period.

(1) CNI will operate in an weekend/evening mode. Bookings appearing in the calendar during this time period will be charged weekend/evening rates – https://cni.stanford.edu/wiki/Getting_Started#Billing_Policies

(2) CNI staff will not be on-site during this three week period. Remote support will be available the first week of shutdown (Saturday, December 12 – Sunday, December 20). Only emergency remote support will be available Monday, December 21 – Sunday, January 3.

(3) Janitorial support will be limited, being performed twice weekly. For the health and safety for all users, it is imperative that all CNI users perform all required COVID-19 mitigation cleaning scrupulously before and after their scans.

(4) During the CNI shutdown, all users must follow all university on-site requirements including being registered in ORMS and doing daily health checks.  The University also follows the Santa Clara County guidelines, and we will alert you should  any significant changes be announced.

(5) Parking enforcement will continue during the Winter shutdown – https://transportation.stanford.edu/news/parking-enforcement-continues-during-holiday-season-winter-closure

(6) Normal CNI operations will resume on Monday, January 4, 2021.

Please reach out to the CNI team for any additional questions or concerns.

The CNI team

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.

1. 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 properly boot up.  This was diagnosed as a failed power supply that provides power to much of the scan room interface equipment.  GE replaced the supply by cannibalizing another system, but this added more than a day to our schedule.
2. Lengthy calibration process: Given the advanced nature of our system, GE decided to repeat an extensive calibration process that usually only happens during a new system installation. This was expected to be only a day given our system was already in spec. Good news is that our system met all the calibration requirements, bad news is the hoped-for duration of one day wasn’t met.
3. DICOM server configuration change: We spent a considerable amount of time diagnosing a problem with Flywheel not being able to connect to the scanner DICOM server. This eventually turned out to be a change in the server name that wasn’t obvious.  This issue has been resolved and connectivity with Flywheel has been restored.
4. New coil configuration format: An unexpected change (to us) was a new coil configuration format.  This effects all of our research coils (NOVA 32 channel, NOVA 16 channel, the 32-channel baby prototype) and prevented them from operating on the updated system.  After scouring other systems we were able to find the configuration file for the NOVA 32 channel system and it is now functioning. We hope to get the new format configuration for the NOVA 16 channel from either NovaMedical or by working with GE engineers over the next week.
5. Research sequence incompatibility: Most of our research or modified product PSDs are installed and working correctly.  However, our research SMS or MUX sequences (BOLD and DTI) are not yet operational. The CNI spiral fieldmap sequence is also failing to correctly go through auto-prescan. We have made progress on enabling some debug utilities on the scanner and hope to diagnose the problems with these sequences soon.

Our hope is to solve the issues with the research sequences and test their integration with offline Flywheel reconstruction by today.  If we are not done, then we will continue to work over the weekend.  Because of the uncertainty, we have currently extended our service time through EOB Monday.   We will send out another update before 3pm Sunday, hopefully with good news.

Thanks for your patience!

The CNI Team

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 all research groups.  These changes are implemented in the scheduler, which enables users to clearly reserve space.  By explicitly scheduling the use of these spaces, users will more easily meet the space requirements for health safety.

We describe the changes in the research guidelines and then we describe the changes in space scheduling and other important notes.

1. New Human Subject Research Guidelines

As described on the Stanford Research Recovery site, the guidelines for non-clinical human subject research have been considerably relaxed.  As of October 21, community research subjects that are considered low risk for COVID-19 (not over the age of 65, and without medical conditions known to create serious risk) are allowed to participate on-campus as long as the PI has completed all other university requirements outlined on this site.  Please note that all PIs need to be familiar with the specific guidelines and restrictions on the Stanford Research Recovery site — we’ve chosen not to replicate or distill them into our SOP as they are continually evolving.

2. New CNI SOP

Our CNI SOP has been updated to explicitly add access to the CNI conference room.  While this room is under the 250 sq. ft. nominal requirement in order to have 2 occupants, we have received permission to use it in this manner.  However, we recommend keeping one or both windows open in order to improve ventilation.  We also have included markings on the conference table indicating where the two occupants should sit in order to observe 6′ of social distancing.

3. Additional CNI Scheduler Resources

We expanded the room reservation authority in the CNI scheduler to include the CNI conference room and the CNI lobby for anyone who is currently able to reserve the CNI mock scanner or testing room.  We are adding the CNI lobby as a resource in order to help ensure there aren’t any conflicts for this space between groups given the occupancy limits.  Please also note that the intent is for users to be reserving these extra spaces immediately prior to or after a scan session.  If you would like access to these spaces without a corresponding scan reservation please contact us in advance for approval.

4. Important note about entering the building and the CNI space

Please note that if you are a Stanford affiliate visiting the CNI, you should be entered into the Onsite Role Management System (ORMS) and have completed Stanford HealthCheck.  There are no exceptions.

The ORMS system uses badge swipes at door entries to record onsite personnel and ensure compliance with Stanford guidelines (HealthCheck, ORMS entry).  All Stanford affiliates should swipe their badge at the Building 420 external entry and CNI entry.

5. Important note about parking for researchers and participants

The Q parking spaces are not currently available so a virtual daily A parking permit needs to be purchased for participants. We recommend creating a departmental-level account with Stanford Transportation (see https://transportation.stanford.edu/parking/purchase-a-parking-permit/how-to-purchase). For each participant you will need to first add the vehicle details and then purchase a daily permit for them. If you are part of the Psychology Department they already have a web form based process for securing daily virtual A permits — please contact Lisa Ewan for more information. We will revisit the option of reacquiring the Q parking spaces as research activity increases.

Additionally please remember that on-campus parking in now enforced 24/7. There are only ‘A’ and ‘C’ spaces available, all visitor parking spaces have been removed. All researchers will need to purchase either an ‘A’ or a ‘C’ parking pass to park anywhere on campus during normal hours.  A free after-hours permit is available through the transportation portal as well.

Thanks and stay safe!

The CNI Team 

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 with Protocol Development time, and as a result some groups are having difficulty getting scheduled for basic research time.  We all benefit by prioritizing scheduling access for users running funded scans because this keeps the CNI viable.

Consequently, we propose to return to our normal policy regarding advance booking of Protocol Development time beginning Oct. 1, 2020.  Effectively this means Protocol Development time can be scheduled for regular daytime hours (8am-6pm M-F) no more than 48 hours in advance. Protocol Development for off-peak hours may be booked up to 5 days in advance.  Please note that these restrictions are not enforced by the scheduling system, so please note the rules when you schedule your times.

Please remember that Protocol Development time may not be used for publishable research data.  It is intended for establishing and testing protocol settings and to ensure any stimulus presentation and scan synchronization are working. 

Even with the return to normal policy, we expect that there will be plenty of Protocol Development time for people who are restarting their research projects.

For your convenience, we note that the CNI scheduling policy is described in some detail on the CNI wiki page, here.

The CNI Team

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 minutes) such as when passing other groups in the waiting room or hallways.  The intent of this modification is to allow groups to be using the mock scanner room while others are using the scan room.

If you find yourself in a situation where too many people are congregating in the waiting room or elsewhere, please relocate so that density requirements are being followed. This may mean waiting outside of CNI for a short while until other groups have left.

Back to Normal Hours

We are removing the restrictions of limiting scanning between 9am-6pm — CNI users who have the appropriate level of training are allowed to scan at off hours.  We ask that users who are new to operations under the new SOP come in during normal business hours in order to have CNI staff available to answer any questions.

Protocol Development Time

We will still be allowing protocol development time to be booked out up to 7 days  in advance.  If the CNI schedule starts to become more congested we will reinstate the 48 hour advance booking time limit and inform users accordingly.  Please remember that protocol development time may not be used for acquiring any research product.  It is meant only for establishing and testing protocol settings and to ensure any stimulus presentation and scan synchronization are working.

The CNI Team

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 anyone already coming to Stanford main campus.  We would like to suggest PIs utilize the Slack CNI workplace #general channel for recruiting volunteers among CNI users.  This will help keep interactions more local to just CNI users, as well as bringing in volunteers who are already familiar with the CNI and our COVID19 SOP.  Please note this is just a suggestion and not a requirement.

The CNI Team

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, non-clinical human subjects research activities that take place on campus may restart beginning July 15, 2020, for protocols that have met all of the following criteria:

1. Subjects are exclusively Stanford affiliates who are authorized by their departments and/or schools to be on the same campus location as the research facility for allowable business, and are registered in ORMS,Both subjects and researchers involved in in-person protocols are ready and willing to participate, in compliance with IRB recruitment and consent procedures.
2. Volunteer subjects should be recruited and recorded in ways that ensure willingness to participate is uninfluenced by supervision relationships (e.g., solicitations and decisions of whether or not to participate is kept confidential and anonymized for supervisors).
3. PIs have submitted Standard Operating Procedure (SOP) documentation that conforms to all requirements for Stage 2 Laboratories Research in the https://cardinalrecovery.stanford.edu/research/research-recovery/ (e.g., density criteria, hygiene, laboratory headcount and building population density), and the SOP documentation has been reviewed and approved by the appropriate department and/or school;
4. PIs commit to providing timely feedback, relevant insights, and challenges to the non-clinical human subjects’ research recovery working group about restart procedures and lessons learned while restarting.
5. Compliance with all rules, Standard Operating Procedures (SOPs), and scheduling programs for the research facility/building are being routinely monitored and deviations immediately reported.

Other non-clinical human subjects research should continue to be postponed or conducted online until a safe return to campus is possible.

The CNI Team

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 that we define in our SOP are entirely independent of the general University research recovery (URR) stages.  The University may be going to Stage 2 as of June 22nd — but human subjects research will remain at HSR-stage 1 — or same-group research subjects only until the University says otherwise.  The University may also adopt a more granular approach of reintroducing human subjects research such as: same-group subjects, same-department subjects, and so on.

We have also added a CNI SOP Slideshow to our Getting Started page that presents a pictorial view of the main processes in our SOP for scanning.

We have received a number of questions regarding the SOP and generally how to restart research on campus.  Many of these questions will be clarified as individual departments publish more information on the departmental & building SOPs, but we attempt to answer some of these below to the best of our ability.

FAQ

1. Q: What do I need to do besides the CNI training described on the CNI Wiki Getting Started page in order to start scanning?  A: Anyone coming to campus needs to be listed in the new On-site Role Management (OSRM) system.  Your departmental manager should have access to the system. If you were previously in the Essential Roles Smartsheet, you will have been automatically included in the list on the OSRM.  Your PI also needs to have an SOP approved by their appropriate department or school.  This should refer to the CNI SOP, and should also describe the process for recruiting same-group research subjects without any coercion.  If there are any additional interactions with the human subject (behavioral tests, training, etc.), then the process for executing these in a safe manner should also be described.
2. Q: What are the hours that CNI will be open for scanning?   A: We will be initially open on normal business workdays from 9AM – 6PM.  This is so that CNI staff can be onsite to answer questions about implementation of the CNI SOP, as well as to answer questions on the use of the new UHP scanner.  As demand ramps up, we will open up the schedule as needed.  Please feel free to email us if you would like an exception to the current hours.
3. Q: Can we use Protocol Development time? What are the rules for scheduling this time?   A: Yes.  We encourage groups to use Protocol Development time to familiarize themselves with the new scanner, and how to put the new COVID-19 Mitigation SOP into practice.  The more experience all our groups acquire with this SOP, the more positive feedback we can provide to the Human Subjects Research Recovery Subcommittee on CNI users’ preparation to restart research with a broader subject base.  Until further notice, it is acceptable to book Prototype Development time up to 1 week in advance (note this is all on the honor system).  Please exercise reasonable judgment on how much time you book — if the schedule is starting to look full please be considerate of others’ needs.
4. Q: How do I book a slot on the CNI scanner?   A: Use the regular scheduler, but make sure there are 1/2-hour blocks of “COVID19-Mitigation” before and after your booking. Note that only a single 1/2-hour “COVID19-Mitigation” block needs to be between scans.  In this case, researchers from the previous and following scan will each have 15 minutes of the 1/2-hour block for their disinfection protocol.  Only one group of researchers should be in CNI at a time.
5. Q: Can we use the Mock Scanner room or another room while another group is scanning?   A: Sorry – no.  In order to satisfy University requirements on reduced density, we cannot make these rooms available at present.  As the University progresses through the URR-stages, it may be possible to relax this restriction.  We are also investigating whether we can use the neighboring 050 Classroom for extended CNI use.  If this is permitted, we will be able to provide concurrent use of this room while another group is scanning.
6. Q: Do I need to follow Jordan Hall rules for entry and exit?   A: Yes! Jordan Hall will likely have a QR code posted at the primary entrance (Main Psychology entrance facing the Oval) directing you to an entry and exit Google form for tracking personnel.  You are required to complete any such posted requests.  You must also follow all posted social distancing marks and other signage. Note that only the rear elevator has room for 2 people — the front elevator has single occupancy only.  Entry and exit from Jordan Hall is currently also planned to be restricted to only the single main entry — you are required to follow any such restriction and not exit from any other door.
7. Q: Do PIs need to keep track of who is scanning and being scanned?   A: Yes! In the event of a COVID-19 detected infection, County contact tracers will be reaching out to CNI to find out who was in the MRI suite during and after the infected individual was present.  CNI will use it’s calendar to contact PI representatives to find out exactly who was present.
8. Q: What will the process for new user training look like?   A: As described on the CNI Wiki Getting Started page, new users need to register on Canvas for the online training and also register with the provided Zoom link for the CNI orientation session.  At this point they will be Level 2 users, and will need to accompany Level 3 operators to get hands-on training on the MRI system.  Given the University requirements to limit research personnel to a maximum of 2 on campus at any one time, Level 2 users will be limited to scanning phantoms ONLY with the assistance of their Level 3 labmate.  On request, CNI staff can join a Level 2 user to assist in scanning a labmate for instructional purposes and grant Level 3 status. If a lab does not have any Level 3 members, CNI staff can assist a Level 2 user in getting scan experience.
9. Q: What is the process for wearing and changing gloves?   A: New gloves should be put on for any interaction with a scan subject and removed afterwards. Scan subjects themselves do not need to wear gloves but should have either washed or sanitized their hands. We also recommend wearing gloves whenever performing the disinfection protocol. Gloves may be worn in the waiting area and scanner control room, but frequent hand washing or sanitization is also acceptable.
10. Q: I can’t find any Super-Sani wipes.  What do I do?  A: Disinfecting wipes continue to be at extreme shortage.  Please use our available Clorox wipes (4-minute contact time) or paper towels soaked with Sani-Prime spray (3-minute contact time).  Note: it is advisable to spray towels first and use, rather than spray a surface as this can aerosolize any surface virions. Remember, the purpose is to leave the surface noticeably moist with disinfectant.
11. Q: How do I manage to follow posted density requirements and get a subject into the scanner?   A: This is more of an issue when we are allowed to scan non-same-group subjects.  In this case, there will be 3 individuals entering the CNI. We suggest that one researcher remain in the scan room, while the second meets and screens the subject external to Jordan Hall. The second researcher will then escort the subject to CNI, perform the MRI screening and informed consent, have the subject change, and then pass them off to the first researcher in the scan room. This will ensure no posted density limits in CNI are exceeded.  In addition, density requirements will be relaxed as the University progresses to further URR stages.
12. Q: My scan subject feels claustrophobic wearing the mask in the scanner?  Can they remove it?   A: NO! We recognize this is likely to be a significant issue, but approval of our SOP includes the requirement for the scan subject to wear a mask and this is standard procedure for Stanford Radiology.  If the subject cannot tolerate wearing the mask inside the scanner, you need to exit them and cancel your scan.  Remember that scan subjects must wear an MRI-safe mask from which the metal ribbon has been removed.  Researchers that are in the scan room may wear an unmodified mask — CNI staff have tested the masks we have and there is very little attractive force and the ribbon is useful for conforming the mask to the face.

The CNI Team

Partial opening

The CNI will partially re-open this Wednesday, June 10th.  We expect much of the rest of the month of June to be used for protocol development (new UHP) and training on the new procedures (COVID-19).  For this initial period scheduling protocol development time up to 1 week in advance is permitted, and the CNI will be open weekdays from 9am to 6pm.

Before signing up for time, researchers should complete the CNI online re-certification training. You can sign up for time using the CNI scheduler - please remember to set at least a one-half hour block between studies.  The inter-session time sign-up is charged to the COVID-19 Mitigation grant.  Users will be granted access to the COVID-19 Mitigation grant after they have completed the required online re-certification training.

CNI requirements

Please consult the Getting Started page and the University Research Recovery Handbook.  We emphasize the key points here.

Lab requirements

These are Stanford requirements that are immediately relevant for labs to start measuring at the CNI.

1. Subjects must be members of the same research team as PIs
2. PIs and subjects are willing and ready to start and in compliance with IRB consent procedures, specifically
   • The consent process must explicitly explain that a decision to participate – or not – will not affect employment
   • It is recommended that PIs do not consent their reports
3. PIs must have a Standard Operating Procedure (SOP) for their lab that conforms to the density criteria and hygiene requirements for Stage 1 Laboratories Research (see the Research Recovery Handbook).
4. Departmental approval is required.
5. PIs are expected to provide feedback and share information with the research recovery working group

For the Stage 1 recovery, PIs will need to have a simple SOP for their labs.  For later stages, PIs will need a more extensive SOP

N.B. The CNI SOP  has been updated with the latest information (June 6, 2020).  Material from that page can be incorporated by reference.

Stanford requirements

Please note these Stanford requirements for all research activity that are particularly relevant to the CNI.

1. Each group is limited to having two group members on campus at a time.  At the CNI this means one person can be in the scanner and the other operating the console.  Or two people – physically distanced and wearing PPE – can measure a phantom.
2. Every group must keep a record of who came to the CNI for each session

Safety first

Personal protective equipment (PPE) will be available and required.  We encourage people who have their own masks – and this should be everybody – to bring them. Gloves, face shields, sanitizer, water, plastic face shields will arrive shortly and are required.  We are preparing a video to illustrate our current understanding of safe practices.

The CNI Team

The CNI Team believes that we can re-open safely.  There are issues beyond the CNI environment that the University must consider prior to giving us permission.  We report, however, that our confidence that the CNI environment can be safe is high. A blog post and Slack Channel messages will be sent out when CNI has been cleared for scanning and the dates for specific session are posted.

The items below describe our plans and why we will be ready to open when the University and County give us permission.

New Operating procedures

The CNI has drafted a standard operating procedures (SOP) document for safely resuming  human research studies. In preparation for restarting – and we don’t know when that will be – we ask CNI users to familiarize themselves with the new policies and protocols for scanning human subjects.

The  SOP document was developed in collaboration with people representing Environmental Health and Safety and Human Subjects Research policies at Stanford University. The principal safety tools in the plan

• use signage to make the rules clear to all participants, including restrict the area that needs frequent cleaning
• restrict the number of participants to meet the density restrictions using the facility and require physical distancing
• require and provide PPE  to all participants including masks and hand-washing prior to entry
• require Stanford health checks prior to entering the CNI

Re-certification

To be sure the new procedures are clear,  users must re-certify for scanning privileges.  This can be done by completing CNI Covid-19 training.  The steps and documents for recertification for scanning at CNI are posted on the CNI “Getting Started” Wiki  in the new “COVID-19″ section at the top of the page. 

In addition to being cleared to scan by their PI and the usual safety training, the new certification steps are: 

1. Review the CNI SOP. The CNI SOP covers the procedures for participant screenings, enhanced cleaning procedures, and required behavior during a research session.
2. Complete the quiz/verification form link from the COVID-19 section at the top of the CNI “Getting Started” Wiki page quiz/verification form
3. Complete the EHS training on COVID19 hygiene best practices (STARS Course Code EHS-2470-WEB)

New procedure: visitor forms

For each scanning session participants must complete an additional CNI COVID-19 SCREENING, MITIGATION AND ASSUMPTION OF RISKS form.  This document informs all visitors to the CNI what steps we are taking to mitigate the risk of COVID-19 transmission.  These precautions  significantly reduce the risk of infection, but  visitors should recognize that the level of risk of COVID-19 infection increases as it would for any activity outside the home.

The screening questions must be completed by all CNI visitors and users; links to the form are also posted on the  CNI “Getting Started” Wiki page. When completed, the form must be left in the labelled box (labelled “CNI forms”) located by the CNI printer in the CNI control room at the conclusion of each scanning session.

New user training

Please  fill out the registration form for the session that you would like to attend. Enrollment to each session is limited to eight people. There will also be some changes for the new user orientation sessions, which will now be Zoom sessions. For new users to CNI, new user training will be the following:

1. CNI user training begins with the completion of the Level 1 and Level 2 on-line training modules in Canvas. The links to the training module are on the CNI “Getting Started” Wiki  page.
2. Completion of the on-line training is now followed by registration in a Level1/Level2 Zoom orientation session. The in-person orientation sessions have are discontinued and replaced with a one hour Zoom session. The Zoom orientation sessions will be held on Thursdays from 9-10AM. Current sessions will be listed on the CNI “Getting Started” Wiki page.
3. All new users will be additionally required to complete the CNI Covid-19 training already described in this blog. The steps and documents for this training are posted on the CNI Wiki “Getting Started” page in the new “COVID-19″ section.

Feedback regarding all the new procedures is always encouraged and appreciated by the CNI team.

The CNI Team

We have updated the CNI IRB page  to consolidate and simplify the descriptions and classifications of equipment and devices at CNI.  The new documentation consolidates the Device description to include the new UHP MRI scanner, software and coils in your IRB applications.  These do not need to called out separately. This updated information was prepared and approved in consultation with the Human Subjects Committee.

As aids you can use the CNI IRB and CNI consent forms posted on the CNI IRB Wiki page. These documents are the most recent modfications, which include scanning on the new 3T UHP system, and also the ability to scan both at CNI and at the Lucas Center. You will also need to attach the CNI participant screening form to your submission, which is also posted on the CNI IRB Wiki page.

If you already have modified or created a new IRB that describes the CNI UHP scanner and auxiliary equipment that has been approved, there’s no need to start a new modification.  If you are planning to write such an update, we suggest you use this information.

The CNI Team

Our conversations with the University make it seem likely that when research starts up again there will be various COVID19-mitigation related issues that impact users directly.  This post is one in a series that we will share as the University policy evolves.

Safe operations - The CNI has developed a standard operating procedures (SOP) document  for when studies are resumed.  The document defines the procedures we see as critical for the safe operation of the CNI facility. The policies and procedures discussed in this document were developed in collaboration with people representing Environmental Health and Safety and Human Subjects Research policies at Stanford University. We will share the full document with you as well as our implementation plans over the course of the next week or two; here we provide an overview.

We have designed the document to define how Human Subject Research can be undertaken at CNI with minimal risk of COVID-19 transmission.  We believe that we will achieve this goal if the procedures, which include redundant mechanisms to ensure adequate disinfection protocols,  are rigorously followed.

A document is only as valuable if it has the support of facility users.  It is essential that people understand the procedures and that we work as a whole community to follow protocols.  This means being willing to do more than your fair share.

To be sure that people understand the protocols, we will require users to do CNI Covid-19 training prior to resumption of their scanning privileges at CNI. All users who have been cleared to scan by their PI must complete this recertification, no exceptions. The steps for recertification are posted on the CNI Wiki “Getting Started” in a new “COVID-19″ section and are also listed here.

1. Review of the CNI SOP posted on-line and completion of the quiz/verification form. The CNI SOP covers procedures for participant screenings, enhanced cleaning procedures, and other general required behavior during a research session as well as Stanford’s recommendations for employee screening as to whether they can come in to work.
2. Completion of the EHS training on COVID19 hygiene best practices (STARS Course Code EHS-2470-WEB)
   

Because cleaning is important, and the time and expense of cleaning increases with space, we plan to restrict access to parts of the CNI for essential functions. This will reduce the amount of space that requires frequent cleaning.  To limit the chance of transmission, we will limit the number of people in the facility at any one time. If you typically brought four or five people as helpers to the scan, we will ask you to bring fewer.  Research groups will also be restricted to just a single group using the center at a time.  

The most important elements of the new scanning protocols to keep in mind at CNI are:

1. On the day of their scan, researchers must have confirmed that they meet Stanford’s requirements for employees coming into work prior to arriving at CNI.  This will be facilitated by the use of the Stanford HealthCheck Form https://healthcheck.stanford.edu/.  
2. Researchers must be diligent in screening subjects prior to enrolling them in a study, and they must screen them again 24-48 hours in advance of the planned scan time, and again when subjects arrive to CNI as described in the CNI SOP. As much as possible researchers will practice social distancing, maintaining 6 feet of separation between each other and research subjects. 
   
3. For each scan, researchers will arrive 15-30 minutes in advance of their subject to perform the required cleaning procedures outlined in the CNI SOP for the stations that will be used for their particular research session.
   
4. Following their research session researchers will perform cleaning procedures at each of the stations they or their subject have utilized for their research session as outlined in the CNI SOP for those stations.

Feedback regarding all the new procedures is always encouraged and appreciated by the CNI team.

The CNI team continues to meet twice-a-week through the shutdown. We hope to be fully ready on the first-day that the University opens. We continue to monitor best practices and anticipated regulations so that we can be ready to open safely.  This message describes some of the additional work we are doing.

We have created a Slack workspace for CNI (https://stanford-cni.slack.com) where you can send us your thoughts about issues we might address during the shut down.  If you haven’t used Slack before, please checkout these resources (https://uit.stanford.edu/service/slack/resources).   We hope Slack will become a way for CNI users to share information broadly — not just with CNI staff.

Equipment infrastructure (Adam)

The installation and conversion of pulse sequences is largely finished. After this major change, we needed to do a lot of testing and some infrastructure management.  These are not glamorous tasks, but they are absolutely essential for high quality data. Fortunately, our application to grant Adam and Laima an Essential Role status was accepted, so they have been continuing to work with the Stanford Facilities team.

An important part of the new system is heat management; by improving the remote monitoring & control of the cooling system for the scanner we can now improve our ability to deal with generated heat.  This is important for data stability when running long scans with the new, powerful gradients. Related, the chilled water pump speed is now running at 85% of maximum.  For the moment there is a noticeable noise from the pump, but we expect this will be fixed when making some changes to the secondary loop on May 4.  (This installation is subject to clearing any shelter-in-place orders for a single plumber to do the work). On that day we will be installing a new heat exchanger, reworking some of the plumbing, and overhauling the pump.  These changes are all needed to take full advantage of the new, powerful gradient system.

Pulse sequence upgrades and validation (Hua)

Hua has posted on the cni.flywheel.io site some comparisons between the UHP and other scanners under the project ‘scanner_comparison’. The current comparisons mostly focus on temporal SNR and stability measurements of BOLD time series, and we use phantom data as a benchmark of those measurements. The result shows superior temporal SNR on the UHP comparing to our previous scanner, the MR750, for both regular and multi-band BOLD sequences. It also shows a significant reduction in signal center frequency drift on the UHP comparing to the MR750 during long BOLD time series. We also collected a limited number of in vivo scans on different scanners.

For those interested in backwards compatibility, we found that enforcing the UHP to use the same peak gradient amplitude as the MR750, we were able to achieve very comparable diffusion timing on both systems.

One of several motivations for the upgrade was to permit us to perform new kinds of neuroimaging measurements.   We are very interested in comparing the performance of the diffusion sequences, an area where the new system should excel. There will be new sequences that should permit sub-millimeter diffusion measurements for  diffusion-related statistical assessments and tractography.  These may provide new information about the pathways near the cortical surface as well as be helpful in sorting through crossing fiber regions.  Understanding the value of these new methods always takes some time and involves collaboration between the MR physics team and Neuroimaging teams. We look forward to starting these collaborations as soon as we are open.

Modifying IRBs for the UHP (Laima)

We are in the process of updating the CNI IRB page  to consolidate and simplify the descriptions and classifications of equipment and of devices at CNI.  The new documentation consolidates the Device description and with the new UHP MRI scanner, software, coils, and eye-tracking system in your IRB applications.  Please note that if you already have modified or created a new IRB that describes the CNI UHP scanner and auxiliary equipment that’s been approved, there’s no need to start a new modification–this text is just to simplify the process for IRBs that still need to be updated to include the UHP scanner. We expect the new text will be posted to the Wiki during next week (April 13).

The CNI Team

Today’s ‘shelter-in-place’ announcement (March 16, 2020) means that the CNI (and Jordan Hall) are closed to all non-essential personal.  The CNI staff can be reached online through the usual email and text methods.

In the coming days we plan to send out messages about CNI plans for the future when we all return. We wish you all good health during this challenging period.

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.

1. Please ask all volunteers and participants, before they arrive at CNI, if they have experienced any of the symptoms associated with the COVID-19 virus or if they have any family members with symptoms of the illness listed below. If they have any of the following symptoms or have traveled outside the US in the last two weeks do not bring them to CNI.
   • Fever
   • Cough
   • Breathing difficulty.
2. As with all infection and disease control, to prevent the spread of infection, use good hand washing technique:
   • Wet your hands with clean, running water (warm or cold), then turn off tap.
   • Apply soap.
   • Lather your hands by rubbing them together with the soap.
   • Lather the backs of your hands, between your fingers, and under your nails.
   • Scrub your hands for at least 20 seconds.
3. Be hyper-vigilant when cleaning up after your subject always, but especially now. Wipe all surfaces, sponges, and equipment with disenfecting wipes. Be sure to include RF coil, button box, squeeze ball, PPG, resp. belt and everything else a subject (or you) might have touched. You should include keyboards and mouse. Use the hand sanitizers or hand soap frequently.
4. If you or your scanning colleagues feel sick, please stay home.
5. Janitorial staff will be disinfecting regularly touched surfaces (door handles and immediate surroundings, bathroom faucets, etc.) twice daily.

In addition, in order to remove any incentive for users to scan against contraindications we are waiving all cancellation fees for at least the next month.  However, we ask  that everyone still abide by our underlying tenet of scheduling scan time only when there is a confirmed subject available.  Once the COVID situation has been resolved we will send out an update and cancellation fees will be reinstated at that time.

CNI staff will also be actively monitoring the CNI facility for cleanliness. Please take seriously our communal responsibility to care for each other.

— The CNI Team

We changed the location of the CNI User’s meeting to the Rotunda room (E241).  This room is directly above the (closed) pub.  If you are entering from the front the room is up the stairs.

The time is still 10:30-11:30.

We still plan to create a Zoom link for everyone to use.  We will send this in the morning.

Sorry for the last minute change.

The CNI Team

HOLD THE DATE:   User meeting March 6th, 10:30am

The installation is proceeding roughly on time.  The equipment installation has now passed all of the tests required for clinical scanning.  Our site is ‘special’, so there remains a great deal of specialization work that Adam, Hua, Laima and Michael have to do to get back to our specific configuration.  This will take approximately another two weeks – if all goes well.  That should be about March 2nd.

The system will open up in three steps.

• First, around or just after March 2nd we will permit groups to sign up to test protocols (protocol development time).  The CNI team will be around to help make sure that your protocols are working as you expect.  The calendar is currently closed, but once the team is ready they will release times that you can use for protocol testing.
• Second, the calendar will open Monday, February 17th for reservations 4 weeks later (Monday, March 16th).
• Third, on Monday, February 24th at 9am we will extend the advanced booking to 8 weeks (Monday, April 20th).   This is the standard advanced booking of 8 weeks that was used prior to the upgrade.  The slots March 23 through April 20 will open up all at once at that time.

HOLD THE DATE:   User meeting March 6th, 10:30am

The GE and CNI teams have been working intensely on the installation of the new gradient and electronics systems.  The electronics cabinets – including the new gradient amplifiers, cabinets, and a massive amount of wiring – have been installed.  The new gradient coil has arrived and is ready for installation.

There was a setback a couple of days ago that briefly had us worried.  One of the protective elements of the new coil was shipped with improper labeling.  This created a dangerous situation that required us to ramp down the main field.  The situation has resolved, and the magnet is being brought back up to field strength.  The incident may have impacted the schedule by a couple of days – but it may also be possible that we lost only a very little time.

Throughout this complex process the GE and CNI teams worked together with some intensity and for very long hours.  There are very few coils in the world like the one we are installing, and GE has not carried out this particular upgrade many times.  There is always a learning curve and this is a very large and complex instrument.  We will tell you more details at the user meeting.

We remain on target for re-opening in early March.  There will be a series of messages from all of us at the CNI as the system starts up.  These will pertain to scheduling, new protocols, and image quality reports.  Please communicate these to other CNI users to make sure that the community as a whole stays up to date.

For now, we urge all PIs to to update your IRB protocols.

A picture of the new coil is shown below.  In addition, and unconnected to the install, a few days ago Adam had a serious injury while bicycling - a car door swung open into his path and the incident broke the index finger on his right hand.  He had to undergo surgery.  What a life – but he is soldiering on and barely missed a beat.

The CNI Team

The CNI scanner upgrade has begun! As you can see from the picture – the guts have been pulled out.

 


 
Adam and the CNI team are in constant discussion with the Stanford Construction team (led once again by Fred Sutton!) who is overseeing the modifications to infrastructure, and with the GE team that is disassembling the current system and installing the new one.  Mostly progress is straight ahead. But there are issues, too. For example, Adam is making calculations about the heat exchanger that removes heat from the MRI scanner, using the campus chilled water system.  The contractor ordered a replacement system that is far bigger than we need (purple thing).  The exchanger is over-qualified and will take up a lot of space and make other work inconvenient.  Adam is considering possible solutions to the problem; this was the topic of today’s CNI management meeting.  In addition to the parts, we had a discussion about some new quantitative information about the critical nature of controlling the temperature of the water. Despite the heat exchanger issue, the schedule for the upgrade remains unchanged. Of course, it is not possible for us to be 100% certain about this timing, so please view the following dates as our current best estimates rather than a hard commitment.  We will keep updating our best estimates, but we want to offer them now so that people who are planning subject recruitment can make more informed decisions.

• System installation should be complete by March 6; that’s when GE leaves
• The next week (March 9-13) we will be testing,  adjusting protocols, and and user training  for the new operating system
• We anticipate that we will be ready on March 16 for normal scanning.

For those of you scheduling subjects, our plan is to open up the calendar for new signups one month in advance (mid-February). We plan to send additional updates every few days, sooner if there is something new to report.

The CNI Team

Dear CNI Users: 

Charges at a service center like the CNI are closely monitored by Stanford’s financial officers.  The principles are to set the rates so that the service center does not make or lose much money in any given year.  The costs of running the CNI are the staff salaries, scanner maintenance, and supplies.  In case you are wondering, our center is extremely inexpensive compared to most in the country.

There is a second principle worth noting: most of the charges are made to NIH grants.  It is a government rule that charges to a grant must benefit the NIH grant itself, not some future user. This limits the ability to purchase new equipment that will benefit only future users. For example, we cannot purchase a new head coil that will be installed next year based on this year’s income.

This year

For a few reasons, this year the CNI has a surplus.  The surplus arises because of the scheduling improvements we made earlier this year, and some reduced costs.

We are permitted to have a surplus of up to 15% of our annual expenses but no more.  To comply with service center rules we must adjust our rates at this time.

The rate adjustment

Starting from June 1, the CNI hourly rates will be reduced by 25%. These rates will be in place until March 1, 2020.  After March 1 the rates will  rise to a level that is similar to where they have been, subject to approval by Stanford’s financial officers.

New hourly scan rates

8:00AM to 6:00PM weekdays (Monday-Friday)         - $320/hour

6:00PM to Midnight weekdays (Monday-Friday)       - $245/hour
8:00AM to Midnight weekends (Saturday-Sunday)   - $245/hour
8:00AM to Midnight University Holidays or Closure – $245/hour

Midnight to 8:00AM any day (Monday-Sunday)         - $75/hour

EEG usage charge is an additional $50/hour at any time

Many of you are interested in Artificial Intelligence approaches to Medical Imaging.  If so, this conference is for you.  But you have to register!
The workshop will include talks, panel discussions and interactive demos that highlight:

(If you are a student who can’t afford the $35 dollars for the registration, which pays for food, let me know.  I might be able to help.  Or your adviser might).

Brian