CNI – April 10 update

April 10th, 2020
April 10th, 2020

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 ( 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 (   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 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

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