Recent advances in in-vivo spectroscopy methods at CNI Background Interest in measuring metabolic changes via MRS techniques and combining that information with functional MRI measurements in neuroscience studies continues to grow. CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities read more…

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 read more…

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 read more…

This week we are reminding everyone about two items: shared space usage and scheduling policies.  We need your help in maintaining a safe and productive environment at CNI. First, we need everyone to help keep the CNI shared space clean and orderly. Some of the important guidelines are below. Second, the facility is being heavily used.  We ask all of you read more…

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 read more…

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 read more…

Recent advances in In-vivo spectroscopy methods at the CNI Background A growing number of people at the CNI are interested in measuring metabolic changes in the brain using in-vivo spectroscopy (MRS) techniques.  Often, they combine this information with functional MRI measurements. The special interest spectroscopy group at CNI  develops and supports new MRS data acquisition and read more…

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

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 read more…

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

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

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

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 read more…

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

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

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

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

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

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

Funding opportunity – Please see the funding opportunity below, sent on behalf of the Wu Tsai Human Performance Alliance: The Wu Tsai Human Performance Alliance is a new interdisciplinary research initiative whose mission is to transform human health and wellness on a global scale through the discovery and translation of the underlying principles which govern human performance. We read more…

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

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

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

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 read more…

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 read more…

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 read more…

1. Introduction Good news — after a lot of hard work over the weekend by the CNI staff, we are most of the way back to normal operation with our upgrade to GE’s RX28 release.  The significant accomplishments over the weekend include solving the issues with the research SMS sequences as well as the spiral read more…

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

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

The software controlling the new UHP system will be significantly upgraded in early November.  This post describes the system upgrade. We also describe the valuable features of a new display we recently installed in the control room. 1. MR Software Upgrade Our 3T Ultra-High Performance system is scheduled for a host computer and operating system upgrade over read more…

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

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

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

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

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

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

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

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

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 read more…

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 read more…

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 read more…

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 read more…

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 read more…

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. read more…

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

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

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

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 read more…

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

The CNI users’ meeting will held on Friday, March 6, 10:30 to 11:30AM in the new Wu Tsai Neurosciences Building Room E153. We look forward to sharing the latest on the system upgrade. Also – stay tuned for another blog posting soon regarding opening of the CNI calendar for times earlier than the week March 16. read more…