Brian Wandell

CNI Technology Update

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 CNI Technology Update

Reopening the CNI - safe operations - part 2

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 Reopening the CNI - safe operations - part 2

Updated CNI IRB information

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 Updated CNI IRB information

CNI - April 10 update

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 CNI - April 10 update

CNI Update: Shelter-in-place

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 CNI Update: Shelter-in-place

CNI Users Meeting (3/6/2020): Room location change

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 CNI Users Meeting (3/6/2020): Room location change

CNI Upgrade News (II)

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… Read more CNI Upgrade News (II)

CNI - Upgrade update (Feb 10)

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… Read more CNI - Upgrade update (Feb 10)

CNI: Notes from the Underground

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… Read more CNI: Notes from the Underground

CNI Users meeting - September 6th, 2019

Dear CNI Users:  We are inviting you to a User Meeting 10:30-11:30AM on Friday Sept. 6 in Bldg 380, Rm 380C.  This is in the Math building and is easily accessed from the sublevel patio just outside CNI. We will use this meeting to discuss issues surrounding the upgrade of the CNI scanner beginning in January, 2020.  The… Read more CNI Users meeting - September 6th, 2019

CNI hourly scan rate adjustments

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… Read more CNI hourly scan rate adjustments

CNI upgrade planning

Planning for an MRI scanner upgrade at the CNI The MRI scanner we have (GE DVMR 750) is about 8 years old. There have been advances over the years that we incorporated through compute infrastructure and software. It is now time for us to consider the opportunity for a hardware upgrade. In anticipation of the hardware… Read more CNI upgrade planning

Medical Imaging and Artificial Intelligence conference at Stanford

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… Read more Medical Imaging and Artificial Intelligence conference at Stanford

Flywheel: Part Four

Flywheel We are on track to switch over to Flywheel on Saturday, September 1.  As of that day, new data collected at CNI will not be placed in NIMS.  New data will be sent  to Flywheel directly (https://cni.flywheel.io).  NIMS will be kept online as legacy only. Logins for the Flywheel site is managed by Stanford authentication, via Google. So to login… Read more Flywheel: Part Four

Flywheel: Part Three

Thanks to all of you who have started to take a look at the Flywheel data management system. A few notes and reminders. 1.  We are still on track for a September 1 change over.  Having said this, Michael is considering transitioning a little bit sooner.  The reason is that the very heavy use of… Read more Flywheel: Part Three

NIMS transition to Flywheel: Part Two

Main point The Flywheel data management system has been running smoothly for several months at the CNI.  The main purpose of this message is to encourage you to explore Flywheel (https://cni.flywheel.io). A number of groups have already switched from NIMS to take advantage of Flywheel’s features. After Michael completes further testing, which we anticipate to be around September 1, we will… Read more NIMS transition to Flywheel: Part Two

Laima measures GABA

You may have been wondering about Laima’s experimental work over the last few years.  You can now read about it in a paper co-authored by folks who work at the CNI, GE, and Lucas.  Nice collaboration! GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence Meng Gu, Ralph Hurd, Ralph Noeske, Laima Baltusis, Roeland Hancock, Matthew D. Sacchet, Ian H. Gotlib, Frederick T. Chin, Daniel M. Spielman… Read more Laima measures GABA

Choosing an MRI protocol for your experiment

The CNI’s Wiki pages offer general advice about how to set up your scan protocols and save the information for later use. The wiki pages take you through the template protocols we think are most widely used. These protocols can be found on the the scanner console, saved under “CNI/head” within the protocol pool. The… Read more Choosing an MRI protocol for your experiment

Bob Dougherty farewell

Please come by the CNI this Friday (May 5th) at 5-6:30pm to share some nibbles and to wish Bob well;  he will  be moving out of the CNI to his new office space at Mindstrong. A good time will be had by all.   Laima, Adam, Michael, Hua, and Brian

CNI - A new team

Hi Everyone, About three weeks ago Bob Dougherty let the CNI board know that he was considering taking a position in an interesting new company, Mindstrong Health, a startup in health management. We tried to change Bob’s mind, but it is strong; we were not successful. Bob’s last official day at the CNI is March 31st, though… Read more CNI - A new team

CNI 5th Year - Thanks and links to videos of the presentations

The CNI Team sends a thanks to the many of you who took the time to come to the talks and celebrate the CNI’s fifth year.  We hope you enjoyed the morning. A special thanks to Nisa Cao, who organized the room, food, and posters, with great help from Roz Grayson and Porsche Williams.  Nisa and the… Read more CNI 5th Year - Thanks and links to videos of the presentations

CNI - Celebrating Five Years (Save the Date, October 14th)

Save the Date:  The morning of Friday, October 14th The CNI team invites you to join us for a celebration to mark our first five years of operation.  The celebration will take place the morning of October 14th.  We have not yet secured a room, but we remain hopeful ;-).  The time is a bit uncertain because the room… Read more CNI - Celebrating Five Years (Save the Date, October 14th)

Data management and storage at the CNI

In planning the CNI environment, we made a risky decision: We committed to providing the community with data management services. Many of you know that most MRI centers do no more than hand the user a DVD at the end of the session, and wish them well. Or perhaps they allow the user to copy the data… Read more Data management and storage at the CNI

Planning for hardware upgrades

The CNI is planning for a significant equipment upgrade, which we expect to be available in about a year. This message describes our plans, which are rather uncertain. Despite this uncertainty, we thought it best to write this note to give you plenty of time to plan. About a year ago, Siemens released a new scanner… Read more Planning for hardware upgrades