Archive for the ‘Uncategorized’ Category

CNI scanner upgrade to DV26

November 9th, 2017

After weeks of testing, the CNI will upgrade the scanner’s software to DV26 on Monday, Nov 12, 2017. All existing protocols will be migrated to the new platform, and we fully expect they will perform as they do on the current platform. Data will continue to be stored in NIMS as they are now as we continue to make progress on migrating NIMS to our new data management platform, Flywheel (more on that soon). Please contact us if you notice any issues with your protocol or data.

The DV26 interface will feel a whole lot like the current platform (DV25), so we don’t expect any of you to be disoriented when we switch. There are, however, some very minor differences that we want you to be aware of.

SAR limit settings. What follows are step-by-step instructions for setting the SAR limit in DV26 — note that these changes don’t affect most sequences:

  1. When starting an exam, in the dialog window for selecting operating mode the first level dB/dt and SAR limit are selected by default: you can click the “Accept” button directly to enter the exam unless you want to change the operating mode.
  2. By default the system will automatically run a “SAR Scout” scan for SAR limit calculation before the localizer in each exam. This scan will show up in the list of Task as series 0. The Scout is 6s long and doesn’t generate images.

Spectroscopy. If you are using spectroscopy sequences, please refer to the CNI wiki for a description of how to prescribe a rotated voxel acquisition. GE has committed to working on a solution which does not require this workaround, but we don’t yet have an expected date for when this will be available.

SMS BOLD and DTI. Our current SMS BOLD and DTI sequences (muxarcepi and muxepi2) will be available, and they will still work as in DV25. While the DV26 software supports the product SMS DTI sequence known as Hyperband DTI, we recommend users to continue using our research sequences until we have had the opportunity to fully evaluate the Hyperband DTI sequence.


Laima measures GABA

August 31st, 2017

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 (

The CNI Team

Choosing an MRI protocol for your experiment

May 5th, 2017

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 protocol templates are organized by category.  One set is based on conventional multislice (2D) or 3D methods, a second set is based on the new simultaneous multislice (SMS) protocols (also called mux or multiband), and a third set are some special methods (spectroscopy and qMRI).

We provide a variety of templates in each category and some recommendations about choosing the right template based on our experience. You can get help in customizing the parameters from the CNI staff (ask Hua, Adam, or Laima).

Here is a brief description of the templates.  All the protocols start with ‘CNI Example’.  The examples below show several ‘presets’ for different types of scans.  You can change the parameters in most cases.

  • CNI Example Anatomical  - A great opening item for most experiments
    • T1w (0.8/0.9/1 mm, sag/ax)
    • T2w (0.8 mm, sag, w/o FLAIR/PROMO)
    • T2w/PDw
  • CNI Example basic fMRI - The GE classic BOLD product sequence, a customer favorite
    • BOLD EPI full brain coverage (2.9mm)
    • BOLD EPI partial brain coverage (1.8mm)
  • CNI Example basic DWI
    • DTI (b=1000, dir=60) – If you plan to use a diffusion tensor model, this will do
    • HARDI (b=2000/2500, dir=80/96) – For more advanced models these parameters are better
  • CNI Example SMS fMRI – Prepared specially our CNI chefs, and now offered nationwide
    • BOLD EPI (mux=6/8, 2.4/2 mm) – BOLD imaging goes forth to SMS, locally grown
    • Multi-echo EPI (3 echoes) – Useful for looking at T2* in BOLD
  • CNI Example SMS DWI – If you are in a hurry for a nutritious scan
    • HARDI (b=2500/3000, dir=80/96)
    • Multi-shell (2-shell, 3-shell)
  • CNI Example qMR – For those devoted to quantification
    • T1 map (2mm)
    • T1 map + PD map (1mm)
  • CNI Example Spectroscopy – Laima’s secret sauce
    • IMSPECIAL (new GABA measurement)
    • Probe-P general (more metabolites)

If you would like to run a different protocol from the ones listed here, please contact us.  We can very likely help configure the protocol.  For example, we can help users who would like to run multi-shell DWI used by NODDI, or with other sequences.

Hua and Brian


Bob Dougherty farewell

May 3rd, 2017

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

March 22nd, 2017

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 he will remain with us as a visitor for one additional month. We wish him well in his new adventure!

I write to explain our plan for the future CNI organization.

First, I am glad to say that Laima, Hua and I will still be here and helping as usual. You can still go to Laima for safety training, scheduling, and general help with scanning as before. Hua will take on some additional responsibilities to help users; she will particularly help with scanner issues such as helping you decide on your sequences and also helping with scanner issues during the times when Laima is not at her desk.

Two people, Adam Kerr and Michael Perry, will join the staff of the CNI. Adam will oversee the MR system, including pulse sequence development and big hardware.  Michael Perry will take responsibility for data management and processing. They will share responsibilities for managing the various physical devices that are used for experiments (button boxes, displays, physiological data, sound, etc.).

Adam has worked with us at the CNI for several years. His main appointment is in the EE department. Adam, along with Kangrong, Hua and Bob, was a key developer of the SMS sequences that are widely deployed at the CNI and that are the basis for the GE SMS product that will ship in the next few months. In addition to a general help with your protocols, Adam will have primary responsibility for managing the big hardware including overseeing the planned system upgrades. These tasks were about half of Bob’s time, and Adam will be a 50% time staff of the CNI.

Michael has worked with Bob at the CNI supporting the computer infrastructure, including hardware maintenance and data management for several years. He is increasing his commitment to 50% to cover the data management parts of Bob’s job (recon failures, data download issues).  Michael will be overseeing the upgrade of the data management system, including both new hardware and software, that will take place over the next few months.

We will announce some CNI social events shortly so that you can visit with all of us and share your ideas about the new organization and to meet any of the people you do not yet know. We will be glad to tell you what we are thinking and to hear back from you.  Next week we will send out some messages about specific times.

It has been a real pleasure for me to work with Bob for nearly twenty years, the last five at the CNI.  He will be missed.  Laima, Hua, Adam, Michael, and I are committed to continuing to support your work and we will try to live up to the standards of the past five years.


Brian Wandell

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

October 19th, 2016

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 team made the event happen smoothly, and we are very grateful for their help.

Michael Perry posted videos of the talks as well as a few pictures from the event.  These are hosted at the site he built and maintains.

Brian, Bob and Laima


CNI Fifth Year Celebration

October 5th, 2016

Friday, October 14th – Room 041 Jordan Hall

The CNI team invites you to join us for a celebration to mark our first five years of operation.  The event will take place the morning of October 14th, the day after the SNI Symposium.

Register here

Schedule – Friday, October 14, 2016

9:00 –  Coffee

9:30 –  Welcome, History and Update

10:00 – Professor Nikos Logothetis
Max Planck Institute for Biological Cybernetics, Tübingen

NET-fMRI of Large-Scale Brain Networks:  Mapping Dynamic Connectivity in Epochs of Synaptic and System Consolidation

Neural-Event-Triggered fMRI (NET-fMRI) can potentially map whole-brain activity, associated with individual local events – or their interactions – in various brain structures. In my talk, I will describe a number of characteristic states of widespread cortical and subcortical networks that are associated with the occurrence of thalamic, hippocampal  and pontine events, which may be related to synaptic and systems consolidation of different memories.

10:45 – Professor David Eagleman
Department of Psychiatry and Behavioral Sciences, Stanford University

How the Brain Constructs Reality

11:30 – 1:00 Posters and Lunch

So that we can plan for the proper amount of coffee and food, please Register for this event.

In addition to the scientific presentations, we will host a poster session where we invite all members of the campus-wide neuroimaging community to come and present your projects with other members of the community.

As part of the event the CNI team will update you about the equipment and software plans for the CNI and how we and our colleagues at the Lucas Center are working together to try to provide high quality neuroimaging support for the campus. There will be time for you to provide us with feedback on new features you would like to see implemented.

Brian, Bob, Laima and Hua

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

August 12th, 2016

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 available is a bit uncertain.  So this is just a heads-up about the morning/lunch.

Here is what we do know:  There will be two 45 minute presentations from distinguished colleagues who are visiting Stanford,

In addition to the talks, we will have a poster session where we invite all members of the campus-wide neuroimaging community to share information about your projects and to meet other members of the community.

Finally, as part of the event the CNI team will update you about the equipment and software plans for the CNI and how we and our colleagues at the Lucas Center are working together to try to provide high quality neuroimaging support for the campus. There will be time for you to provide us with feedback on new features you would like to see implemented.

Brian, Bob, Laima and Hua