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Welcome to the CNI Wiki

This site provides technical information for users of the Stanford Center for Cognitive and Neurobiological Imaging (CNI) facilities. All CNI users are invited to contribute their knowledge by editing content here. It is important that you verify the accuracy of any information that you post.

Follow this Getting Started link if you are new to the CNI and would like to learn about the basic facilities and how to get access and help in using the CNI facilities.

• General information is on the CNI administrative site (wordpress)
• To schedule time on the facilities, see the CNI resource scheduler.

If you are experiencing problems with the scanner or the peripherals, please consult the Troubleshooting section.

Mission Statement

Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The Stanford Center for Cognitive and Neurobiological Imaging (CNI) supports scientific investigations into the brain that make rigorous connections between neuroscience and society. Our Mission is to:

1. Support neuroscience discovery for enhancing society
2. Develop and disseminate cognitive and neurobiological imaging methods
3. Create a structured, safe, and innovative teaching environment for human neuroscience research

People

Daily operations of the MRI facility are managed by Adam Kerr (akerr@stanford.edu), the Research Director, and by Laima Baltusis (laimab@stanford.edu), the Facility Manager. The MR Physics work at the CNI is led by Hua Wu (huawu@stanford.edu). Michael Perry oversees the information technology (e.g., NIMS).

The CNI operations are guided by a faculty Advisory Board that includes representatives from the School of Humanities and Sciences, School of Education, the Department of Neurology, the Department of Psychiatry, and the School of Engineering. The Board receives input from colleagues in the Law School and CCRMA.

Stanford University oversight is through the office of the Vice-Provost and Dean of Research.

Facilities

The first CNI project was construction of the MR facility in the basement of Building 420. The MR scanner was delivered on November 13th, 2010 and began running within a year.

In addition to the MRI scanner, there is a mock scanner for training, experimental testing rooms, and integrated experimental equipment (displays and EEG). (See Facilities and Resources for more details and text useful when preparing sections of NIH or other grants.)

Data Management

The scanner is heavily used. We train about 100 new users each year

The Data Management page contains information about how we use Flywheel to store the data collected at the CNI, and to run certain data analyses.

We have some summary statistics for the last few years gleaned from the Flywheel site that has been up since 2017.

• We have collected approximately 1700 data sets (one hour sessions at the scanner) each year
• We have run about 75,000 jobs (Flywheel Gears) per year
• We are storing 540,000 files, including
  • 50,000 T1 anatomical files
  • 30,000 DWI diffusion files
  • 250,000 functional MR files

Computational Resources

At startup time (2011), the CNI received funding from BIO-X Neuroventures for what was then a high-powered compute server which will be used to provide computational resources to CNI users. That system evolved to use Linux containers.

In the early years we implemented a data management systems (NIMS) for storing and distributing all the data collected at the CNI. We also implemented an LXC Page system to support user computations. NIMS was retired in 2017 and the LXC system was retired in 2021.

In 2017 we installed Flywheel, which is a commercialized version of NIMS. That system continues to evolve and holds a great deal of data. It supports cloud-based computations (docker containers, which Flywheel calls Gears).

In 2023 the CNI received funding from C-ShARP to upgrade our computational facilities with advanced GPUs. These are being installed and will be heavily used for advanced reconstruction methods, particularly for quantitative methods developed by Kawin Setsompop's group.

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