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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.

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


Daily operations of the MRI facility are managed by Adam Kerr (, the Research Director, and by Laima Baltusis (, the Facility Manager. The MR Physics work at the CNI is led by Hua Wu ( 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.


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. See some pictures from that day. Since the time it was installed, we train about 100 new users each year. We have collected approximately 15,000 data sets (one hour sessions at the scanner) comprising 25,000 anatomical acquisitions (mostly T1-weighted), 6,000 diffusion-weighted acquisitions, and 63,000 fMRI acquisitions.

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.)

Computational Resources

The CNI has received funding from BIO-X Neuroventures for a high-powered compute server which will be used to provide computational resources to CNI users.

The CNI has recently started providing LXContainers and is moving away from the previous Virtual Machines deployment scheme.

Please visit the LXC Page for information about getting started with computational resources.

Data Management

The Flywheel page contains information about how we use Flywheel to manage all the data collected at the CNI.

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