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Transforming the understanding
and treatment of mental illnesses.

Scientific and Statistical Computing Core

The SSCC is the Scientific and Statistical Computing Core of the NIMH Intramural Research Program. The primary function of this core is to support MRI-related neuroimaging research at the NIH. This includes the development of new data analysis techniques, their implementation in the AFNI software (AFNI = Analysis of Functional NeuroImages, though the software includes tools for several varieties of image types), advising researchers on the analysis methods, and instructing them in the use of software tools.

Support methods:

Developing the AFNI software package ( for MRI visualization and analysis, which includes tools for structural, functional and diffusion-based datasets:

  • Development of AFNI: Dr. Robert Cox started AFNI in 1994 at MCW in Milwaukee, WI, USA; since 2001, AFNI has been primarily developed by the SSCC (NIMH, NIH), though the software is open source and has had contributors from around the globe.
  • Formal and informal instruction in the use of AFNI, including study design, start-to-finish processing, quality control assessment and statistical methodologies.
  • The Core leads multiple 5-day/40 hour “AFNI Bootcamps” each year, both on NIH campus and at hosting institutions around the world; these include both theory lectures and particularly hands-on data analysis tutorials.
    • As of 2021, the Core has led over 90 Bootcamps at NIH and globally.
  • Assisting with installation of AFNI on NIH computers (Linux/Unix, Mac OS, Windows).
  • Realtime monitoring of FMRI data at scanners.
  • Continuing development of new modules for AFNI to meet needs of NIH researchers.

Consultation with NIH and extramural researchers:

  • Most consultations occur for NIMH groups, followed by NINDS and other ICs at NIH, as well as extramural researchers.
  • Meetings both before and after data acquisition: study design, pilot study setup, data analysis, visualization, understanding and statistical methods.
    • Primarily in the context of the AFNI software package, but with some connections to other software as well (e.g., FreeSurfer, TORTOISE, and other community-based tools).
  • In-person consulting in small groups for substantial problems.
  • The Core advises new trainees, such as postbac/IRTAs and postdocs, as well as more established researchers.
    • Web-based message board forum for “quick questions” and longer discussions.
    • Development of new tools to meet researcher/study design needs.
    • One of the most important ways tools grow is through practical applications and novel study designs.