Welcome to the fMRI Course Website

A number of software packages are available for analysis of fMRI data:

AFNI
A set of programs for processing, analyzing, and displaying functional MRI (fMRI) data. It runs on Unix-based systems and is currently freely available.

FSL
FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK

FreeSurfer
A program for reconstruction of the brain's cortical surface and overlay of functional data onto the reconstructed surface, the program is developed by Martin Sereno.

SPM
A powerful set of MATLAB functions for preprocessing, analysis, and display of fMRI and PET data. It is currently freely available.

IMSIM
A MATLAB tool to simulate MRI Imaging - developed inhouse at the UCSD fMRI center.

VoxBo
A package that contains both analysis tools and project management features for tracking the status of analyses. It runs on Unix-based systems and is currently freely available.

Stimulate
An fMRI analysis package that runs on UNIX / Linux based systems. It is currently freely available.

MEDx
A software package for the visualization, processing, and analysis of medical images. It is a commercial product.

BrainVoyager
A Windows-compatible fMRI analysis and visualization software that includes very powerful rendering functions. It is a commercial product.

MRIcro
An easy to use program that allows Windows and Linux computers to view medical images. It is a stand-alone program, but includes tools to complement SPM. It is currently freely available.

ImageJ A versatile easy to use program for viewing and analyzing any digital images (including MRI). Java-based program works under windows, mac or linux.


Last modified September 11, 2014
Produced by the Center for Functional MRI.
Copyright 2009 CFMRI. All rights reserved.