This project is deprecated. See fPrep for an updated version of the core pipeline. Also see MindStorm, which has updated versions of some scripts.
Functional analysis toolbox: a set of scripts defining a pipeline for analysis of fMRI data. The pipeline uses FSL, ANTs, and FreeSurfer. It's designed to improve registration between functional images and high-resolution structural images, co-registration between functional images, and to deal with scan distortions caused by nonlinearities in field gradients.
Scripts are written in Bash in Python, with a high-performance cluster environment in mind. Scripts are optimized for using resources of the Texas Advanced Computing Center (TACC), but should work on any Linux or Unix system.
See the Wiki for detailed documentation. The Preprocessing Tutorial is a good place to start.