http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/%|%FSL%|% stands for FMRIB's Software Library, and is a product of the analysis group at Oxford University's Centre for Functional Magnetic Resonance Imaging of the Brain. FSL is a collection of C++ programs sewed together with bash scripts and tcl/tk GUIs.

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. It runs on Apple and PCs (both Linux, and Windows via a Virtual Machine), and is very easy to install. Most of the tools can be run both from the command line and as GUIs. 


****STRUCTURAL TOOLS****


   *     BET - Brain Extraction Tool - segments brain from non-brain in structural and functional data.
   *     SUSAN - Nonlinear noise reduction.
   *     FAST - FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction.
   *     FLIRT - FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration.
   *     FUGUE - Unwarps distortion in EPI images using B0 field maps.
   *     SIENA - Structural brain change analysis, for estimating brain atrophy. 


****FUNCTIONAL TOOLS****


   *     FEAT - Advanced FMRI analysis with easy-to-use yet powerful GUI. Includes all necessary preprocesing, model-based and semi-model-free statistical analysis, automatic registration to structural and/or standard space, and fixed- and random-effects group statistics.
   *     MCFLIRT - FMRI motion correction.
   *     MELODIC - ICA-based model-free analysis of FMRI (and other 4D) data. 

[http://upload.wikimedia.org/wikipedia/en/thumb/6/64/FSL-GUIs.png/800px-FSL-GUIs.png]

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