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.


  • 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.


  • 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.