The FMRIB Software Library, abbreviated FSL, is a software library containing image analysis and statistical tools for functional, structural and diffusion MRI brain imaging data.
FSL is available as both precompiled binaries and source code for Apple and PC (Linux) computers. It is freely available for non-commercial use.
FSL Functionality
Functional MRI
FABBER
FABBER is a Bayesian model fitting tool intended for use in task modelling of ASL data.
FEAT
Model-based FMRI analysis with straightforward but powerful GUI: data preprocessing (including slice timing correction, MCFLIRT motion correction and PRELUDE+FUGUE EPI unwarping); FILM GLM timeseries analysis with prewhitening; registration to structural and/or standard space images; and fully generalised mixed-effects group analysis using advanced Bayesian techniques.
MELODIC
Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significances ("p-values") to the output spatial maps.
FLOBS
Generation of optimal HRF basis functions and Bayesian activation estimation.
SMM
Spatial mixture modelling – alternative hypothesis testing using histogram mixture modelling with spatial regularisation of the voxel classification into activation and non-activation.
Structural MRI
BET /
BET2
Brain Extraction Tool – segments brain from non-brain in structural and functional data, and models skull and scalp surfaces.[1]
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.[2]
FUGUE
Unwarps geometric distortion in EPI images using B0 field maps.
SIENA
Structural brain change analysis, for estimating brain atrophy.
Diffusion MRI
FDT
FMRIB's Diffusion Toolbox – tools for low-level diffusion parameter reconstruction and probabilistic tractography.
TBSS
Tract-Based Spatial Statistics (part of FMRIB's Diffusion Toolbox) – voxelwise analysis of multi-subject diffusion data.[3]
Other tools
Inference
Various inference/thresholding tools, including: Randomise (permutation-based inference tool for nonparametric statistical thresholding), cluster (cluster-based thresholding using GRF theory for inference), FDR (false discovery rate inference) and Glm (a GUI for creating model design matrices).
FSLeyes
Interactive display tool for 3D and 4D data.
AVWUTILS
Misc utils for converting and processing images.
History and development
FSL is written mainly by members of the FMRIB (Functional Magnetic Resonance Imaging of the Brain) Analysis Group, Oxford
University, UK. The first release of FSL was in 2000; there has been
approximately one major new release each year to date. The FMRIB
Analysis Group is primarily funded by the Wellcome Trust and the UK EPSRC and
MRC Research Councils.
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