The FMRIB Software Library (FSL) is a software library containing image analysis and statistical tools for functional

Functional magnetic resonance imaging

Functional magnetic resonance imaging or functional MRI is a type of specialized MRI scan used to measure the hemodynamic response related to neural activity in the brain or spinal cord of humans or other animals. It is one of the most recently developed forms of neuroimaging...

, structural and diffusion

Diffusion MRI

Diffusion MRI is a magnetic resonance imaging method that produces in vivo images of biological tissues weighted with the local microstructural characteristics of water diffusion, which is capable of showing connections between brain regions...

 MRI brain imaging data.

FSL is available as both precompiled binaries and source code for Apple and PC (Linux and Windows) computers. It is freely available for non-commercial use.

FSL Functionality

Functional MRI
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 General linear model The general linear model is a statistical linear model.It may be written aswhere Y is a matrix with series of multivariate measurements, X is a matrix that might be a design matrix, B is a matrix containing parameters that are usually to be estimated and U is a matrix containing errors or...  timeseries analysis with prewhitening; registration to structural and/or standard space images; and fully generalised mixed-effects group analysis using advanced Bayesian Bayesian inference In statistics, Bayesian inference is a method of statistical inference. It is often used in science and engineering to determine model parameters, make predictions about unknown variables, and to perform model selection...  techniques.
MELODIC	Model-free FMRI analysis using Probabilistic Independent Component Analysis Independent component analysis Independent component analysis is a computational method for separating a multivariate signal into additive subcomponents supposing the mutual statistical independence of the non-Gaussian source signals...  (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.
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 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.
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).
FSLView	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 UK EPSRC and
MRC Research Councils.

See also

• FSL website
• FMRIB Analysis Group
• SPM
  Statistical parametric mapping
  Statistical parametric mapping or SPM is a statistical technique created by Karl Friston for examining differences in brain activity recorded during functional neuroimaging experiments using neuroimaging technologies such as fMRI or PET...
  
  
• Neuroimaging
  Neuroimaging
  Neuroimaging includes the use of various techniques to either directly or indirectly image the structure, function/pharmacology of the brain...