The FMRIB Software Library (FSL) is a software library containing image analysis and statistical tools for functional, structural and diffusion MRI brain imaging data. Functional magnetic resonance imaging (fMRI) is the use of MRI to measure the hemodynamic response related to neural activity in the brain or spinal cord of humans or other animals. ... The mri are a fictional alien species in the Faded Sun Trilogy of C.J. Cherryh. ... Diffusion MRI is a specific Magnetic Resonace Imaging (MRI) modality that produces in vivo images of biological tissues weighted with the local microstructural characteristics of water diffusion. ...
FSL is available as both precompiled binaries and source code for Apple, PC (Linux and Windows) and Sun 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 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.
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.
The general linear model (GLM) is a statistical, linear model. ... Bayesian inference is statistical inference in which evidence or observations are used to update or to newly infer the probability that a hypothesis may be true. ... Independent component analysis (ICA) is a computational method for separating a multivariate signal into additive subcomponents supposing the mutual statistical independence of the non-Gaussian source signals. ...
History and Development
FSL is written mainly by members of the FMRIB 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. The Engineering and Physical Sciences Research Council (EPSRC) is a British Research Council that provides government funding for grants to undertake engineering and science research, mainly to universities in the United Kingdom. ... Current MRC logo The Medical Research Council (MRC) is a UK organisation dedicated to promot[ing] the balanced development of medical and related biological research in the UK. // Organisation The MRC is one of eight Research Councils and is answerable to, although politically independent from, the Office of Science and...
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