Functional MRI

• FEAT - model-based analysis, e.g., for task FMRI

• MELODIC - model-free ICA-based analysis, e.g., for resting FMRI

• FABBER - dual-echo (ASL/BOLD) perfusion FMRI

• BASIL - quantitative resting perfusion analysis from perfusion ASL FMRI

Structural MRI

• fsl_anat - general anatomical pipeline script that calls most of the below tools to provide a "one-stop" comprehensive integrated structural analysis

• BET - brain extraction

• FAST - tissue-type segmentation

• FIRST - segmentation of subcortical structures

• FLIRT & FNIRT - linear and nonlinear registration

• FSLVBM - voxelwise analysis of multi-subject grey-matter density

• SIENA & SIENAX - longitudinal and cross-sectional analysis of structural changes

Diffusion MRI

• FDT - diffusion MRI preprocessing, tensor fitting and tractography

• TBSS - voxelwise analysis of multi-subject diffusion MRI datasets

• EDDY - improved eddy-current and head motion correction for diffusion MRI datasets

• TOPUP - improved distortion correction for diffusion MRI datasets

Perfusion MRI

• BASIL - perfusion quantification using arterial spin labelling

Statistics

• Randomise - permutation-based inference, including TFCE

• PALM - permutation-based inference, including multivariate and handling of surface data

• Dual Regression - Generating subject-specific maps from a group-ICA

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Other tools

• FSLView - 3D/4D image, timeseries and surface viewer

• Nets - various tools relating to network/connectivity analysis

• FDR - false discovery rate thresholding

• Mm - mixture-model thresholding

• Cluster - various cluster-based analyses including GRF-based cluster inference

• Fslutils - miscellaneous command-line programs (including fslmaths and fslstats)

• Atlases - various atlases included with FSL

• SUSAN - nonlinear image noise reduction

• FUGUE - fieldmap-based EPI distortion correction

• MCFLIRT - head-motion correction

• FLOBS - flexible haemodynamic basis functions

• Miscvis - programs for making summary pictures

• lesion_filling - tool for filling lesion masks with non-lesion intensities

• POSSUM - FMRI/MRI image simulator

• Atlasquery - tool for reporting atlas labels for masks or single coordinates