= 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|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|EDDY]] - improved eddy-current and head motion correction for diffusion MRI datasets
 * [[topup|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
 * [[DualRegression|Dual Regression]] - Generating subject-specific maps from a group-ICA

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= Other tools =
 * [[FSLeyes]] - 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

= GPU advice =
 * [[GPU|GPU requirements]] - GPU information for making sure your hardware is compatible with FSL tools