FSL TOOLS
Functional MRI
FEAT	Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.
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 significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.
FLOBS	Generation of optimal HRF basis functions and Bayesian activation estimation.
FABBER	Fast ASL & BOLD Bayesian Estimation Routine. Efficient nonlinear modelling and estimation of BOLD and CBF from dual-echo ASL data, using Variational Bayes.
Structural MRI
BET	Brain Extraction Tool - segments brain from non-brain in structural and functional data, and models skull and scalp surfaces.
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.
FNIRT	FMRIB's Nonlinear Image Registration Tool - nonlinear registration.
FIRST	FMRIB's Integrated Registration and Segmentation Tool. FIRST uses mesh models trained with a large amount of rich hand-segmented training data to segment subcortical brain structures.
FUGUE	Unwarps geometric distortion in EPI images using B0 field maps.
SIENA	Structural brain change analysis, for estimating brain atrophy.
FSL-VBM	VBM-style analysis using FSL tools, for voxelwise analysis of grey-matter density.
SUSAN	Nonlinear noise reduction.
Diffusion MRI
FDT	FMRIB's Diffusion Toolbox - tools for low-level diffusion parameter reconstruction and probabilistic tractography, including crossing-fibre modelling.
TBSS	Tract-Based Spatial Statistics (part of FMRIB's Diffusion Toolbox) - voxelwise analysis of multi-subject diffusion data.
Other tools
POSSUM	Physics-Oriented Simulated Scanner for Understanding MRI. An FMRI data simulator that produces realistic simulated images and FMRI time series given a gradient echo pulse sequence, a segmented object with known tissue parameters, and a motion sequence..
Inference	Various inference/thresholding tools, including: SMM spatial mixture modelling - alternative hypothesis testing using histogram mixture modelling with spatial regularisation of the voxel classification into activation and non-activation; 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.
Atlases	Several complementary brain atlases, integrated into FSLView and Featquery, allowing viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts.
FSLUTILS	Misc utils for converting and processing images.
MISCVIS	Simple (non-interactive) image display utilities and a stats overlay utility.