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.