FSL TOOLS
Functional
FEAT	Model-based FMRI analysis with straightforward but powerful GUI: data preprocessing (including slice timing correction and MCFLIRT motion correction); first-level FILM GLM analysis with time-series prewhitening; registration to structural and standard space; and fully generalised mixed-effects group analysis using advanced Bayesian estimation 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.
Randomise	Randomisation-based inference tool for nonparametric statistical thresholding.
Structural
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.
FDT	FMRIB's Diffusion Toolbox - tools for low-level diffusion parameter reconstruction and probabilistic tractography.
Other tools
FSLView	Interactive display tool for 3D and 4D data.
AVWUTILS	Misc utils for converting and processing images.
MISCVIS	Simple (non-interactive) image display utilities and a stats overlay utility.