Voxel-based lesion-symptom mapping (VLSM)
VLSM is a MATLAB toolbox for evaluating statistical relationships between damage to specific brain regions and resulting deficits (Bates et al., 2003). VLSM can be used for the analysis of both discrete and gradiated lesions (i.e. voxel-based morphometry), and in both cases incorporates permutation tests for robust assessment of statistical significance.
Click to download: VLSM 2.55
Multiview is a MATLAB toolbox for producing publication-quality overlays of structural, functional, and other images, and plotting co-ordinates of interest.
Click to download: Multiview 1.01
This is a MATLAB toolbox for reading, writing and manipulating NIFTI images.
Click to download: Nifti toolbox 1.0
FMRISTAT by Keith Worsley
My favorite toolbox for modeling fMRI data is Keith Worsley's FMRISTAT, due to its simplicity and flexibility. The package and its documentation can still be found on Keith's FMRISTAT website at McGill University. However, in case this material ever disappears, I have created an archive of FMRISTAT and its documentation pages.