Fsl is a comprehensive library of image analysis and statistical tools for fmri, mri and dti brain imaging data. the suite consists of various command line tools, as well as simple guis for its core analysis pipelines. among others, fsl offers implementations of standard glm analysis, white matter tractography, tissue segmentation, affine and non-linear co-registration, and independent component analysis.

fsl interoperates well with other brain imaging related software. this includes caret, freesurfer (cortical flattening and modelling). all fsl tools support the nifti format.