FSL WITH OTHER SOFTWARE
FSL Plugins Wiki
On the FSL Plugins Wiki we provide a list of plugins, extensions, toolboxes, templates and atlases that have been created by other groups and are relevant to users of FSL. FreeSurfer - Cortical flattening and modelling
FreeSurfer is a set of tools for reconstruction/flattening of the brain's cortical surface and subcortical segmentation/registration, produced at MGH, Boston. It can, for example, be used to overlay functional data onto the inflated/flattened cortical surface, or carry out multi-subject FMRI statistics on the cortical surface. We have worked together with MGH to make interoperation of FSL and FreeSurfer as easy as possible. NITRC - Neuroimaging software resource
FSL is just one of many software packages listed at the NITRC neuroimaging tools resource.