FreeSurfer is a set of tools for the automated generation of a complete neuroanatomical description of the human brain from MRI. This includes surface models of the cerebral cortex as well as volumetric labelings of most macroscopically visible neuroanatomical structures. FS-Fast is a set of tools for funtional analysis of neuroimaging data that take advantage of the neuroanatomical models to guide the analysis of the functional data.
FreeSurfer runs on Linux and Mac OS/X and is relatively easy to install and run. The tools can be accessed through the graphical user interface, or from the command line.
For more information, visit the FREESURFER Homepage.