FreeSurfer is an MRI brain imaging software package developed by the Athinoula A. Martinos Center for Biomedical Imaging at Massachusetts General Hospital. It is an important tool in functional brain mapping and facilitates the visualization of the functional regions of the highly-folded cerebral cortex. It contains both volume based and surface based analysis, which primarily use the white matter surface.

FreeSurfer includes tools for the reconstruction of topologically correct and geometrically accurate models of both the gray/white and pial surfaces, for measuring cortical thickness, surface area and folding, and for computing inter-subject registration based on the pattern of cortical folds. In addition, an automated labeling of 35 non-cortical regions is included in the package.

FreeSurfer uses toolkits from MNI MINC, VXL, Tcl/Tk/Tix/BLT, VTK, KWWidgets and Qt, which are all available with the distribution.