FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.

FreeSurfer provides a full processing stream for structural MRI data, including:

  • Skull stripping, B1 bias field correction, and gray-white matter segmentation
  • Reconstruction of cortical surface models (gray-white boundary surface and pial surface)
  • Labeling of regions on the cortical surface, as well as subcortical brain structures
  • Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas
  • Statistical analysis of group morphometry differences


To run FreeSurfer, you simply need to add it to your path and run the setup script:

export FREESURFER_HOME=/gpfs/research/software/freesurfer/freesurfer