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

Usage

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
source $FREESURFER_HOME/SetUpFreeSurfer.sh