Welcome to BU RCS’s FreeSurfer documentation!

FreeSurfer Software Suite is an open source software for processing and analyzing primarily MRI brain images. FreeSurfer applications include: Skullstripping, Image Regisitration, Subcortical Segmentation, Cortical Surface Reconstruction, Cortical Segmentation, Cortical Thickness Estimation, Longitudinal Processing, fMRI Analysis, Tractography, FreeView Visualization GUI, and much more!

This page is designed to show users how to submit batch jobs on the SCC for the FreeSurfer reconstruction application recon-all and how to access the FreeView GUI for viewing/editing brains. For further instructions on FreeSurfer processing pipelines, please see the tutorial materials on the Developer Site.


This project is under active development.


This Freesurfer material has its documentation hosted on Read the Docs.