An open source software suite for processing and analysing human brain MRI images


Bruce Fischl1, Martin Reuter1, Doug Greve1, Anastasia Yendiki1, Lilla Zollei1, Juan Eugenio Iglesias2

Estimated cost



Stable release, V 5.3.0 (require registration and license from Massachusetts General Hospital)

FreeSurfer is a software package for analysis and visualization of structural and functional neuroimaging data

FreeSurfer has been developed for post-processing cross-sectional or longitudinal studies employing the following imaging modalities:

  • Structural MRI: 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 morphometric differences
    • Hippocampus sub-field segmentation
    • Dedicated processing and statistics tools for longitudinal data analysis
  • Functional MRI: A set of tools for performing functional MRI data analyses on the cortical surface named “FreeSurfer Functional Analysis Stream” (FS-FAST) is provided.
  • Diffusion MRI: TRACULA is a tool for automated global probabilistic tractography with anatomical priors.
  • PET Partial Volume Correction (PVC) and Kinetic Modeling: PETSurfer is a tool for performing ROI-based, surface-based, and whole-brain analysis of PET data integrated with FreeSurfer anatomical analysis.
  • Combining with other modalities: FreeSurfer offers a range of tools for both within-subject and across-subject registration.

FreeSurfer can be controlled from the command line allowing for fully automatized post-processing. Alternatively, it has different graphical user interfaces (GUI) for data visualization, analysis and management.



1Massachusetts General Hospital, Harvard-MIT HST, A.A. Martinos Center, Laboratory for Computational Neuroimaging, Boston, MA, USA

2Translational Imaging Group, Medical Physics and Biomedical Engineering Department, London, England