FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. FreeSurfer is the structural MRI analysis software of choice for the Human Connectome Project.

Our tools

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 morphometry differences

For more information, see:

Functional MRI

Diffusion MRI

* TRActs Constrained by UnderLying Anatomy (TRACULA): TRACULA is a tool for automated global probabilistic tractography with anatomical priors. It reconstructs a set of major white-matter pathways by incorporating prior information on the structural segmentation labels that each pathway goes through or next to, as a function of position along the length of the pathway. It includes a specialized stream for processing longitudinal diffusion MRI data.

* AnatomiCuts : An unsupervised hierarchical streamline clustering algorithm based on anatomical similarity. AnatomiCuts is currently in the developing branch (

* DiffusionTool : This tool can help generating the configuration file of TRACULA and setting up the parameters to run AnatomiCuts. The DiffusionTool is currently in the developing branch (

PET Partial Volume Correction (PVC) and Kinetic Modeling

  • PETSurfer: PETSurfer is a tool for performing ROI-based, surface-based, and whole-brain analysis of PET data integrated with FreeSurfer anatomical analysis.


  • Registration tools: FreeSurfer offers a range of tools for both within-subject and across-subject registration.

Quick Links for LCN Members

  • LCN Members can navigate to the LcnInternal wiki page with quicklinks to regularly requested resources or wiki pages

Home (last edited 2012-03-26 16:59:00 by NickSchmansky)