FreeSurfer

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 Martinos Center for Biomedical Imaging.

• License: The license agreement that allows you to use FreeSurfer

• Release notes: New features and changes in each version of FreeSurfer - current stable release is v5.3.0

• Installation guide: How to download and install FreeSurfer on your computer

• Documentation: Getting started, step-by-step tutorials, FAQ, Glossary

• Citing FreeSurfer: Short description and citations for core FreeSurfer methods

• Publications: A Zotero library of articles on the methods in FreeSurfer and the studies that use FreeSurfer

• User support: How to get help with problems that you encounter when using FreeSurfer

• Hands-on training: Information on the FreeSurfer courses that we organize in Boston and around the world

• User contributions: Scripts and techniques from users of FreeSurfer

• Other software: Third-party software packages that are interoperable or related to FreeSurfer

• Acknowledgements: The funding agencies and collaborators that have contributed to the research behind FreeSurfer

• Social media: Find us on Facebook as FreeSurferMRI , follow us on Twitter or join our LinkedIn group .

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:

• Overview

• WorkFlows - Information on how the FreeSurfer tools are used in a processing stream.

• ToolsAndCommands - GUI and command-line tool documentation.

• FileFormats - Description of native FreeSurfer file formats, as well as external file formats used by FreeSurfer.

• CoordinateSystems - Details on the voxel and RAS coordinate systems used in FreeSurfer.

• Recommended acquisition protocols:

  • Suggested Morphometry Protocols for Optimal FreeSurfer Reconstruction

  • Alternative Morphometry Protocols, from ADNI

• Longitudinal studies:

  • The longitudinal !FreeSurfer stream

  • Longitudinal linear mixed effects statistics

• Troubleshooting:

  • Manual Editing: see Edits and LongitudinalEdits for an overview and check the Tutorials for examples.

  • ReconAllTableStableV5.3 - An at-a-glance table showing the FreeSurfer files used & created during the recommended processing stream.

Diffusion MRI

• TRACULA - Documentation on TRActs Constrained by UnderLying Anatomy, a tool for automated probabilistic tractography.

Multimodal

• Registration Tools - Documentation of FreeSurfer's registration tools.