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 Athinoula A. Martinos Center for Biomedical Imaging.

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

• Release notes: New features and changes in each version of FreeSurfer - current stable release is v6.0.0

• 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: General description of the functionality 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 for the basic stream and for the longitudinal stream

  • Output files: A table of files created and used during a standard FreeSurfer analysis

• Advanced:

  • Work flows: How to use the FreeSurfer stream to accomplish specific tasks

  • Tools and commands: GUI and command-line tool documentation

  • File formats: Description of native FreeSurfer file formats, as well as external file formats recognized by FreeSurfer

  • Coordinate systems: Details on the voxel and RAS coordinate systems used in FreeSurfer

Functional MRI

• FreeSurfer Functional Analysis Stream (FS-FAST): FS-FAST is a set of tools for performing functional MRI data analyses on the cortical surface.

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.

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.

Multimodal

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