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
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
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:
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
FreeSurfer Functional Analysis Stream (FS-FAST): FS-FAST is a set of tools for performing functional MRI data analyses on the cortical surface.
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
Registration tools: FreeSurfer offers a range of tools for both within-subject and across-subject registration.