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* 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.
|* [[FreeSurferAnalysisPipelineOverview|Overview]] - General description of the functionality in !FreeSurfer|
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* 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.
* Manual editing [[Edits|for the basic stream]] and [[LongitudinalEdits|for the longitudinal stream]]
* [[ReconAllTableStableV5.3|Output files]] - A table of files created and used during a standard !FreeSurfer analysis
* [[WorkFlows|Work flows]] - How to use the !FreeSurfer stream to accomplish specific tasks
* [[ToolsAndCommands|Tools and commands]] - GUI and command-line tool documentation
* [[FileFormats|File formats]] - Description of native !FreeSurfer file formats, as well as external file formats recognized by !FreeSurfer
* [[CoordinateSystems|Coordinate systems]] - Details on the voxel and RAS coordinate systems used in !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
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 .
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:
- Longitudinal studies:
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.
TRACULA - Documentation on TRActs Constrained by UnderLying Anatomy, a tool for automated probabilistic tractography.
Registration Tools - Documentation of FreeSurfer's registration tools.