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| * [[FreeSurferAnalysisPipelineOverview|Overview]] - General description of the functionality in !FreeSurfer | * [[FreeSurferAnalysisPipelineOverview|Overview:]] General description of the functionality in !FreeSurfer |
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| * [[ReconAllTableStableV5.3|Output files]] - A table of files created and used during a standard !FreeSurfer analysis | * [[ReconAllTableStableV5.3|Output files:]] A table of files created and used during a standard !FreeSurfer analysis |
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* [[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. |
* [[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 |
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| * [[Tracula|TRACULA]] - Documentation on TRActs Constrained by !UnderLying Anatomy, a tool for automated probabilistic tractography. | * [[Tracula|TRActs Constrained by !UnderLying Anatomy (TRACULA):]] TRACULA is a tool for automated 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, at every point long the pathway's trajectory. It includes a specialized stream for processing longitudinal diffusion MRI data. |
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| * [[FreeSurferCommandsRegistration|Registration Tools]] - Documentation of !FreeSurfer's registration tools. | * [[FreeSurferCommandsRegistration|Registration tools:]] !FreeSurfer offers a range of tools for within-subject and across-subject registration |
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: General description of the functionality in FreeSurfer
- Recommended acquisition protocols:
- Longitudinal studies:
- 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
Diffusion MRI
TRActs Constrained by !UnderLying Anatomy (TRACULA): TRACULA is a tool for automated 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, at every point long the pathway's trajectory. It includes a specialized stream for processing longitudinal diffusion MRI data.
Multimodal
Registration tools: FreeSurfer offers a range of tools for within-subject and across-subject registration