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 * [[FreeSurferSupport | User support:]] How to get help with problems that you encounter when using !FreeSurfer
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 * '''Encounter a problem with !FreeSurfer?''': Search the [[http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/|mailing list]] to see if this problem has already been covered on there. If you can't find anything that helps you, questions about !FreeSurfer as well as BugReporting should be directed to the <<MailTo(freesurfer AT nmr DOT mgh DOT harvard DOT edu, freesurfer mailing list)>> (subscribe to the list [[http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer|here]]). See FreeSurferSupport for information on mailing lists relating to FreeSurfer.

 * '''What you can do for !FreeSurfer''': Unable to find documentation on some command or process? Once you figure out how to do it, add documentation for everyone else! To contribute to the Wiki, you will need a WikiUserName. Please see GettingAccess to obtain a WikiUserName and then document away. To create a new page once you have an account, just goto the URL you want to create. For instance, goto this link for a page you would name !MyNewPage: https://surfer.nmr.mgh.harvard.edu/fswiki/MyNewPage and note the link that says 'Create new empty page'. Just click on that and type away (but please don't use !MyNewPage as a page name!).


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.

FreeSurfer provides many anatomical analysis tools, including: representation of the cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from the rest of the brain, skull stripping, B1 bias field correction, nonlinear registration of the cortical surface of an individual with a stereotaxic atlas, labeling of regions of the cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures and much more ...

  • NEW USERS: Please see the Getting Started section of the QuickInstall page.

  • 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

  • Social Media: Find us on Facebook as FreeSurferMRI Find FreeSurferMRI on Facebook, follow us on Twitter Follow FreeSurferMRI on Twitter or join our LinkedIn group !LinkedIn FreeSurfer Group.



Overview of FreeSurfer

  • FreeSurferAnalysisPipelineOverview - Overview of the FreeSurfer analysis pipeline.

  • Tutorials - A walk-through of a FreeSurfer workflow, covering editing and troubleshooting techniques in-depth, group analysis, longitudinal analysis, fMRI analysis, and diffusion analysis.

  • FAQ

  • Glossary

MRI Sequences


Some of Our Tools

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

  • LongitudinalProcessing - A description of the longitudinal stream in FreeSurfer.

  • LongitudinalStatistics - Longitudinal linear mixed effects model MATLAB tools

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

More Details about FreeSurfer Processing

  • 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.

  • How to cite FreeSurfer: Short description and citations for core FreeSurfer methods

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

  • User contributions: Scripts and techniques from users of FreeSurfer.

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

FreeSurferWiki (last edited 2022-06-02 11:07:58 by AndrewHoopes)