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 * [[https://www.zotero.org/freesurfer|Publications:]] A Zotero library of articles on the methods in !FreeSurfer or studies that use !FreeSurfer  * [[https://www.zotero.org/freesurfer|Publications:]] A Zotero library of articles on the methods in !FreeSurfer and the studies that use !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.

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.

  • How to cite 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.

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

  • 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.

FreeSurferWiki (last edited 2019-07-18 11:36:01 by 172)