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 * [[FreeSurferAnalysisPipelineOverview|Overview]]
 * 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
 * Advanced:
  * [[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

  • 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 Find FreeSurferMRI on Facebook, follow us on Twitter Follow FreeSurferMRI on Twitter or join our LinkedIn group !LinkedIn FreeSurfer 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:

Diffusion MRI

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


FreeSurferWiki (last edited 2021-07-12 14:00:49 by AndrewHoopes)