• FreeSurferWiki

Welcome

• Welcome to the FreeSurferWiki. The FreeSurferWiki is the central documentation and download source for FreeSurfer, a software application developed at the Martinos Center for Biomedical Imaging.

• NEW USERS: Please see the FreeSurferBeginnersGuide to get started. See also the FAQ page and FreeSurferSupport.

• If you would like to contribute to the Wiki you will need a WikiUserName. Please see GettingAccess to obtain a WikiUserName.

• See FreeSurferSupport for information on mailing lists relating to FreeSurfer. General questions about FreeSurfer, and BugReporting, should be directed to the freesurfer mailing list <freesurfer AT nmr DOT mgh DOT harvard DOT edu> (subscribe to the list here).

• If you would like to sign up for our course mailing list in order to receive announcements about upcoming FreeSurfer courses, you can do so here.

• References

Software

• FreeSurfer download and install - Current stable release: v5.0.0 - See ReleaseNotes

• Miscellaneous downloads

• Information for internal (Martinos Center) users

• Information on FTP file exchange and email file-drop

• Information on remote access

• 3D Slicer

• FSL - FMRIB Software Library

• AFNI/NIfTI/SUMA

• SPM - Statistical Parametric Mapping

• NITRC

• iSurf - iPhone/iPad app

• Nipype - Neuroimaging in Python, w/ FreeSurfer interfaces

Documentation

• Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction

• Alternative Morphometry Sequences, from ADNI

• FreeSurferAnalysisPipelineOverview - Overview of the FreeSurfer analysis pipeline.

• ArticlesSlidesAndPosters - Background describing the techniques used in the FreeSurfer tools, and their usage in research.

• Tutorials - A walk-through of a FreeSurfer workflow, covering editing and troubleshooting techniques in-depth, as well as a group study example. There is also an FS-FAST tutorial.

• FAQ

• Glossary

• ReconAllDevTable - An at-a-glance table showing the FreeSurfer files used & created during the recommended processing stream.

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

• 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.

• DevelopersGuide - Information for developers of the FreeSurfer code-base (Martinos Center internal).

• UserContributions - Scripts and techniques from users. This section is new, but if you have something you'd like to share, please do so.

• How to describe and cite Freesurfer - This document has a short description of Freesurfer methods to be used when citing Freesurfer. Alternatively, the text is available on the wiki at FreeSurferMethodsCitation

Acknowledgements

• Support for this research was provided in part by the National Center for Research Resources (P41-RR14075, R01 RR16594-01A1 and the NCRR BIRN Morphometric Project BIRN002, U24 RR021382), the National Institute for Neurological Disorders and Stroke (R01 NS052585-01)), the National Institute of Biomedical Imaging and Bioengineering, as well as the Mental Illness and Neuroscience Discovery (MIND) Institute, and is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

• Thanks to Ron Kikinis, Steve Pieper and NA-MIC (NIH Roadmap for Medical Research Grant U54 EB005149) for providing engineering advice and support for testing and open-sourcing of FreeSurfer.

• Thanks to Avi Snyder (Washington University School of Medicine) for porting his Talairach alignment implementation to FreeSurfer.

References

When citing Freesurfer, here is some boilerplate text.