Welcome

• Welcome to the FreeSurferWiki. The FreeSurferWiki is the central documentation source for FreeSurfer, a software application developed at the [http://www.nmr.mgh.harvard.edu/martinos/noFlashHome.php Martinos Center for Biomedical Imaging].

• NEW USERS: Please see the FreeSurferBeginnersGuide to get started.

• 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 should be directed to the MailTo(freesurfer AT nmr DOT mgh DOT harvard DOT edu, freesurfer mailing list). BugReporting should be directed to the MailTo(analysis-bugs AT nmr DOT mgh DOT harvard DOT edu, analysis-bugs mailing list).

Software

• [wiki:DownloadAndInstall FreeSurfer download and install] - New! Current stable release is v3.0.5

• [wiki:MiscellaneousDownloads Miscellaneous downloads]

• [wiki:InternalFreeSurferDistributions Information for internal (Martinos Center) users]

• [wiki:FtpFileExchange Information on FTP file exchange] and [https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html email file-drop]

• [wiki:RemoteAccess Information on remote access]

• [wiki:Slicer 3D Slicer]

Documentation

• FreeSurferAnalysisPipelineOverview - Overview of the FreeSurfer analysis pipeline.

• WorkFlows - Information on the how the FreeSurfer tools are used in a processing stream.

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

• ["Tutorials"] - A walk-through of a FreeSurfer work-flow, covering editing and troubleshooting techniques in-depth, as well as a group study example.

• ["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).

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

• ReconAllBlockDiagram - A block diagram showing the FreeSurfer work flow (same information as the Dev Table above, different presentation).

Support

• FreeSurferSupport - Mailing lists and helplines which provide user support for FreeSurfer

WikiGuidelines

• CulturalGuidelines

• StyleGuidelines

BeginnersGuides

• WikiBeginnersGuide

• FreeSurferBeginnersGuide

Acknowledgements

• Support for this research was provided in part by the [http://www.ncrr.nih.gov/ National Center for Research Resources] (P41-RR14075, R01 RR16594-01A1 and the NCRR [http://www.nbirn.net/research/testbeds/morphometry/index.shtm BIRN Morphometric Project] BIRN002, U24 RR021382), the [http://www.ninds.nih.gov/ National Institute for Neurological Disorders and Stroke] (R01 NS052585-01) as well as the [http://www.themindinstitute.org/ Mental Illness and Neuroscience Discovery] (MIND) Institute, and is part of the [http://www.na-mic.org/ National Alliance for Medical Image Computing] (NAMIC), funded by the [http://www.nih.gov/ National Institutes of Health] through the [http://nihroadmap.nih.gov/ 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.

attachment:NAMIC.jpg attachment:NINDS.jpg BR attachment:NCRR.jpg attachment:MIND.jpg

References

Include(Articles)