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  Welcome to the FreeSurferWiki. FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. The FreeSurferWiki provides a documentation forum for investigators at the [http://www.martinos.org Athinoula A. Martinos Center For Biomedical Imaging].  * Welcome to the FreeSurferWiki. The FreeSurferWiki is the central documentation source for [http://surfer.nmr.mgh.harvard.edu 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. See also the [http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ FAQ] page.

 * 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:Self:DownloadAndInstall FreeSurfer download and install] - '''Current stable release is v4.0.2''' - See ReleaseNotes
 * [wiki:Self:MiscellaneousDownloads Miscellaneous downloads]
 * [wiki:Self:InternalFreeSurferDistributions Information for internal (Martinos Center) users]
 * [wiki:Self:FtpFileExchange Information on FTP file exchange] and [https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html email file-drop]
 * [wiki:Self:RemoteAccess Information on remote access]
 * [wiki:Self:Slicer 3D Slicer]
 * [http://www.fmrib.ox.ac.uk/fsl/ FSL - FMRIB Software Library]
 * [http://afni.nimh.nih.gov/ AFNI/NIfTI/SUMA]
 * [http://www.fil.ion.ucl.ac.uk/spm/ SPM - Statistical Parametric Mapping]
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  * FreeSurferInstallation
  * FreeSurferGuide
  * FreeSurferTutorial
  * FreeSurferTools		  * 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 and FS-FAST workflows, covering editing and troubleshooting techniques in-depth, as well as a group study example.
 * ReconAllDevTable - An at-a-glance table showing the !FreeSurfer files used & created during the recommended processing stream.
 * 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. See also the [http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ FAQ] page.
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  FreeSurferSupport  * FreeSurferSupport - Mailing lists and helplines which provide user support for !FreeSurfer

= WikiGuidelines =
 * CulturalGuidelines
 * StyleGuidelines

= BeginnersGuides =
 * WikiBeginnersGuide
 * FreeSurferBeginnersGuide
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FreeSurfer is brought to you by [http://www.cortechs.net CorTechs] and NCRR/P41RR14075  * 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/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)), the [http://www.nibib.nih.gov/ National Institute of Biomedical Imaging and Bioengineering], 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.
 * Thanks to Avi Snyder (Washington University School of Medicine) for porting his Talairach alignment implementation to !FreeSurfer.
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= MoinMoin Wiki =

A WikiWikiWeb is a collaborative hypertext environment, with an emphasis on easy access to and modification of information. This wiki can also link to InterWiki space.

MoinMoin is a Python Wiki:WikiClone, based on Wiki:PikiPiki. The name is a common German slang expression explained on the MoinMoin page. If you run a Wiki using MoinMoin, please add it to the MoinMoin:MoinMoinWikis page. Contributed code is on the MoinMoin:MacroMarket, MoinMoin:ActionMarket and MoinMoin:ParserMarket pages. For more details and further topics, see the MoinMoin page.

----
You can edit any page by pressing the link at the bottom of the page. Capitalized words joined together form a WikiName, which hyperlinks to another page. The highlighted title searches for all pages that link to the current page. Pages which do not yet exist are linked with a question mark: just follow the link and you can add a definition.

To get an overview over this site and what it contains, see the SiteNavigation page.

To learn more about what a WikiWikiWeb is, read about MoinMoin:WhyWikiWorks and the MoinMoin:WikiNature. Also, consult the MoinMoin:WikiWikiWebFaq.

----
Interesting starting points:
  * RecentChanges: see where people are currently working
  * HelpForBeginners: to get you going
  * WikiSandBox: feel free to change this page and experiment with editing
  * FindPage: search or browse the database in various ways
  * SyntaxReference
 = References =
[[Include(Articles)]]

Welcome

Software

Documentation

  • 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 and FS-FAST workflows, covering editing and troubleshooting techniques in-depth, as well as a group study example.

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

  • 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. See also the [http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ FAQ] page.

Support

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

WikiGuidelines

BeginnersGuides

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/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)), the [http://www.nibib.nih.gov/ National Institute of Biomedical Imaging and Bioengineering], 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.

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

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

References

Include(Articles)

FreeSurferWiki (last edited 2023-06-14 23:16:55 by buildqa)