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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 FreeSurfer. * '''''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:Self:DownloadAndInstall FreeSurfer download and install] - '''New! Current stable release is v3.0.5''' * [wiki:Self:MiscellaneousDownloads Miscellaneous downloads] * [wiki:Self:InternalFreeSurferDistributions Information for internal (Martinos Center) users] * [wiki:Self:FtpFileExchange Information on FTP file exchange and email file-drop] * [wiki:Self:RemoteAccess Information on remote access] * [wiki:Self:Slicer 3D Slicer] |
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| * FreeSurferInstallation * FreeSurferGuide * FreeSurferTutorial * FreeSurferTools |
* 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). |
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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/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 |
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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
Welcome to the FreeSurferWiki. The FreeSurferWiki is the central documentation source for FreeSurfer.
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 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
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/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