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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)]]. Bugs reports 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 stable release v3.0!''' * [wiki:Self:MiscellaneousDownloads Miscellaneous downloads] * [wiki:Self:InternalFreeSurferDistributions Information for internal (Martinos Center) users] * [wiki:Self:FtpFileExchange Information on FTP file exchange] * [wiki:Self:RemoteAccess Information on remote access] |
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| * FreeSurferInstallation * FreeSurferGuide * FreeSurferTutorial * FreeSurferTools |
## * FreeSurferDistributions - Description of !FreeSurfer distributions * 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). |
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| FreeSurferSupport | * FreeSurferSupport - Mailing lists and helplines which provide user support for !FreeSurfer = WikiGuidelines = * CulturalGuidelines * StyleGuidelines = BeginnersGuides = * WikiBeginnersGuide * FreeSurferBeginnersGuide = Feedback = * The FreeSurfer development team values your feedback. Please take a moment to visit the ["Priorities"] page and register your priority. Thanks. * You can add your comments or suggestions on our FeedBack page. |
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| FreeSurfer is brought to you by [http://www.cortechs.net CorTechs] and NCRR/P41RR14075 | * !FreeSurfer is brought to you by [http://www.cortechs.net CorTechs], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6641264&p_grant_num=5P41RR014075-05&p_query=&ticket=10459360&p_audit_session_id=48433183&p_keywords= NCRR/P41RR14075], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6936484&p_grant_num=5R01RR01659404&p_query=&ticket=16737375&p_audit_session_id=78570196&p_keywords= R01 RR16594-01A1], and our ["Contributors"]. |
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| = MoinMoin Wiki = | = References = |
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| 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. | Published material describing the techniques used in !FreeSurfer ([http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/cite.php please cite our software!]): |
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| 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. | * '''''surface reconstruction:''''' * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/dale99-recon1.pdf Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction], Dale, A.M., Fischl, B., Sereno, M.I., (1999). NeuroImage 9(2):179-194 * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99b-recon2.pdf Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System], Fischl, B., Sereno, M.I., Dale, A.M., (1999). NeuroImage, 9(2):195-207. * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl01-topology-fixing.pdf Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex], Fischl, B., Liu, A. and Dale, A.M., (2001). IEEE Transactions on Medical Imaging, 20(1):70-80. * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/dalesereno93-ms.pdf Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction: A linear approach], Dale, A.M., and Sereno, M.I. (1993). Journal of Cognitive Neuroscience 5:162-176. * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/segonne05.pdf A Hybrid Approach to the Skull-Stripping Problem in MRI], Ségonne, F., Dale, A.M., Busa, E., Glessner, M., Salvolini, U., Hahn, H.K., Fischl, B. (2004). NeuroImage, 22:1160-1075. * '''''inter-subject spherical averaging:''''' * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99-morphing.pdf High-resolution inter-subject averaging and a coordinate system for the cortical surface], Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999). * '''''thickness measurement:''''' * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl00-cortical-thickness.pdf Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images], Fischl, B., and Dale, A.M., (2000). Proceedings of the National Academy of Sciences, 97:11044-11049. * '''''cortical parcellation:''''' * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Automatically Parcellating the Human Cerebral Cortex], Fischl et al., (2004). Cerebral Cortex, 14:11-22. * '''''subcortical segmentation:''''' * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/montillo02-labeling.pdf Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain], Montillo et al., (2002). Neuron, 33:341-355. * [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-segmentation.pdf Sequence-Independent Segmentation of Magnetic Resonance Images], Fischl, B., Salat. D.H., van der Kouwe, A.J.W., Makris, N., Ségonne, F., and Dale, A.M. (2004) NeuroImage Jul;22(3):1060-75. |
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| ---- 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 |
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). Bugs reports 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 stable release v3.0!
[wiki:MiscellaneousDownloads Miscellaneous downloads]
[wiki:InternalFreeSurferDistributions Information for internal (Martinos Center) users]
[wiki:FtpFileExchange Information on FTP file exchange]
[wiki:RemoteAccess Information on remote access]
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).
Support
FreeSurferSupport - Mailing lists and helplines which provide user support for FreeSurfer
WikiGuidelines
BeginnersGuides
Feedback
The FreeSurfer development team values your feedback. Please take a moment to visit the ["Priorities"] page and register your priority. Thanks.
You can add your comments or suggestions on our FeedBack page.
Acknowledgements
FreeSurfer is brought to you by [http://www.cortechs.net CorTechs], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6641264&p_grant_num=5P41RR014075-05&p_query=&ticket=10459360&p_audit_session_id=48433183&p_keywords= NCRR/P41RR14075], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6936484&p_grant_num=5R01RR01659404&p_query=&ticket=16737375&p_audit_session_id=78570196&p_keywords= R01 RR16594-01A1], and our ["Contributors"].
References
Published material describing the techniques used in FreeSurfer ([http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/cite.php please cite our software!]):
surface reconstruction:
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/dale99-recon1.pdf Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction], Dale, A.M., Fischl, B., Sereno, M.I., (1999). NeuroImage 9(2):179-194
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99b-recon2.pdf Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System], Fischl, B., Sereno, M.I., Dale, A.M., (1999). NeuroImage, 9(2):195-207.
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl01-topology-fixing.pdf Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex], Fischl, B., Liu, A. and Dale, A.M., (2001). IEEE Transactions on Medical Imaging, 20(1):70-80.
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/dalesereno93-ms.pdf Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction: A linear approach], Dale, A.M., and Sereno, M.I. (1993). Journal of Cognitive Neuroscience 5:162-176.
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/segonne05.pdf A Hybrid Approach to the Skull-Stripping Problem in MRI], Ségonne, F., Dale, A.M., Busa, E., Glessner, M., Salvolini, U., Hahn, H.K., Fischl, B. (2004). NeuroImage, 22:1160-1075.
inter-subject spherical averaging:
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99-morphing.pdf High-resolution inter-subject averaging and a coordinate system for the cortical surface], Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999).
thickness measurement:
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl00-cortical-thickness.pdf Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images], Fischl, B., and Dale, A.M., (2000). Proceedings of the National Academy of Sciences, 97:11044-11049.
cortical parcellation:
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Automatically Parcellating the Human Cerebral Cortex], Fischl et al., (2004). Cerebral Cortex, 14:11-22.
subcortical segmentation:
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/montillo02-labeling.pdf Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain], Montillo et al., (2002). Neuron, 33:341-355.
[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-segmentation.pdf Sequence-Independent Segmentation of Magnetic Resonance Images], Fischl, B., Salat. D.H., van der Kouwe, A.J.W., Makris, N., Ségonne, F., and Dale, A.M. (2004) NeuroImage Jul;22(3):1060-75.