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| #acl AdminGroup:read,write,delete,revert All:read = Welcome = ---- ## * '''''ANNOUNCEMENT:''''' A Freesurfer Tutorial and Workshop will be held January 20 & 21st, 2009. [[CourseDescription|Details here!]] * Welcome to the FreeSurferWiki. The FreeSurferWiki is the central documentation and download 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]]. |
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| = Welcome = 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]. |
* '''''NEW USERS:''''' Please see the FreeSurferBeginnersGuide to get started. See also the [[http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ|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 <<MailTo(freesurfer AT nmr DOT mgh DOT harvard DOT edu, freesurfer mailing list)>> (subscribe to the list [[http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer|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 [[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi|here]]. * [[FreeSurferWiki#References|References]] = Software = ---- * [[DownloadAndInstall|FreeSurfer download and install]] - '''Current stable release: v5.0.0''' - See ReleaseNotes * [[MiscellaneousDownloads|Miscellaneous downloads]] * [[InternalFreeSurferDistributions|Information for internal (Martinos Center) users]] * [[FtpFileExchange|Information on FTP file exchange]] and [[https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html|email file-drop]] * [[RemoteAccess|Information on remote access]] * [[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]] * [[http://www.nitrc.org/|NITRC]] * [[http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8|iSurf]] - iPhone/iPad app * [[http://nipy.sourceforge.net/nipype/index.html|Nipype]] - Neuroimaging in Python, w/ FreeSurfer interfaces |
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| ---- * [[http://martinos.org/~andre/|Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction]] * [[http://adni.loni.ucla.edu/research/protocols/mri-protocols/|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. * [[http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ|FAQ]] * [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Glossary|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. * [[attachment:freesurfer_methods.doc|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 |
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| * FreeSurferInstallation * FreeSurferGuide * FreeSurferTutorial * FreeSurferTools |
##= 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/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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| = Support = FreeSurferSupport |
||<tablewidth="270px" tableheight="169px">[[http://www.nih.gov/|{{attachment:NIH.gif|http://www.nih.gov/}}]] ||[[http://www.ncrr.nih.gov/|{{attachment:NCRR.png|http://www.ncrr.nih.gov/}}]] ||[[http://www.nbirn.net/|{{attachment:BIRN.jpg|http://www.nbirn.net/}}]] || ||[[http://www.ninds.nih.gov/|{{attachment:NINDS.jpg|http://www.ninds.nih.gov/}}]]'''NINDS''' ||[[http://www.na-mic.org/|{{attachment:NAMIC.jpg|http://www.na-mic.org/}}]] '''NAMIC''' ||[[http://www.nibib.nih.gov/|{{attachment:NIBIB.jpg|http://www.nibib.nih.gov/}}]] || |
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| = Acknowledgements = FreeSurfer is brought to you by [http://www.cortechs.net CorTechs] and NCRR/P41RR14075 |
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| = MoinMoin Wiki = | ||[[http://www.nitrc.org/projects/freesurfer/|{{attachment:NITRC_logo_Listed.jpg|http://www.nitrc.org/projects/freesurfer/}}]] || |
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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. | |
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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. |
= References = When citing Freesurfer, [[FreeSurferMethodsCitation|here is some boilerplate text]]. |
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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 |
. <<Include(Articles)>> |
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.
Software
FreeSurfer download and install - Current stable release: v5.0.0 - See ReleaseNotes
iSurf - iPhone/iPad app
Nipype - Neuroimaging in Python, w/ FreeSurfer interfaces
Documentation
Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction
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.
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.