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| * 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]. | * 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]]. |
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| * '''''NEW USERS:''''' Please see the FreeSurferBeginnersGuide to get started. See also the [http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ FAQ] page. | * '''''NEW USERS:''''' Please see the FreeSurferBeginnersGuide to get started. See also the [[http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ|FAQ]] page. |
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| * 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)]]. | * 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)>>. |
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| * [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] |
* [[DownloadAndInstall|FreeSurfer download and install]] - '''New stable release v4.0.3''' - 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]] |
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| * ["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. | * [[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. |
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| * ["ToolsAndCommands"] - GUI and command-line tool documentation. | * [[ToolsAndCommands]] - GUI and command-line tool documentation. |
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| * 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. | * 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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| * 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. | * 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. |
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| [[Include(Articles)]] | <<Include(Articles)>> |
Welcome
Welcome to the FreeSurferWiki. The FreeSurferWiki is the central documentation 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.
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 freesurfer mailing list <freesurfer AT nmr DOT mgh DOT harvard DOT edu>. BugReporting should be directed to the analysis-bugs mailing list <analysis-bugs AT nmr DOT mgh DOT harvard DOT edu>.
Software
FreeSurfer download and install - New stable release v4.0.3 - See ReleaseNotes
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 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.
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 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 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