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| * 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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| * '''''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. | 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]]. <<Include(FreeSurfer)>> * '''''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 for any questions you may have. * '''!FreeSurfer Courses''': If you would like to be notified about upcoming !FreeSurfer courses, sign up for the course mailing list [[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi|here]]. General information about course can be found on the CourseDescription page. |
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* Social Media ''FreeSurferMRI'': Find us on Facebook [[http://facebook.com/FreeSurferMRI|{{attachment:facebook_32.png|Find FreeSurferMRI on Facebook|width=25}}]] or follow us on Twitter [[http://www.twitter.com/FreeSurferMRI|{{http://twitter-badges.s3.amazonaws.com/t_small-a.png|Follow FreeSurferMRI on Twitter}}]]. * [[FreeSurferWiki#References|References]] |
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| * [[DownloadAndInstall|FreeSurfer download and install]] - '''Current stable release: v4.5.0''' - See ReleaseNotes | * [[DownloadAndInstall|FreeSurfer download and install]] - '''New stable release: v5.1.0''' - See ReleaseNotes |
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| * [[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]] | * [[attachment:FreeSurfer_Suggested_Morphometry_Protocols.pdf|Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction]] * [[http://adni.loni.ucla.edu/research/protocols/mri-protocols/|Alternative Morphometry Sequences, from ADNI]] |
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| * [[http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ|FAQ]] * [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Glossary|Glossary]] |
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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. |
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| When citing Freesurfer, [[FreeSurferMethodsCitation|here is some boilerplate text]]. |
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.
FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.
FreeSurfer provides many anatomical analysis tools, including: representation of the cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from the rest of the brain, skull stripping, B1 bias field correction, nonlinear registration of the cortical surface of an individual with an stereotaxic atlas, labeling of regions of the cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures and much more ...
NEW USERS: Please see the FreeSurferBeginnersGuide to get started. See also the FAQ page and FreeSurferSupport for any questions you may have.
FreeSurfer Courses: If you would like to be notified about upcoming FreeSurfer courses, sign up for the course mailing list here. General information about course can be found on the CourseDescription 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, and BugReporting, should be directed to the freesurfer mailing list <freesurfer AT nmr DOT mgh DOT harvard DOT edu> (subscribe to the list here).
Social Media FreeSurferMRI: Find us on Facebook
or follow us on Twitter 
.
Software
FreeSurfer download and install - New stable release: v5.1.0 - 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.