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| #acl LcnGroup:read,write,delete,revert All:read = F = ---- 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]] by the [[http://martinos.org/lcn/|Laboratory for Computational Neuroimaging]]. |
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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]. |
##<<Include(FreeSurfer)>> !FreeSurfer is a set of tools for analysis and visualization of structural, functional, and diffusion MRI 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 a 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 [[https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall#GetStarted.21|Getting Started]] section of the QuickInstall page. * '''!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 the course can be found on the CourseDescription page. * '''Encounter a problem with !FreeSurfer?''': Search the [[http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/|mailing list]] to see if this problem has already been covered on there. If you can't find anything that helps you, questions about !FreeSurfer as well as 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]]). See FreeSurferSupport for information on mailing lists relating to FreeSurfer. * '''What you can do for !FreeSurfer''': Unable to find documentation on some command or process? Once you figure out how to do it, add documentation for everyone else! To contribute to the Wiki, you will need a WikiUserName. Please see GettingAccess to obtain a WikiUserName and then document away. To create a new page once you have an account, just goto the URL you want to create. For instance, goto this link for a page you would name !MyNewPage: https://surfer.nmr.mgh.harvard.edu/fswiki/MyNewPage and note the link that says 'Create new empty page'. Just click on that and type away (but please don't use !MyNewPage as a page name!). * '''Social Media''': Find us on Facebook as ''FreeSurferMRI'' [[http://facebook.com/FreeSurferMRI|{{attachment:facebook_32.png|Find FreeSurferMRI on Facebook|width="25"}}]], follow us on Twitter [[http://www.twitter.com/FreeSurferMRI|{{attachment:twitter_32.png|Follow FreeSurferMRI on Twitter}}]] or join our LinkedIn group [[https://www.linkedin.com/groups/FreeSurfer-8173404|{{attachment:linkedin_32.png|!LinkedIn FreeSurfer Group}}]]. * [[https://www.zotero.org/freesurfer|FreeSurfer Publications]] = Software = ---- * [[http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense|License]] * [[DownloadAndInstall|FreeSurfer download and install]] - '''Current stable release is v5.3.0''' - 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]] * [[FSL]] * [[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 * [[http://mindboggle.info/data.html|Mindboggle-101 data]] - Manually labeled anatomical regions for 101 healthy subjects * [[http://martinos.org/mne/|MNE - M/EEG data analysis using FreeSurfer meshes and surface registration]] * [[http://neuroimage.usc.edu/brainstorm/Introduction|Brainstorm]] - See [[Brainstorm|Integration with FreeSurfer]] |
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| ---- === Overview of FreeSurfer === * FreeSurferAnalysisPipelineOverview - Overview of the !FreeSurfer analysis pipeline. * [[https://www.zotero.org/freesurfer|Publications]] - 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, group analysis, longitudinal analysis, fMRI analysis, and diffusion analysis. * [[UserContributions/FAQ|FAQ]] * [[FsTutorial/Glossary|Glossary]] |
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| * FreeSurferInstallation * FreeSurferGuide * FreeSurferTutorial * FreeSurferComponents |
=== MRI Sequences === * [[attachment:FreeSurfer_Suggested_Morphometry_Protocols.pdf|Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction|&do=get]] * [[http://adni.loni.usc.edu/methods/documents/mri-protocols/|Alternative Morphometry Sequences, from ADNI]] |
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| = Support = FreeSurferSupport |
=== Troubleshooting === * Manual Editing: see [[Edits]] and LongitudinalEdits for an overview and check the [[Tutorials]] for examples. * [[ReconAllTableStableV5.3]] - An at-a-glance table showing the !FreeSurfer files used & created during the recommended processing stream. |
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| = Acknowledgements = FreeSurfer is brought to you by [http://www.cortechs.net CorTechs] and NCRR/P41RR14075 |
=== Some of Our Tools === * [[FreeSurferCommandsRegistration|Registration Tools]] - Documentation of !FreeSurfer's registration tools. * LongitudinalProcessing - A description of the longitudinal stream in !FreeSurfer. * LongitudinalStatistics - Longitudinal linear mixed effects model MATLAB tools * [[Tracula|TRACULA]] - Documentation on TRActs Constrained by !UnderLying Anatomy, a tool for automated probabilistic tractography. |
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| = MoinMoin Wiki = | === More Details about FreeSurfer Processing === * 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. |
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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. | === Sharing What You Learned === ## * 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. * [[http://brainder.org/|Brainder.org]] - Several fantastic Freesurfer contributions described on this site. |
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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. | = Publications = ---- '''Our publications are now organized in a [[https://www.zotero.org/freesurfer|Zotero Library]]'''. |
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| * [[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 [[FreesurferAcknowledgements|Funding and acknowledgements]] |
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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. | * Support for this research was provided in part by the [[http://www.nih.gov/about/almanac/organization/NCRR.htm/|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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| To get an overview over this site and what it contains, see the SiteNavigation page. | ||<tablewidth="270px" tableheight="169px">[[http://www.nih.gov/|{{attachment:NIH.gif|http://www.nih.gov/}}]] ||[[http://www.nih.gov/about/almanac/organization/NCRR.htm|{{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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| To learn more about what a WikiWikiWeb is, read about MoinMoin:WhyWikiWorks and the MoinMoin:WikiNature. Also, consult the MoinMoin:WikiWikiWebFaq. | |
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| ---- 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 |
||[[http://www.nitrc.org/projects/freesurfer/|{{attachment:NITRC_logo_Listed.jpg|http://www.nitrc.org/projects/freesurfer/}}]] || |
F
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 by the Laboratory for Computational Neuroimaging.
FreeSurfer is a set of tools for analysis and visualization of structural, functional, and diffusion MRI 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 a 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 Getting Started section of the QuickInstall page.
FreeSurfer Courses: If you would like to be notified about upcoming FreeSurfer courses, sign up for the course mailing list here. General information about the course can be found on the CourseDescription page.
Encounter a problem with FreeSurfer?: Search the mailing list to see if this problem has already been covered on there. If you can't find anything that helps you, questions about FreeSurfer as well as BugReporting should be directed to the freesurfer mailing list <freesurfer AT nmr DOT mgh DOT harvard DOT edu> (subscribe to the list here). See FreeSurferSupport for information on mailing lists relating to FreeSurfer.
What you can do for FreeSurfer: Unable to find documentation on some command or process? Once you figure out how to do it, add documentation for everyone else! To contribute to the Wiki, you will need a WikiUserName. Please see GettingAccess to obtain a WikiUserName and then document away. To create a new page once you have an account, just goto the URL you want to create. For instance, goto this link for a page you would name MyNewPage: https://surfer.nmr.mgh.harvard.edu/fswiki/MyNewPage and note the link that says 'Create new empty page'. Just click on that and type away (but please don't use MyNewPage as a page name!).
Social Media: Find us on Facebook as FreeSurferMRI
, follow us on Twitter 
or join our LinkedIn group 
.
Software
FreeSurfer download and install - Current stable release is v5.3.0 - See ReleaseNotes
iSurf - iPhone/iPad app
Nipype - Neuroimaging in Python, w/ FreeSurfer interfaces
Mindboggle-101 data - Manually labeled anatomical regions for 101 healthy subjects
MNE - M/EEG data analysis using FreeSurfer meshes and surface registration
Documentation
Overview of FreeSurfer
FreeSurferAnalysisPipelineOverview - Overview of the FreeSurfer analysis pipeline.
Publications - 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, group analysis, longitudinal analysis, fMRI analysis, and diffusion analysis.
MRI Sequences
Troubleshooting
Manual Editing: see Edits and LongitudinalEdits for an overview and check the Tutorials for examples.
ReconAllTableStableV5.3 - An at-a-glance table showing the FreeSurfer files used & created during the recommended processing stream.
Some of Our Tools
Registration Tools - Documentation of FreeSurfer's registration tools.
LongitudinalProcessing - A description of the longitudinal stream in FreeSurfer.
LongitudinalStatistics - Longitudinal linear mixed effects model MATLAB tools
TRACULA - Documentation on TRActs Constrained by UnderLying Anatomy, a tool for automated probabilistic tractography.
More Details about FreeSurfer Processing
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.
Sharing What You Learned
UserContributions - Scripts and techniques from users. This section is new, but if you have something you'd like to share, please do so.
Brainder.org - Several fantastic Freesurfer contributions described on this site.
Publications
Our publications are now organized in a Zotero Library.
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
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.
