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| #acl LcnGroup:read,write,delete,revert All:read = FreeSurfer = |
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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 software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the [[http://martinos.org/lcn/|Laboratory for Computational Neuroimaging]] at the [[http://www.nmr.mgh.harvard.edu|Martinos Center for Biomedical Imaging.]] !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 ... * '''[[FreeSurferSoftwareLicense|License:]]''' The license agreement that allows you to use !FreeSurfer * '''[[ReleaseNotes|Release notes:]]''' New features and changes in each version of !FreeSurfer - '''current stable release is v5.3.0''' * '''[[DownloadAndInstall|Download:]]''' How to download and install !FreeSurfer on your computer * '''Documentation:''' [[QuickInstall|Getting started,]] [[Tutorials|step-by-step tutorials,]] [[UserContributions/FAQ|FAQ,]] [[FsTutorial/Glossary|Glossary]] * '''[[FreeSurferMethodsCitation|Citing FreeSurfer:]]''' Short description and citations for core !FreeSurfer methods * '''[[https://www.zotero.org/freesurfer|Publications:]]''' A Zotero library of articles on the methods in !FreeSurfer and the studies that use !FreeSurfer * '''[[FreeSurferSupport | User support:]]''' How to get help with problems that you encounter when using !FreeSurfer * '''[[CourseDescription | Hands-on training:]]''' Information on the !FreeSurfer courses that we organize in Boston and around the world * '''[[UserContributions | User contributions:]]''' Scripts and techniques from users of !FreeSurfer. * '''[[FreesurferAcknowledgements|Acknowledgements:]]''' The funding agencies and collaborators that have contributed to the research behind !FreeSurfer * '''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}}]]. = Software = ---- * [[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. * |
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| * FreeSurferInstallation * FreeSurferGuide * FreeSurferTutorial * FreeSurferTools |
=== 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. 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. ---- 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 |
## * DevelopersGuide - Information for developers of the !FreeSurfer code-base (Martinos Center internal). |
FreeSurfer
FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging.
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 ...
License: The license agreement that allows you to use FreeSurfer
Release notes: New features and changes in each version of FreeSurfer - current stable release is v5.3.0
Download: How to download and install FreeSurfer on your computer
Documentation: Getting started, step-by-step tutorials, FAQ, Glossary
Citing FreeSurfer: Short description and citations for core FreeSurfer methods
Publications: A Zotero library of articles on the methods in FreeSurfer and the studies that use FreeSurfer
User support: How to get help with problems that you encounter when using FreeSurfer
Hands-on training: Information on the FreeSurfer courses that we organize in Boston and around the world
User contributions: Scripts and techniques from users of FreeSurfer.
Acknowledgements: The funding agencies and collaborators that have contributed to the research behind FreeSurfer
Social media: Find us on Facebook as FreeSurferMRI
, follow us on Twitter 
or join our LinkedIn group 
.
Software
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.
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.