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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.]] |
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| = Documentation = | * '''[[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|Installation guide:]]''' How to download and install !FreeSurfer on your computer |
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| * FreeSurferInstallation * FreeSurferGuide * FreeSurferTutorial * FreeSurferTools |
* '''Documentation:''' [[QuickInstall|Getting started,]] [[Tutorials|step-by-step tutorials,]] [[UserContributions/FAQ|FAQ,]] [[FsTutorial/Glossary|Glossary]] |
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| = Support = FreeSurferSupport |
* '''[[FreeSurferMethodsCitation|Citing FreeSurfer:]]''' Short description and citations for core !FreeSurfer methods |
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| = Acknowledgements = FreeSurfer is brought to you by [http://www.cortechs.net CorTechs] and NCRR/P41RR14075 |
* '''[[https://www.zotero.org/freesurfer|Publications:]]''' A Zotero library of articles on the methods in !FreeSurfer and the studies that use !FreeSurfer |
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| = MoinMoin Wiki = | * '''[[FreeSurferSupport | User support:]]''' How to get help with problems that you encounter when using !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. | * '''[[CourseDescription | Hands-on training:]]''' Information on the !FreeSurfer courses that we organize in Boston and around the world |
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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. | * '''[[UserContributions | User contributions:]]''' Scripts and techniques from users of !FreeSurfer |
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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. |
* '''[[ThirdPartySoftware | Other software:]]''' Third-party software packages that are interoperable or related to !FreeSurfer |
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| To get an overview over this site and what it contains, see the SiteNavigation page. | * '''[[FreesurferAcknowledgements|Acknowledgements:]]''' The funding agencies and collaborators that have contributed to the research behind !FreeSurfer |
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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. | * '''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}}]]. |
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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 |
= Our tools = |
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| === Structural MRI === !FreeSurfer provides a full processing stream for structural MRI data, including: * Skull stripping, B1 bias field correction, and gray-white matter segmentation * Reconstruction of cortical surface models (gray-white boundary surface and pial surface) * Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas * Labeling of regions on the cortical surface, as well as subcortical brain structures * Statistical analysis of group morphometry differences For more information, see: * FreeSurferAnalysisPipelineOverview - Overview of the !FreeSurfer analysis pipeline. === 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]] === 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 === * [[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. === 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. ## * 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.
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
Installation guide: 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
Other software: Third-party software packages that are interoperable or related to 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 
.
Our tools
Structural MRI
FreeSurfer provides a full processing stream for structural MRI data, including:
- Skull stripping, B1 bias field correction, and gray-white matter segmentation
- Reconstruction of cortical surface models (gray-white boundary surface and pial surface)
- Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas
- Labeling of regions on the cortical surface, as well as subcortical brain structures
- Statistical analysis of group morphometry differences
For more information, see:
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.