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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://martinos.org/|Athinoula A. Martinos Center for Biomedical Imaging.]]
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= Documentation =  * '''[[FreeSurferSoftwareLicense|License:]]''' The open source 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 [[http://facebook.com/FreeSurferMRI|Facebook]] [[http://facebook.com/FreeSurferMRI|{{attachment:facebook_32.png|Find FreeSurferMRI on Facebook|height="18"}}]] as ''FreeSurferMRI'', follow us on [[http://www.twitter.com/FreeSurferMRI|Twitter]] [[http://www.twitter.com/FreeSurferMRI|{{attachment:twitter_32.png|Follow FreeSurferMRI on Twitter|height="20"}}]] or join our [[https://www.linkedin.com/groups/FreeSurfer-8173404|LinkedIn]] group [[https://www.linkedin.com/groups/FreeSurfer-8173404|{{attachment:linkedin_32.png|!LinkedIn FreeSurfer Group|height="20"}}]].
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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)
 * Labeling of regions on the cortical surface, as well as subcortical brain structures
 * Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas
 * Statistical analysis of group morphometry differences

For more information, see:
 * '''[[FreeSurferAnalysisPipelineOverview|Overview:]]''' General description of the functionality in !FreeSurfer
 * '''Recommended acquisition protocols:'''
  * [[attachment:FreeSurfer_Suggested_Morphometry_Protocols.pdf|Suggested morphometry protocols for optimal FreeSurfer reconstruction|&do=get]]
  * [[http://adni.loni.usc.edu/methods/documents/mri-protocols/|Alternative morphometry protocols, from ADNI]]
 * '''Longitudinal studies:'''
  * [[LongitudinalProcessing|The longitudinal FreeSurfer stream]]
  * [[LongitudinalStatistics | Longitudinal linear mixed effects statistics]]
 * '''Troubleshooting:'''
  * Manual editing [[Edits|for the basic stream]] and [[LongitudinalEdits|for the longitudinal stream]]
  * [[ReconAllTableStableV5.3|Output files:]] A table of files created and used during a standard !FreeSurfer analysis
 * '''Advanced:'''
  * [[WorkFlows|Work flows:]] How to use the !FreeSurfer stream to accomplish specific tasks
  * [[ToolsAndCommands|Tools and commands:]] GUI and command-line tool documentation
  * [[FileFormats|File formats:]] Description of native !FreeSurfer file formats, as well as external file formats recognized by !FreeSurfer
  * [[CoordinateSystems|Coordinate systems:]] Details on the voxel and RAS coordinate systems used in !FreeSurfer

=== Functional MRI ===
 * '''[[FsFast|FreeSurfer Functional Analysis Stream (FS-FAST):]]''' FS-FAST is a set of tools for performing functional MRI data analyses on the cortical surface.

=== Diffusion MRI ===
 * '''[[Tracula|TRActs Constrained by UnderLying Anatomy (TRACULA):]]''' TRACULA is a tool for automated global probabilistic tractography with anatomical priors. It reconstructs a set of major white-matter pathways by incorporating prior information on the structural segmentation labels that each pathway goes through or next to, as a function of position along the length of the pathway. It includes a specialized stream for processing longitudinal diffusion MRI data.

=== PET Partial Volume Correction (PVC) and Kinetic Modeling ===
 * '''[[PetSurfer|PETSurfer:]]''' PETSurfer is a tool for performing
ROI-based, surface-based, and whole-brain analysis of PET data
integrated with FreeSurfer anatomical analysis.

=== Multimodal ===
 * '''[[FreeSurferCommandsRegistration|Registration tools:]]''' !FreeSurfer offers a range of tools for both within-subject and across-subject registration.

## * 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 Athinoula A. Martinos Center for Biomedical Imaging.

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)
  • Labeling of regions on the cortical surface, as well as subcortical brain structures
  • Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas
  • Statistical analysis of group morphometry differences

For more information, see:

Functional MRI

Diffusion MRI

  • TRActs Constrained by UnderLying Anatomy (TRACULA): TRACULA is a tool for automated global probabilistic tractography with anatomical priors. It reconstructs a set of major white-matter pathways by incorporating prior information on the structural segmentation labels that each pathway goes through or next to, as a function of position along the length of the pathway. It includes a specialized stream for processing longitudinal diffusion MRI data.

PET Partial Volume Correction (PVC) and Kinetic Modeling

ROI-based, surface-based, and whole-brain analysis of PET data integrated with FreeSurfer anatomical analysis.

Multimodal

  • Registration tools: FreeSurfer offers a range of tools for both within-subject and across-subject registration.

FreeSurferWiki (last edited 2023-06-14 23:16:55 by buildqa)