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#acl WikiUserGroup:read,write,delete,revert All:read #acl LcnGroup:read,write,delete,revert All:read
= FreeSurfer =
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= Welcome =
 * Welcome to the FreeSurferWiki. The FreeSurferWiki provides a documentation forum for investigators at the MartinosCenter for Biomedical Imaging and for the !FreeSurfer user community at large. 		##<<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 [[https://www.martinos.org/lab/lcn|Laboratory for Computational Neuroimaging]] at the [[http://martinos.org/|Athinoula A. Martinos Center for Biomedical Imaging.]] !FreeSurfer is the structural MRI analysis software of choice for the [[https://github.com/Washington-University/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage|Human Connectome Project.]]
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 * To gain access to the Wiki to make additions or improvements, see GettingAccess. Once you have access, see the WikiBeginnersGuide to get started.  * '''[[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 v7.4.1'''
 * '''[[DownloadAndInstall|Installation guide:]]''' How to download and install !FreeSurfer on your computer
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 * Most of the Wiki is publicly readable, and is the central source for !FreeSurfer usage documentation.  * '''Documentation:''' [[QuickInstall|Getting started]]; [[Tutorials|step-by-step tutorials]]; [[UserContributions/FAQ|FAQ]]; [[FsTutorial/Glossary|glossary]]; [[ReconAllTable | Table of commands in processing stream]]
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 * Please feel free to email [[MailTo(fswiki DASH help AT nmr DOT mgh DOT harvard DOT edu, fswiki-help)]] if you have any questions or encounter any difficulties.  * '''[[FreeSurferMethodsCitation|Citing FreeSurfer:]]''' Short description and citations for core !FreeSurfer methods
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= Software =  * '''[[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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 * For external users: FreeSurferDistributions
 * For NMR users: InternalFreeSurferDistributions
 * FtpFileExchange
 * RemoteAccess		  * '''[[FreeSurferSupport | User support:]]''' How to get help with problems that you encounter when using !FreeSurfer
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= Documentation =  * '''[[CourseDescription | Hands-on training:]]''' Information on the !FreeSurfer courses that we organize in Boston and around the world
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 * WorkFlows
 * ["Tools"]
 * ["Commands"]
 * ["Articles"]
 * ["Guides"]
 * ["Tutorials"]
 * FileFormats
 * CoordinateSystems
 * DevelopersGuide		  * '''[[FsStats | Stats:]]''' Stats on !FreeSurfer usage, citations, and development
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= Support =
 * FreeSurferSupport		  * '''[[UserContributions | User contributions:]]''' Scripts and techniques from users of !FreeSurfer
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= WikiGuidelines =
 * CulturalGuidelines
 * StyleGuidelines		  * '''[[ThirdPartySoftware | Other software:]]''' Third-party software packages that are interoperable or related to !FreeSurfer
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= BeginnersGuides =
 * WikiBeginnersGuide
 * FreeSurferBeginnersGuide		  * '''[[FreesurferAcknowledgements|Acknowledgements:]]''' The funding agencies and collaborators that have contributed to the research behind !FreeSurfer
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= Acknowledgements =
FreeSurfer is brought to you by [http://www.cortechs.net CorTechs], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6641264&p_grant_num=5P41RR014075-05&p_query=&ticket=10459360&p_audit_session_id=48433183&p_keywords= NCRR/P41RR14075], R01 RR16594-01A1, and our ["Contributors"].		  * '''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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 * '''[[DiversityAndInclusion|Diversity and Inclusion]]'''

= 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:
 * '''[[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]]
  * [[ReconAllTableStableV6.0|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.

* '''AnatomiCuts''' : An unsupervised hierarchical streamline clustering algorithm based on anatomical similarity. AnatomiCuts is currently in the developing branch (https://github.com/freesurfer/freesurfer/tree/dev/anatomicuts).

* '''DiffusionTool''' : This tool can help generating the configuration file of TRACULA and setting up the parameters to run AnatomiCuts. The DiffusionTool is currently in the developing branch (https://github.com/freesurfer/freesurfer/tree/dev/diffusion_tool).

=== PETsurfer PET Kinetic Modeling and Partial Volume Correction (PVC) ===
 * '''[[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).

=== Quick Links for LCN Members ===

 * LCN Members can navigate to the LcnInternal wiki page with quicklinks to regularly requested resources or wiki pages

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. FreeSurfer is the structural MRI analysis software of choice for the Human Connectome Project.

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.

* AnatomiCuts : An unsupervised hierarchical streamline clustering algorithm based on anatomical similarity. AnatomiCuts is currently in the developing branch (https://github.com/freesurfer/freesurfer/tree/dev/anatomicuts).

* DiffusionTool : This tool can help generating the configuration file of TRACULA and setting up the parameters to run AnatomiCuts. The DiffusionTool is currently in the developing branch (https://github.com/freesurfer/freesurfer/tree/dev/diffusion_tool).

PETsurfer PET Kinetic Modeling and Partial Volume Correction (PVC)

  • PETSurfer: PETSurfer is a tool for performing 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.

  • LCN Members can navigate to the LcnInternal wiki page with quicklinks to regularly requested resources or wiki pages

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