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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 ... * '''''NEW USERS:''''' Please see the [[https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall#GetStarted.21|Getting Started]] section of the QuickInstall page. * [[FreeSurferMethodsCitation|How to cite 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 = ---- * [[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. * [[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 * FreeSurferWorkFlows * 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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| * FileFormats * CoordinateSystems |
=== 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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| * DevelopersGuide | === 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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| = Support = FreeSurferSupport |
=== 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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| = WikiGuidelines = * ["Content"] * ["Style"] = BeginnersGuide = * BeginnersGuide 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 = Acknowledgements = FreeSurfer is brought to you by [http://www.cortechs.net CorTechs] and [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] |
## * 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 ...
NEW USERS: Please see the Getting Started section of the QuickInstall page.
How to cite 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
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.
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.