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| ---- Welcome to the '''FreeSurferWiki'''. The FreeSurferWiki is the central documentation and download source for [[http://surfer.nmr.mgh.harvard.edu|FreeSurfer]], a software application developed at the [[http://www.nmr.mgh.harvard.edu/martinos/noFlashHome.php|Martinos Center for Biomedical Imaging]] by the [[http://martinos.org/lcn/|Laboratory for Computational Neuroimaging]]. |
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| !FreeSurfer is a set of tools for analysis and visualization of structural, functional, and diffusion MRI brain imaging data. !FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data. | !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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| * '''!FreeSurfer Courses''': If you would like to be notified about upcoming !FreeSurfer courses, sign up for the course mailing list [[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi|here]]. General information about the course can be found on the CourseDescription page. | * [[FreeSurferSupport | User support:]] How to get help with problems that you encounter when using !FreeSurfer |
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| * '''Encounter a problem with !FreeSurfer?''': Search the [[http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/|mailing list]] to see if this problem has already been covered on there. If you can't find anything that helps you, questions about !FreeSurfer as well as BugReporting should be directed to the <<MailTo(freesurfer AT nmr DOT mgh DOT harvard DOT edu, freesurfer mailing list)>> (subscribe to the list [[http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer|here]]). See FreeSurferSupport for information on mailing lists relating to FreeSurfer. * '''What you can do for !FreeSurfer''': Unable to find documentation on some command or process? Once you figure out how to do it, add documentation for everyone else! To contribute to the Wiki, you will need a WikiUserName. Please see GettingAccess to obtain a WikiUserName and then document away. To create a new page once you have an account, just goto the URL you want to create. For instance, goto this link for a page you would name !MyNewPage: https://surfer.nmr.mgh.harvard.edu/fswiki/MyNewPage and note the link that says 'Create new empty page'. Just click on that and type away (but please don't use !MyNewPage as a page name!). |
* [[CourseDescription | Hands-on training:]] Information on the !FreeSurfer courses that we organize in Boston and around the world |
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* [[https://www.zotero.org/freesurfer|FreeSurfer Publications]] |
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| * [[https://www.zotero.org/freesurfer|Publications]] - Background describing the techniques used in the !FreeSurfer tools, and their usage in research. | |
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| * [[UserContributions | User contributions:]] Scripts and techniques from users of !FreeSurfer. | * [[FreeSurferMethodsCitation|How to cite FreeSurfer:]] Short description and citations for core !FreeSurfer methods |
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| * [[FreeSurferMethodsCitation|How to cite FreeSurfer:]] Short description and citations for core !FreeSurfer methods | * [[UserContributions | User contributions:]] Scripts and techniques from users of !FreeSurfer. |
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| * [[FreesurferAcknowledgements|Funding and acknowledgements:]] The funding agencies and collaborators that have contributed to the research behind !FreeSurfer | * [[FreesurferAcknowledgements|Acknowledgements:]] The funding agencies and collaborators that have contributed to the research behind !FreeSurfer |
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.
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
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.
How to cite FreeSurfer: Short description and citations for core FreeSurfer methods
Publications: A Zotero library of articles on the methods in FreeSurfer or studies that use FreeSurfer
User contributions: Scripts and techniques from users of FreeSurfer.
Acknowledgements: The funding agencies and collaborators that have contributed to the research behind FreeSurfer