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 * [[ReleaseNotes|Release notes:]] New features and changes in each version of !FreeSurfer - '''current stable release is v5.3.0'''
 * [[DownloadAndInstall|Download:]] How to download and install !FreeSurfer on your computer
 * '''[[ReleaseNotes|Release notes:]]''' New features and changes in each version of !FreeSurfer - '''current stable release is v5.3.0'''
 * '''[[DownloadAndInstall|Download:]]''' How to download and install !FreeSurfer on your computer
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 * [[FreeSurferMethodsCitation|How to cite FreeSurfer:]] Short description and citations for core !FreeSurfer methods  * '''[[FreeSurferMethodsCitation|Citing FreeSurfer:]]''' Short description and citations for core !FreeSurfer methods
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 * [[https://www.zotero.org/freesurfer|Publications:]] A Zotero library of articles on the methods in !FreeSurfer and the studies that use !FreeSurfer  * '''[[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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 * [[FreeSurferSupport | User support:]] How to get help with problems that you encounter when using !FreeSurfer  * '''[[FreeSurferSupport | User support:]]''' How to get help with problems that you encounter when using !FreeSurfer
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 * [[CourseDescription | Hands-on training:]] Information on the !FreeSurfer courses that we organize in Boston and around the world  * '''[[CourseDescription | Hands-on training:]]''' Information on the !FreeSurfer courses that we organize in Boston and around the world
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 * [[UserContributions | User contributions:]] Scripts and techniques from users of !FreeSurfer.  * '''[[UserContributions | User contributions:]]''' Scripts and techniques from users of !FreeSurfer.
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 * [[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}}]].
 * '''[[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}}]].

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 ...

  • 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

  • Download: 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.

  • Acknowledgements: The funding agencies and collaborators that have contributed to the research behind FreeSurfer

  • Social media: Find us on Facebook as FreeSurferMRI Find FreeSurferMRI on Facebook, follow us on Twitter Follow FreeSurferMRI on Twitter or join our LinkedIn group !LinkedIn FreeSurfer Group.

Software


Documentation


Overview of FreeSurfer

MRI Sequences

Troubleshooting

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.

FreeSurferWiki (last edited 2019-07-18 11:36:01 by 172)