##language:en #pragma section-numbers off #acl AdminGroup:read,write,delete,revert All:read = Welcome = ---- ## * '''''ANNOUNCEMENT:''''' A Freesurfer Tutorial and Workshop will be held January 20 & 21st, 2009. [[CourseDescription|Details here!]] * 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]]. * '''''NEW USERS:''''' Please see the FreeSurferBeginnersGuide to get started. See also the [[http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ|FAQ]] page and FreeSurferSupport. * If you would like to contribute to the Wiki you will need a WikiUserName. Please see GettingAccess to obtain a WikiUserName. * See FreeSurferSupport for information on mailing lists relating to FreeSurfer. General questions about !FreeSurfer, and BugReporting, should be directed to the <> (subscribe to the list [[http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer|here]]). = Software = ---- * [[DownloadAndInstall|FreeSurfer download and install]] - '''New stable release! v4.5.0''' - 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]] * [[http://www.fmrib.ox.ac.uk/fsl/|FSL - FMRIB Software Library]] * [[http://afni.nimh.nih.gov/|AFNI/NIfTI/SUMA]] * [[http://www.fil.ion.ucl.ac.uk/spm/|SPM - Statistical Parametric Mapping]] = Documentation = ---- * FreeSurferAnalysisPipelineOverview - Overview of the !FreeSurfer analysis pipeline. * ArticlesSlidesAndPosters - Background describing the techniques used in the !FreeSurfer tools, and their usage in research. * [[Tutorials]] - A walk-through of a !FreeSurfer workflow, covering editing and troubleshooting techniques in-depth, as well as a group study example. There is also an FS-FAST tutorial. * ReconAllDevTable - An at-a-glance table showing the !FreeSurfer files used & created during the recommended processing stream. * [[LongitudinalProcessing]] - A description of the longitudinal stream in !FreeSurfer. * 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. * DevelopersGuide - Information for developers of the !FreeSurfer code-base (Martinos Center internal). * UserContributions - Scripts and techniques from users. This section is new, but if you have something you'd like to share, please do so. See also the [[http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ|FAQ]] page. * [[attachment:freesurfer_methods.doc|How to describe and cite Freesurfer]] - This document has a short description of Freesurfer methods to be used when citing Freesurfer. Alternatively, the text is available on the wiki at [[FreeSurferMethodsCitation]] ##= Support = ##---- ## * FreeSurferSupport - Mailing lists and helplines which provide user support for !FreeSurfer ##= WikiGuidelines = ## * CulturalGuidelines ## * StyleGuidelines ##= BeginnersGuides = ## * WikiBeginnersGuide ## * FreeSurferBeginnersGuide = Acknowledgements = ---- * Support for this research was provided in part by the [[http://www.ncrr.nih.gov/|National Center for Research Resources]] (P41-RR14075, R01 RR16594-01A1 and the NCRR [[http://www.nbirn.net/research/morphometry/index.shtm|BIRN Morphometric Project]] BIRN002, U24 RR021382), the [[http://www.ninds.nih.gov/|National Institute for Neurological Disorders and Stroke]] (R01 NS052585-01)), the [[http://www.nibib.nih.gov/|National Institute of Biomedical Imaging and Bioengineering]], as well as the [[http://www.themindinstitute.org/|Mental Illness and Neuroscience Discovery]] (MIND) Institute, and is part of the [[http://www.na-mic.org/|National Alliance for Medical Image Computing]] (NAMIC), funded by the [[http://www.nih.gov/|National Institutes of Health]] through the [[http://nihroadmap.nih.gov/|NIH Roadmap for Medical Research]], Grant U54 EB005149. * Thanks to Ron Kikinis, Steve Pieper and NA-MIC (NIH Roadmap for Medical Research Grant U54 EB005149) for providing engineering advice and support for testing and open-sourcing of !FreeSurfer. * Thanks to Avi Snyder (Washington University School of Medicine) for porting his Talairach alignment implementation to !FreeSurfer. ||[[http://www.nih.gov/|{{attachment:NIH.gif|http://www.nih.gov/}}]] || [[http://www.ncrr.nih.gov/|{{attachment:NCRR.png|http://www.ncrr.nih.gov/}}]] || [[http://www.nbirn.net/|{{attachment:BIRN.jpg|http://www.nbirn.net/}}]] || ||[[http://www.ninds.nih.gov/|{{attachment:NINDSsm.jpg|http://www.ninds.nih.gov/}}]] || [[http://www.na-mic.org/|{{attachment:NAMIC.jpg|http://www.na-mic.org/}}]] || [[http://www.nibib.nih.gov/|{{attachment:NIBIB.jpg|http://www.nibib.nih.gov/}}]] || ||[[http://www.nitrc.org/projects/freesurfer/|{{attachment:NITRC_logo_Listed.jpg|http://www.nitrc.org/projects/freesurfer/}}]] || = References = ---- . <>