Welcome

• Welcome to the FreeSurferWiki. The FreeSurferWiki is the central documentation source for FreeSurfer.

• NEW USERS: Please see the FreeSurferBeginnersGuide to get started.

• 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 should be directed to the MailTo(freesurfer AT nmr DOT mgh DOT harvard DOT edu, freesurfer mailing list). Bugs reports should be directed to the MailTo(analysis-bugs AT nmr DOT mgh DOT harvard DOT edu, analysis-bugs mailing list).

Software

• [wiki:DownloadAndInstall FreeSurfer download and install] - New stable release v3.0.1 now available!

• [wiki:MiscellaneousDownloads Miscellaneous downloads]

• [wiki:InternalFreeSurferDistributions Information for internal (Martinos Center) users]

• [wiki:FtpFileExchange Information on FTP file exchange]

• [wiki:RemoteAccess Information on remote access]

Documentation

• FreeSurferAnalysisPipelineOverview - Overview of the FreeSurfer analysis pipeline.

• WorkFlows - Information on the how the FreeSurfer tools are used in a processing stream.

• ArticlesSlidesAndPosters - Background describing the techniques used in the FreeSurfer tools, and their usage in research.

• ["Tutorials"] - A walk-through of a FreeSurfer work-flow, covering editing and troubleshooting techniques in-depth, as well as a group study example.

• ["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).

• ReconAllDevTable - An at-a-glance table showing the FreeSurfer files used & created during the recommended processing stream.

Support

• FreeSurferSupport - Mailing lists and helplines which provide user support for FreeSurfer

WikiGuidelines

• CulturalGuidelines

• StyleGuidelines

BeginnersGuides

• WikiBeginnersGuide

• FreeSurferBeginnersGuide

Feedback

• The FreeSurfer development team values your feedback. Please take a moment to visit the ["Priorities"] page and register your priority. Thanks.

• You can add your comments or suggestions on our FeedBack page.

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], [http://crisp.cit.nih.gov/crisp/CRISP_LIB.getdoc?textkey=6936484&p_grant_num=5R01RR01659404&p_query=&ticket=16737375&p_audit_session_id=78570196&p_keywords= R01 RR16594-01A1], and our ["Contributors"].

References

• Published material describing the techniques used in FreeSurfer ([http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/cite.php please cite our software!]):

• surface reconstruction:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/dale99-recon1.pdf Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction], Dale, A.M., Fischl, B., Sereno, M.I., (1999). NeuroImage 9(2):179-194

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99b-recon2.pdf Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System], Fischl, B., Sereno, M.I., Dale, A.M., (1999). NeuroImage, 9(2):195-207.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl01-topology-fixing.pdf Automated Manifold Surgery: Constructing Geometrically Accurate and Topologically Correct Models of the Human Cerebral Cortex], Fischl, B., Liu, A. and Dale, A.M., (2001). IEEE Transactions on Medical Imaging, 20(1):70-80.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/dalesereno93-ms.pdf Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction: A linear approach], Dale, A.M., and Sereno, M.I. (1993). Journal of Cognitive Neuroscience 5:162-176.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/segonne05.pdf A Hybrid Approach to the Skull-Stripping Problem in MRI], Ségonne, F., Dale, A.M., Busa, E., Glessner, M., Salvolini, U., Hahn, H.K., Fischl, B. (2004). NeuroImage, 22:1160-1075.

• inter-subject spherical averaging:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99-morphing.pdf High-resolution inter-subject averaging and a coordinate system for the cortical surface], Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999).

• thickness measurement:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl00-cortical-thickness.pdf Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Images], Fischl, B., and Dale, A.M., (2000). Proceedings of the National Academy of Sciences, 97:11044-11049.

• cortical parcellation:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Automatically Parcellating the Human Cerebral Cortex], Fischl et al., (2004). Cerebral Cortex, 14:11-22.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest], Desikan et al., (2006). NeuroImage, in press.

• subcortical segmentation:

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/montillo02-labeling.pdf Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain], Montillo et al., (2002). Neuron, 33:341-355.

  • [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-segmentation.pdf Sequence-Independent Segmentation of Magnetic Resonance Images], Fischl, B., Salat. D.H., van der Kouwe, A.J.W., Makris, N., Ségonne, F., and Dale, A.M. (2004) NeuroImage Jul;22(3):1060-75.