Welcome

Welcome to the FreeSurferWiki. The FreeSurferWiki is the central documentation and download source for FreeSurfer, a software application developed at the Martinos Center for Biomedical Imaging.

FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.

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 an 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: In addition to the FreeSurferBeginnersGuide also be sure to check out the FAQ.

• FreeSurfer Courses: If you would like to be notified about upcoming FreeSurfer courses, sign up for the course mailing list here. General information about course can be found on the CourseDescription page.

• Ran into a problem with FreeSurfer?: Search the 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 freesurfer mailing list <freesurfer AT nmr DOT mgh DOT harvard DOT edu> (subscribe to the list 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.

• Social Media: Find us on Facebook as FreeSurferMRI or follow us on Twitter .

• FreeSurfer Articles

Software

• FreeSurfer download and install - New stable release: v5.1.0 - See ReleaseNotes

• Miscellaneous downloads

• Information for internal (Martinos Center) users

• Information on FTP file exchange and email file-drop

• Information on remote access

• 3D Slicer

• FSL - FMRIB Software Library

• AFNI/NIfTI/SUMA

• SPM - Statistical Parametric Mapping

• NITRC

• iSurf - iPhone/iPad app

• Nipype - Neuroimaging in Python, w/ FreeSurfer interfaces

Documentation

Overview to FreeSurfer

• 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, group analysis, longitudinal analysis, fMRI analysis, and diffusion analysis.

• FAQ

• Glossary

MRI Sequences

• Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction

• Alternative Morphometry Sequences, from ADNI

Troubleshooting

• Manual Editing: see Edits and LongitudinalEdits for an overview and check the Tutorials for examples.

• ReconAllDevTable - 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.

• 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.

Sharing What You Learned

• UserContributions - Scripts and techniques from users. This section is new, but if you have something you'd like to share, please do so.

Citing FreeSurfer

• 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

Acknowledgements

• Support for this research was provided in part by the National Center for Research Resources (P41-RR14075, R01 RR16594-01A1 and the NCRR BIRN Morphometric Project BIRN002, U24 RR021382), the National Institute for Neurological Disorders and Stroke (R01 NS052585-01)), the National Institute of Biomedical Imaging and Bioengineering, as well as the Mental Illness and Neuroscience Discovery (MIND) Institute, and is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the 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.

References

When citing Freesurfer, here is some boilerplate text.