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| !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 ... * [[http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense|License:]] The license agreement that allows you to use !FreeSurfer * [[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 |
* '''[[FreeSurferSoftwareLicense|License:]]''' The license agreement that allows you to use !FreeSurfer * '''[[ReleaseNotes|Release notes:]]''' New features and changes in each version of !FreeSurfer - '''current stable release is v5.3.0''' * '''[[DownloadAndInstall|Installation guide:]]''' 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}}]]. |
* '''[[ThirdPartySoftware | Other software:]]''' Third-party software packages that are interoperable or related to !FreeSurfer |
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| = Software = ---- * [[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]] * [[FSL]] * [[http://afni.nimh.nih.gov/|AFNI/NIfTI/SUMA]] * [[http://www.fil.ion.ucl.ac.uk/spm/|SPM - Statistical Parametric Mapping]] * [[http://www.nitrc.org/|NITRC]] * [[http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8|iSurf]] - iPhone/iPad app * [[http://nipy.sourceforge.net/nipype/index.html|Nipype]] - Neuroimaging in Python, w/ FreeSurfer interfaces * [[http://mindboggle.info/data.html|Mindboggle-101 data]] - Manually labeled anatomical regions for 101 healthy subjects * [[http://martinos.org/mne/|MNE - M/EEG data analysis using FreeSurfer meshes and surface registration]] * [[http://neuroimage.usc.edu/brainstorm/Introduction|Brainstorm]] - See [[Brainstorm|Integration with FreeSurfer]] |
* '''[[FreesurferAcknowledgements|Acknowledgements:]]''' The funding agencies and collaborators that have contributed to the research behind !FreeSurfer |
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| = Documentation = ---- === Overview of FreeSurfer === * FreeSurferAnalysisPipelineOverview - Overview of the !FreeSurfer analysis pipeline. * |
* '''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}}]]. |
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| === MRI Sequences === * [[attachment:FreeSurfer_Suggested_Morphometry_Protocols.pdf|Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction|&do=get]] * [[http://adni.loni.usc.edu/methods/documents/mri-protocols/|Alternative Morphometry Sequences, from ADNI]] |
= Our tools = |
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| === 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. |
=== Structural MRI === |
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| === Some of Our Tools === * [[FreeSurferCommandsRegistration|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|TRACULA]] - Documentation on TRActs Constrained by !UnderLying Anatomy, a tool for automated probabilistic tractography. |
!FreeSurfer provides a full processing stream for structural MRI data, including: * Skull stripping, B1 bias field correction, and gray-white matter segmentation * Reconstruction of cortical surface models (gray-white boundary surface and pial surface) * Labeling of regions on the cortical surface, as well as subcortical brain structures * Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas * Statistical analysis of group morphometry differences |
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| === More Details about FreeSurfer Processing === | For more information, see: * [[FreeSurferAnalysisPipelineOverview|Overview]] |
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| * Recommended acquisition protocols: * [[attachment:FreeSurfer_Suggested_Morphometry_Protocols.pdf|Suggested Morphometry Protocols for Optimal FreeSurfer Reconstruction|&do=get]] * [[http://adni.loni.usc.edu/methods/documents/mri-protocols/|Alternative Morphometry Protocols, from ADNI]] * Longitudinal studies: * [[LongitudinalProcessing|The longitudinal !FreeSurfer stream]] * [[LongitudinalStatistics | Longitudinal linear mixed effects statistics]] * 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. === Diffusion MRI === * [[Tracula|TRACULA]] - Documentation on TRActs Constrained by !UnderLying Anatomy, a tool for automated probabilistic tractography. === Multimodal === * [[FreeSurferCommandsRegistration|Registration Tools]] - Documentation of !FreeSurfer's registration tools. |
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.
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
Installation guide: 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
Other software: Third-party software packages that are interoperable or related to FreeSurfer
Acknowledgements: The funding agencies and collaborators that have contributed to the research behind FreeSurfer
Social media: Find us on Facebook as FreeSurferMRI
, follow us on Twitter 
or join our LinkedIn group 
.
Our tools
Structural MRI
FreeSurfer provides a full processing stream for structural MRI data, including:
- Skull stripping, B1 bias field correction, and gray-white matter segmentation
- Reconstruction of cortical surface models (gray-white boundary surface and pial surface)
- Labeling of regions on the cortical surface, as well as subcortical brain structures
- Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas
- Statistical analysis of group morphometry differences
For more information, see:
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.
- Recommended acquisition protocols:
- Longitudinal studies:
- 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.
Diffusion MRI
TRACULA - Documentation on TRActs Constrained by UnderLying Anatomy, a tool for automated probabilistic tractography.
Multimodal
Registration Tools - Documentation of FreeSurfer's registration tools.