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= Welcome =
----
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]] by the [[http://martinos.org/lcn/|Laboratory for Computational Neuroimaging]].		 = FreeSurfer =
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!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 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 [[https://www.martinos.org/lab/lcn|Laboratory for Computational Neuroimaging]] at the [[http://martinos.org/|Athinoula A. Martinos Center for Biomedical Imaging.]] !FreeSurfer is the structural MRI analysis software of choice for the [[https://github.com/Washington-University/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage|Human Connectome Project.]]
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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 ...  * '''[[FreeSurferSoftwareLicense|License:]]''' The open source license agreement that allows you to use !FreeSurfer
 * '''[[ReleaseNotes|Release notes:]]''' New features and changes in each version of !FreeSurfer - '''current stable release is v7.4.1'''
 * '''[[DownloadAndInstall|Installation guide:]]''' How to download and install !FreeSurfer on your computer
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 * '''''NEW USERS:''''' Please see the [[https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall#GetStarted.21|Getting Started]] section of the QuickInstall page.  * '''Documentation:''' [[QuickInstall|Getting started]]; [[Tutorials|step-by-step tutorials]]; [[UserContributions/FAQ|FAQ]]; [[FsTutorial/Glossary|glossary]]; [[ReconAllTable | Table of commands in processing stream]]
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 * '''!FreeSurfer Courses''': If you would like to be notified about upcoming !FreeSurfer courses, sign up for the course mailing list [[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi|here]]. General information about the course can be found on the CourseDescription page.  * '''[[FreeSurferMethodsCitation|Citing FreeSurfer:]]''' Short description and citations for core !FreeSurfer methods
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 * '''Encounter a problem with !FreeSurfer?''': Search the [[http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/|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 <<MailTo(freesurfer AT nmr DOT mgh DOT harvard DOT edu, freesurfer mailing list)>> (subscribe to the list [[http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer|here]]). See FreeSurferSupport for information on mailing lists relating to 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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 * '''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. To create a new page once you have an account, just goto the URL you want to create. For instance, goto this link for a page you would name !MyNewPage: https://surfer.nmr.mgh.harvard.edu/fswiki/MyNewPage and note the link that says 'Create new empty page'. Just click on that and type away (but please don't use !MyNewPage as a page name!).  * '''[[FreeSurferSupport | User support:]]''' How to get help with problems that you encounter when using !FreeSurfer
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 * '''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}}]].  * '''[[CourseDescription | Hands-on training:]]''' Information on the !FreeSurfer courses that we organize in Boston and around the world
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 * [[https://www.zotero.org/freesurfer|FreeSurfer Publications]]  * '''[[FsStats | Stats:]]''' Stats on !FreeSurfer usage, citations, and development
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= Software =
----
 * [[http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense|License]]
 * [[DownloadAndInstall|FreeSurfer download and install]] - '''Current stable release is v5.3.0''' - 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]]
 * [[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]]		  * '''[[UserContributions | User contributions:]]''' Scripts and techniques from users of !FreeSurfer
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= Documentation =
----
=== Overview of FreeSurfer ===
 * FreeSurferAnalysisPipelineOverview - Overview of the !FreeSurfer analysis pipeline.
 * [[https://www.zotero.org/freesurfer|Publications]] - 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.
 * [[UserContributions/FAQ|FAQ]]
 * [[FsTutorial/Glossary|Glossary]]		  * '''[[ThirdPartySoftware | Other software:]]''' Third-party software packages that are interoperable or related to !FreeSurfer
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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]]		  * '''[[FreesurferAcknowledgements|Acknowledgements:]]''' The funding agencies and collaborators that have contributed to the research behind !FreeSurfer
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=== 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.		  * '''Social media''': Find us on [[http://facebook.com/FreeSurferMRI|Facebook]] [[http://facebook.com/FreeSurferMRI|{{attachment:facebook_32.png|Find FreeSurferMRI on Facebook|height="18"}}]] as ''FreeSurferMRI'', follow us on [[http://www.twitter.com/FreeSurferMRI|Twitter]] [[http://www.twitter.com/FreeSurferMRI|{{attachment:twitter_32.png|Follow FreeSurferMRI on Twitter|height="20"}}]] or join our [[https://www.linkedin.com/groups/FreeSurfer-8173404|LinkedIn]] group [[https://www.linkedin.com/groups/FreeSurfer-8173404|{{attachment:linkedin_32.png|!LinkedIn FreeSurfer Group|height="20"}}]].
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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.		  * '''[[DiversityAndInclusion|Diversity and Inclusion]]'''
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=== 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.		 = Our tools =
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=== Sharing What You Learned === === 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:
 * '''[[FreeSurferAnalysisPipelineOverview|Overview:]]''' General description of the functionality in !FreeSurfer
 * '''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 [[Edits|for the basic stream]] and [[LongitudinalEdits|for the longitudinal stream]]
  * [[ReconAllTableStableV6.0|Output files:]] A table of files created and used during a standard !FreeSurfer analysis
 * '''Advanced:'''
  * [[WorkFlows|Work flows:]] How to use the !FreeSurfer stream to accomplish specific tasks
  * [[ToolsAndCommands|Tools and commands:]] GUI and command-line tool documentation
  * [[FileFormats|File formats:]] Description of native !FreeSurfer file formats, as well as external file formats recognized by !FreeSurfer
  * [[CoordinateSystems|Coordinate systems:]] Details on the voxel and RAS coordinate systems used in !FreeSurfer

=== Functional MRI ===
 * '''[[FsFast|FreeSurfer Functional Analysis Stream (FS-FAST):]]''' FS-FAST is a set of tools for performing functional MRI data analyses on the cortical surface.

=== Diffusion MRI ===
* '''[[Tracula|TRActs Constrained by UnderLying Anatomy (TRACULA):]]''' TRACULA is a tool for automated global probabilistic tractography with anatomical priors. It reconstructs a set of major white-matter pathways by incorporating prior information on the structural segmentation labels that each pathway goes through or next to, as a function of position along the length of the pathway. It includes a specialized stream for processing longitudinal diffusion MRI data.

* '''AnatomiCuts''' : An unsupervised hierarchical streamline clustering algorithm based on anatomical similarity. AnatomiCuts is currently in the developing branch (https://github.com/freesurfer/freesurfer/tree/dev/anatomicuts).

* '''DiffusionTool''' : This tool can help generating the configuration file of TRACULA and setting up the parameters to run AnatomiCuts. The DiffusionTool is currently in the developing branch (https://github.com/freesurfer/freesurfer/tree/dev/diffusion_tool).

=== PETsurfer PET Kinetic Modeling and Partial Volume Correction (PVC) ===
 * '''[[PetSurfer|PETSurfer:]]''' PETSurfer is a tool for performing ROI-based, surface-based, and whole-brain analysis of PET data integrated with FreeSurfer anatomical analysis.

=== Multimodal ===
 * '''[[FreeSurferCommandsRegistration|Registration tools:]]''' !FreeSurfer offers a range of tools for both within-subject and across-subject registration.
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 * UserContributions - Scripts and techniques from users. This section is new, but if you have something you'd like to share, please do so.
 * [[http://brainder.org/|Brainder.org]] - Several fantastic Freesurfer contributions described on this site.
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= Publications =
----
'''Our publications are now organized in a [[https://www.zotero.org/freesurfer|Zotero Library]]'''.		 === Quick Links for LCN Members ===
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 * [[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


= Acknowledgements =
----
 * Support for this research was provided in part by the [[http://www.nih.gov/about/almanac/organization/NCRR.htm/|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.

||<tablewidth="270px" tableheight="169px">[[http://www.nih.gov/|{{attachment:NIH.gif|http://www.nih.gov/}}]] ||[[http://www.nih.gov/about/almanac/organization/NCRR.htm|{{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:NINDS.jpg|http://www.ninds.nih.gov/}}]]'''NINDS''' ||[[http://www.na-mic.org/|{{attachment:NAMIC.jpg|http://www.na-mic.org/}}]] '''NAMIC''' ||[[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/}}]] ||		  * LCN Members can navigate to the LcnInternal wiki page with quicklinks to regularly requested resources or wiki pages

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 Athinoula A. Martinos Center for Biomedical Imaging. FreeSurfer is the structural MRI analysis software of choice for the Human Connectome Project.

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:

Functional MRI

Diffusion MRI

* TRActs Constrained by UnderLying Anatomy (TRACULA): TRACULA is a tool for automated global probabilistic tractography with anatomical priors. It reconstructs a set of major white-matter pathways by incorporating prior information on the structural segmentation labels that each pathway goes through or next to, as a function of position along the length of the pathway. It includes a specialized stream for processing longitudinal diffusion MRI data.

* AnatomiCuts : An unsupervised hierarchical streamline clustering algorithm based on anatomical similarity. AnatomiCuts is currently in the developing branch (https://github.com/freesurfer/freesurfer/tree/dev/anatomicuts).

* DiffusionTool : This tool can help generating the configuration file of TRACULA and setting up the parameters to run AnatomiCuts. The DiffusionTool is currently in the developing branch (https://github.com/freesurfer/freesurfer/tree/dev/diffusion_tool).

PETsurfer PET Kinetic Modeling and Partial Volume Correction (PVC)

  • PETSurfer: PETSurfer is a tool for performing ROI-based, surface-based, and whole-brain analysis of PET data integrated with FreeSurfer anatomical analysis.

Multimodal

  • Registration tools: FreeSurfer offers a range of tools for both within-subject and across-subject registration.

  • LCN Members can navigate to the LcnInternal wiki page with quicklinks to regularly requested resources or wiki pages

FreeSurferWiki (last edited 2023-06-14 23:16:55 by buildqa)