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!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 [[http://martinos.org/lcn/|Laboratory for Computational Neuroimaging]] at the [[http://www.nmr.mgh.harvard.edu|Martinos Center for Biomedical Imaging.]] !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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 * '''[[ReleaseNotes|Release notes:]]''' New features and changes in each version of !FreeSurfer - '''current stable release is v5.3.0'''  * '''[[ReleaseNotes|Release notes and downloads:]]''' New features and changes in each version of !FreeSurfer - '''current stable release is v7.4.1'''
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 * '''Documentation:''' [[QuickInstall|Getting started,]] [[Tutorials|step-by-step tutorials,]] [[UserContributions/FAQ|FAQ,]] [[FsTutorial/Glossary|Glossary]]  * '''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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 * '''[[FreeSurferMethodsCitation|Citing FreeSurfer:]]''' Short description and citations for core !FreeSurfer methods   * '''[[FreeSurferMethodsCitation|Citing FreeSurfer:]]''' Short description and citations for core !FreeSurfer methods
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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. '''We are currently accepting registrations for the 2026 Virtual Course! [[VirtualCourse|See this page for more details]]'''
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 * '''[[UserContributions | User contributions:]]''' Scripts and techniques from users of !FreeSurfer  * '''[[FsStats|Stats:]]''' Stats on !FreeSurfer usage, citations, and development
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 * '''[[ThirdPartySoftware | Other software:]]''' Third-party software packages that are interoperable or related to !FreeSurfer  * '''[[UserContributions|User contributions:]]''' Scripts and techniques from users of !FreeSurfer

 * '''[[ThirdPartySoftware|Other software:]]''' Third-party software packages that are interoperable or related to !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}}]].  * '''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"}}]].

 * '''[[DiversityAndInclusion|Diversity and Inclusion]]'''
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=== Structural MRI ===
!FreeSurfer provides a full processing stream for structural MRI data, including:
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=== Structural MRI ===

!FreeSurfer provides a full processing stream for structural MRI data, including:
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  * [[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]]		   * [[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]]
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  * [[LongitudinalProcessing|The longitudinal FreeSurfer stream]] 
  * [[LongitudinalStatistics | Longitudinal linear mixed effects statistics]]		   * [[LongitudinalProcessing|The longitudinal FreeSurfer stream]]
  * [[LongitudinalStatistics|Longitudinal linear mixed effects statistics]]
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  * [[ReconAllTableStableV5.3|Output files:]] A table of files created and used during a standard !FreeSurfer analysis   * [[ReconAllTableStableV6.0|Output files:]] A table of files created and used during a standard !FreeSurfer analysis
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 * '''[[FsFast|FreeSurfer Functional Analysis Stream (FS-FAST):]]''' FS-FAST is a set of tools for performing functional MRI data analyses on the cortical surface.   * '''[[FsFast|FreeSurfer Functional Analysis Stream (FS-FAST):]]''' FS-FAST is a set of tools for performing functional MRI data analyses on the cortical surface.
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 * '''[[Tracula|TRActs Constrained by UnderLying Anatomy (TRACULA):]]''' TRACULA is a tool for automated 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, at every point long the pathway's trajectory. It includes a specialized stream for processing longitudinal diffusion MRI data. * '''[[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.
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=== Quick Links for LCN Members ===
 * 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 2026-04-15 10:15:24 by LiamrSennott)