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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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!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 and downloads:]]''' 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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 * '''[[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

 * '''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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 * '''[[UserContributions | User contributions:]]''' Scripts and techniques from users of !FreeSurfer.  * '''[[FsStats | Stats:]]''' Stats on !FreeSurfer usage, citations, and development

 * '''[[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}}]].
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= Software =
----
 * [[MiscellaneousDownloads|Miscellaneous downloads]]
 * [[InternalFreeSurferDistributions|Information for internal (Martinos Center) users]]
 * [[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]]		  * '''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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= Documentation =
----
=== Overview of FreeSurfer ===
 * FreeSurferAnalysisPipelineOverview - Overview of the !FreeSurfer analysis pipeline.
 * 		 * '''[[DiversityAndInclusion|Diversity and Inclusion]]'''
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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 ===
 * 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.		 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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=== 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 2023-06-14 23:16:55 by buildqa)