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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 [[http://martinos.org/lcn/|Laboratory for Computational Neuroimaging]] at the [[http://martinos.org/|Athinoula A. Martinos Center for Biomedical Imaging.]] |
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| * '''[[FreeSurferSoftwareLicense|License:]]''' The license agreement that allows you to use !FreeSurfer | * '''[[FreeSurferSoftwareLicense|License:]]''' The open source license agreement that allows you to use !FreeSurfer |
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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]] |
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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]] as ''FreeSurferMRI'' [[http://facebook.com/FreeSurferMRI|{{attachment:facebook_32.png|Find FreeSurferMRI on Facebook|width="25"}}]], follow us on [[http://www.twitter.com/FreeSurferMRI|Twitter]] [[http://www.twitter.com/FreeSurferMRI|{{attachment:twitter_32.png|Follow FreeSurferMRI on Twitter}}]] 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}}]]. |
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| * [[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]] |
* '''[[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]] |
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| * Troubleshooting: | * '''Troubleshooting:''' |
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| * Advanced: | * '''Advanced:''' |
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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 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. |
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| * [[FreeSurferCommandsRegistration|Registration tools:]] !FreeSurfer offers a range of tools for both within-subject and across-subject registration. | * '''[[FreeSurferCommandsRegistration|Registration tools:]]''' !FreeSurfer offers a range of tools for both within-subject and across-subject registration. |
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.
License: The open source 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:
Overview: General description of the functionality in FreeSurfer
Recommended acquisition protocols:
Longitudinal studies:
Troubleshooting:
Manual editing for the basic stream and for the longitudinal stream
Output files: A table of files created and used during a standard FreeSurfer analysis
Advanced:
Work flows: How to use the FreeSurfer stream to accomplish specific tasks
Tools and commands: GUI and command-line tool documentation
File formats: Description of native FreeSurfer file formats, as well as external file formats recognized by FreeSurfer
Coordinate systems: Details on the voxel and RAS coordinate systems used in FreeSurfer
Functional MRI
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
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.
Multimodal
Registration tools: FreeSurfer offers a range of tools for both within-subject and across-subject registration.