Differences between revisions 323 and 328 (spanning 5 versions)

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:
- Suggested morphometry protocols for optimal FreeSurfer reconstruction
- Alternative morphometry protocols, from ADNI
Longitudinal studies:
- The longitudinal FreeSurfer stream
- Longitudinal linear mixed effects statistics
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 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.

PET Partial Volume Correction (PVC) and Kinetic Modeling

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.

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- * '''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}}]].
+ * '''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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-  * [[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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- * '''[[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.

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