Differences between revisions 312 and 322 (spanning 10 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 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.

-  ⇤ ← Revision 312 as of 2016-05-26 01:33:00 → 
  Size: 4574
  Editor: AnastasiaYendiki
  Comment:
+   ← Revision 322 as of 2016-05-26 11:11:02 → ⇥
  Size: 5370
  Editor: ZekeKaufman
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 7:
-!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.]]
 Line 9:
- * '''[[FreeSurferSoftwareLicense|License:]]''' The license agreement that allows you to use !FreeSurfer
+ * '''[[FreeSurferSoftwareLicense|License:]]''' The open source license agreement that allows you to use !FreeSurfer
 Line 13:
- * '''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]]
 Line 29:
- * '''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}}]].
 Line 43:
- * [[FreeSurferAnalysisPipelineOverview|Overview]]
 * Recommended structural MRI acquisition protocols:
+ * '''[[FreeSurferAnalysisPipelineOverview|Overview:]]''' General description of the functionality in !FreeSurfer
 * '''Recommended acquisition protocols:'''
 Line 47:
+ * '''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]]
  * [[ReconAllTableStableV5.3|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
-Line 48:
+Line 59:
-=== 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.
+=== 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.
-Line 52:
+Line 62:
-=== 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.
+=== Diffusion MRI ===
 * '''[[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.
-Line 58:
+Line 65:
-=== 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.
+=== Multimodal ===
 * '''[[FreeSurferCommandsRegistration|Registration tools:]]''' !FreeSurfer offers a range of tools for both within-subject and across-subject registration.