Differences between revisions 1 and 70 (spanning 69 versions)

FreeSurfer Tutorial

Overview

The FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). This tutorial should familiarize you with FreeSurfer's volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. The tutorial also describes some of FreeSurfer's tools for registering volumetric datasets, performing group analysis on morphology data, and integrating FSL Feat output with FreeSurfer (overlaying color coded parametric maps onto the cortical surface and visualizing plotted results). After completing the tutorial, you should be able to:

perform surface reconstructions;
generate subcortical segmentations;
fix errors encountered during the volume or surface processing;
overlay functional data onto surfaces;
perform group analysis of structural (e.g. thickness) and functional data.

Course Outline

In the following sessions, you will be shown a variety of command strings. Only those that appear between lines should be copy-and-pasted into the terminal for this tutorial. Those commands appear like this:

command arg1 arg2

Additional

Home page: http://surfer.nmr.mgh.harvard.edu
Mailing list: send mail to majordomo@surfer.nmr.mgh.harvard.edu with the following command in the body of your email message: subscribe freesurfer
Getting the tutorial data
Listing of all exercises
FreeSurfer tools
Glossary
References
PDF and HTML snapshot
4pp PDFs: intro4pp.pdf, recon4pp.pdf, group4pp.pdf feat4pp.pdf
Acknowledgements

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+[[FreeSurferWiki|top]]

##= FreeSurfer Slides =
## 1. [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.intro.ppt|Introduction to Freesurfer - Bruce Fischl]]
## 1. [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.recon.ppt|Anatomical Analysis with Freesurfer - Doug Greve]]
## 1. [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ppt|Surface-based Group Analysis - Doug Greve]]
## 1. [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.feat.ppt|Applying FreeSurfer Tools to FSL fMRI Analysis - Doug Greve]]

## 1. [[attachment:freesurfer.intro.2008.ppt|Introduction to Freesurfer - Bruce Fischl]]
## 1. [[attachment:freesurfer.recon.ppt|Anatomical Analysis with Freesurfer - Doug Greve]]
## 1. [[attachment:freesurfer.groupanalysis.ppt|Surface-based Group Analysis - Doug Greve]]
## 1. [[attachment:freesurfer.feat.ppt|Applying FreeSurfer Tools to FSL fMRI Analysis - Doug Greve]]
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+== Overview ==
The !FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). This tutorial should familiarize you with !FreeSurfer's volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. The tutorial also describes some of !FreeSurfer's tools for registering volumetric datasets, performing group analysis on morphology data, and integrating FSL Feat output with !FreeSurfer (overlaying color coded parametric maps onto the cortical surface and visualizing plotted results). After completing the tutorial, you should be able to:
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- [wiki:Self:FsTutorial/Overview 1. Tutorial Overview] [[BR]]
 [wiki:Self:FsTutorial/InstallAndSetup 2. Installation and Setup] [[BR]]
 [wiki:Self:FsTutorial/MorphAndRecon 3. Morphometry and Reconstruction] [[BR]]
 [wiki:Self:FsTutorial/GroupAnalysis 4. Group Analysis] [[BR]]
 [wiki:Self:FsTutorial/Visualization 5. Visualization and Inspection of Group Analysis Results] [[BR]]
 [wiki:Self:FsTutorial/FSLFeatFreeSurfer 6. Applying FreeSurfer Tools to FSL fMRI Analysis (FEAT)] [[BR]]
+ * perform surface reconstructions;
 * generate subcortical segmentations;
 * fix errors encountered during the volume or surface processing;
 * overlay functional data onto surfaces;
 * perform group analysis of structural (e.g. thickness) and functional data.
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+Line 24:
- [wiki:Self:FsTutorial/Exercises Exercise Overview]
+== Course Outline ==
In the following sessions, you will be shown a variety of command strings.  Only those that appear between lines should be copy-and-pasted into the terminal for this tutorial.  Those commands appear like this:
----
{{{
command arg1 arg2
}}}
----
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- [wiki:Self:FsTutorial/FileFormats File Formats]
+<<Include(CourseSchedule)>>
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- [wiki:Self:FsTutorial/Tools FreeSurfer Tools]
+## * '''Session 1'''
##  * [[FsTutorial/OutputData|Session 1a]] - Use the volume and surface viewing tools to observe correctly processed output data.
##  * [[FsTutorial/TroubleshootingData|Session 1b]] - See examples of problematic output data, and learn how to fix the problems.
##  * [[FsTutorial/MorphAndRecon|Extra]] - Long-form tutorial covering Freesurfer's morphometry and reconstruction tool [[recon-all]].
##  * [[ReconAllDevTable|Extra]] - recon-all process-flow reference table.
## * '''Session 2'''
##  * [[FsTutorial/QdecGroupAnalysis|Session 2a]] - Learn how to conduct a group analysis using Qdec, and to visualize and inspect the results.
##  * [[FsTutorial/FslFeatFreeSurfer|Session 2b]] - Applying !FreeSurfer tools to FSL fMRI Analysis (FEAT)
##  * [[FsTutorial/GroupAnalysis|Extra]] - Group Analysis tutorial using mri_glmfit from the command line, prior to the release of Qdec.
##  * [[FsTutorial/Visualization|Extra]] - Visualization and inspection of group analysis results using tksurfer, prior to release of Qdec.
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- [wiki:Self:FsTutorial/Glossary Glossary]
+== Additional ==
 * Home page: http://surfer.nmr.mgh.harvard.edu
 * Mailing list: send mail to majordomo@surfer.nmr.mgh.harvard.edu with the following command in the body of your email message: subscribe freesurfer
 * [[FsTutorial/Data|Getting the tutorial data]]
 * [[FsTutorial/Exercises|Listing of all exercises]]
 * [[FsTutorial/Tools|FreeSurfer tools]]
 * [[FsTutorial/Glossary|Glossary]]
 * [[Articles|References]]
 * [[FsTutorial/SnapShot|PDF and HTML snapshot]]
 * 4pp PDFs: [[attachment:intro4pp.pdf]], [[attachment:recon4pp.pdf]], [[attachment:group4pp.pdf]] [[attachment:feat4pp.pdf]] 
 * [[FsTutorial/Acknowledgements|Acknowledgements]]