|
Size: 2783
Comment:
|
Size: 2445
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 18: | Line 18: |
| * [wiki:Self:FsTutorial/MorphAndRecon Extra] - Long-form tutorial covering Freesurfer's morphometry and reconstruction tool recon-all. | * [wiki:Self:FsTutorial/MorphAndRecon Extra] - Long-form tutorial covering Freesurfer's morphometry and reconstruction tool [wiki:Self:recon-all recon-all]. |
| Line 21: | Line 21: |
| * [wiki:Self:FsTutorial/GroupAnalysis Session 1] - Learn how to conduct a group analysis, including visualization and inspection of results. * [wiki:Self:FsTutorial/FslFeatFreeSurfer Session 2] - Applying !FreeSurfer tools to FSL fMRI Analysis (FEAT) ## old outline: ## 1. [wiki:Self:FsTutorial/Data Tutorial Data] [[BR]] ## 1. [wiki:Self:FsTutorial/Overview Tutorial Overview] [[BR]] ## 1. [wiki:Self:FsTutorial/MorphAndRecon Morphometry and Reconstruction] [[BR]] ## 1. [wiki:Self:FsTutorial/GroupAnalysis Group Analysis] [[BR]] ## 1. [wiki:Self:FsTutorial/Visualization Visualization and Inspection of Group Analysis Results] [[BR]] ## 1. [wiki:Self:FsTutorial/FslFeatFreeSurfer Applying FreeSurfer Tools to FSL fMRI Analysis (FEAT)] [[BR]] ## [wiki:Self:FsTutorial/SpmFreeSurfer 7. *** Under Construction *** Applying FreeSurfer Tools to SPM fMRI Analysis] [[BR]] |
* [wiki:Self:FsTutorial/GroupAnalysis Session 1a] - Learn how to conduct a group analysis. * [wiki:Self:FsTutorial/GroupAnalysis Session 1b] - Perform visualization and inspection of group analysis results. * [wiki:Self:FsTutorial/FslFeatFreeSurfer Session 2] - Applying !FreeSurfer tools to FSL fMRI Analysis (FEAT) |
| Line 34: | Line 26: |
| *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 |
|
| Line 37: | Line 31: |
| *[wiki:Self:FsTutorial/SnapShot PDF and HTML snapshot] | |
| Line 39: | Line 34: |
| *[wiki:Self:FsTutorial/SnapShot PDF and HTML snapshot] |
[wiki:FreeSurferWiki top]
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
Day 1
[wiki:FsTutorial/OutputData Session 1] - Use the volume and surface viewing tools to observe correctly processed output data.
[wiki:FsTutorial/TroubleshootingData Session 2] - See examples of problematic output data, and learn how to fix the problems.
[wiki:FsTutorial/MorphAndRecon Extra] - Long-form tutorial covering Freesurfer's morphometry and reconstruction tool [wiki:recon-all recon-all].
[wiki:ReconAllDevTable Extra] - recon-all process-flow reference table.
Day 2
[wiki:FsTutorial/GroupAnalysis Session 1a] - Learn how to conduct a group analysis.
[wiki:FsTutorial/GroupAnalysis Session 1b] - Perform visualization and inspection of group analysis results.
[wiki:FsTutorial/FslFeatFreeSurfer Session 2] - Applying FreeSurfer tools to FSL fMRI Analysis (FEAT)
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
[wiki:FsTutorial/Data Getting the tutorial data]
[wiki:FsTutorial/Exercises Listing of all exercises]
[wiki:FsTutorial/Tools FreeSurfer tools]
[wiki:FsTutorial/SnapShot PDF and HTML snapshot]
[wiki:FsTutorial/Glossary Glossary]
[wiki:FsTutorial/Acknowledgements Acknowledgements]