|
Size: 720
Comment:
|
Size: 2934
Comment: added slides
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| [wiki:Self:FreeSurferWiki top] |
|
| Line 3: | Line 5: |
| [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]] |
== 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: |
| Line 10: | Line 8: |
| [wiki:Self:FsTutorial/Exercises Exercise Overview] | * 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. |
| Line 12: | Line 14: |
| [wiki:Self:FsTutorial/FileFormats File Formats] | Accompanying slides: * [http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsintro.pdf Introduction to Freesurfer] * [http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsrecon.pdf Cortical Reconstruction with Freesurfer] * [http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsgroupana.pdf Surface-based Group Analysis] * [http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fs+fsl.2006.pdf Applying FreeSurfer Tools to FSL fMRI Analysis] |
| Line 14: | Line 20: |
| [wiki:Self:FsTutorial/Tools FreeSurfer Tools] | == Course Outline == * '''Day 1''' * [wiki:Self:FsTutorial/OutputData Session 1] - Use the volume and surface viewing tools to observe correctly processed output data. * [wiki:Self:FsTutorial/TroubleshootingData Session 2] - See examples of problematic output data, and learn how to fix the problems. * [wiki:Self:FsTutorial/MorphAndRecon Extra] - Long-form tutorial covering Freesurfer's morphometry and reconstruction tool [wiki:Self:recon-all recon-all]. * [wiki:Self:ReconAllDevTable Extra] - recon-all process-flow reference table. * '''Day 2''' * [wiki:Self:FsTutorial/GroupAnalysis Session 1a] - Learn how to conduct a group analysis. * [wiki:Self:FsTutorial/Visualization 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 16: | Line 31: |
| [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 *[wiki:Self:FsTutorial/Data Getting the tutorial data] *[wiki:Self:FsTutorial/Exercises Listing of all exercises] *[wiki:Self:FsTutorial/Tools FreeSurfer tools] *[wiki:Self:FsTutorial/Glossary Glossary] *[wiki:Self:Articles References] *[wiki:Self:FsTutorial/SnapShot PDF and HTML snapshot] *[wiki:Self:FsTutorial/Acknowledgements Acknowledgements] |
[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.
Accompanying slides:
[http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsintro.pdf Introduction to Freesurfer]
[http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsrecon.pdf Cortical Reconstruction with Freesurfer]
[http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsgroupana.pdf Surface-based Group Analysis]
[http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fs+fsl.2006.pdf Applying FreeSurfer Tools to FSL fMRI Analysis]
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/Visualization 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/Glossary Glossary]
[wiki:Articles References]
[wiki:FsTutorial/SnapShot PDF and HTML snapshot]
[wiki:FsTutorial/Acknowledgements Acknowledgements]