[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/QdecGroupAnalysis Session 1] - Learn how to conduct a group analysis, and to visualize and inspect the results.

  • [wiki:FsTutorial/FslFeatFreeSurfer Session 2] - Applying FreeSurfer tools to FSL fMRI Analysis (FEAT)

• [wiki:FsTutorial/GroupAnalysis Extra] - Group Analysis tutorial using mri_glmfit from the command line, prior to the release of Qdec.

• {wiki:FsTutorial/Visualization Extra] - Visualization and inspection of group analysis results using tksurfer, prior to release of Qdec.

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]