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FreeSurfer Tutorial and Workshop

Overview

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

Note: During the tutorial sessions, you will be shown a variety of command strings on the tutorial wiki pages. 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

Laptop damage policy: If liquid is spilled on a provided laptop, then you are liable for payment of the repair costs!

Course Schedule

FreeSurfer/FS-FAST Course, June 4 and 5, 2009

MGH, Charlestown Navy Yard, Conference Room A

Multi Modal Short Course Schedule

Thursday, June 4th - Introduction / Single Subject / Troubleshooting

Time	Title	Type	Lecturer
2:00 - 2:30	Introduction to Freesurfer	talk	Bruce Fischl
2:30 - 3:30	Analyzing the Individual Subject	talk	Doug Greve
3:30 - 3:45	Failure Modes	talk	Bruce Fischl
3:45 - 4:00	Tkmedit/Tksurfer demonstration	demo	Doug Greve
4:00 - 4:15	break
4:15 - 5:00	Inspection of Freesurfer Output	tutorial	staff
5:00 - 6:00	Troubleshooting, Troubleshooting demonstration	tutorial	staff, Allison Stevens

Friday, June 5th - Surface-based Smoothing and Registration / Group Analysis / FS-FAST

Time	Title	Type	Lecturer
9:00 - 9:30	Surface-based Smoothing/Surface-based Registration	talk	Doug Greve
9:30 - 10:30	Group Analysis / GLM / Multiple Comparisons	talk	Doug Greve
10:30 - 11:00	QDEC demonstration	demo	Nick Schmansky
11:00 - 11:15	break
11:15 - 12:15	Group Analysis / Multiple Comparisons - mri_glmfit	tutorial	staff
12:15 - 1:00	Group Analysis - qdec	tutorial	staff
1:00 - 2:00	lunch
2:00 - 3:00	Functional Analysis with FS-FAST	talk	Doug Greve
3:00 - 3:15	break
3:15 - 6:00	FsFastTutorial	tutorial	staff

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 (necessary only if you are not taking a formal course where data is provided)

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-The !FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). The talks and tutorials should familiarize you with !FreeSurfer's volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. The tutorials also describes some of !FreeSurfer's tools for registering volumetric datasets, performing group analysis on morphology data, and integrating multi-modal output with !FreeSurfer (overlaying color coded parametric maps onto the cortical surface and visualizing plotted results). After completing the tutorials, you should be able to:
+The !FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). The talks and tutorials should familiarize you with !FreeSurfer's volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. The tutorials also describe some of !FreeSurfer's tools for registering volumetric datasets, performing group analysis on morphology data, and integrating multi-modal output with !FreeSurfer (overlaying color coded parametric maps onto the cortical surface and visualizing plotted results). After completing the tutorials, you should be able to:
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-'''Laptop damage policy: If liquid is spilled in a provided laptop, then you are liable for payment of the repair costs!'''
+'''Laptop damage policy: If liquid is spilled on a provided laptop, then you are liable for payment of the repair costs!'''
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+## == Question / Suggestion Box ==
## During the course, if you have questions or suggestions, [[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/questions.cgi|please follow this link]] to submit them (anonymously, or not).  We will process them during the course and give feedback at the end. 

## == Course Evaluation ==
## Please fill out our course evaluation [[http://spreadsheets.google.com/viewform?formkey=cHJlMFNVZDFNeDltbUE0RkNhaTBuWFE6MA..|here]]. You can fill it in throughout the course.
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+##<<Include(FsTutorial/April2009CourseSchedule)>>
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