FreeSurfer Tutorial and Workshop
Cape Town, South Africa
11-12 February 2010
Centre for High Performance Computing (CHPC), map
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
Course Schedule
Thursday, February 11th - Introduction / Single Subject / Group Analysis
Time |
Title |
Type |
Lecturer |
8:00 - 8:30 |
optional - Unix Tutorial for FreeSurfer Users 1. Surrey, 2. O'Reilly |
tutorial |
Allison Stevens |
8:45 - 9:00 |
optional - Intro to FreeSurfer Jargon |
talk |
Allison Stevens |
8:30 - 9:00 |
Course Registration |
sign-in |
|
9:00 - 9:30 |
talk |
David Salat |
|
9:30 - 10:30 |
talk |
Doug Greve |
|
10:30 - 10:45 |
break |
|
|
10:45 - 11:15 |
Tkmedit/Tksurfer demonstration |
demo |
Doug Greve |
11:15 - 11:45 |
tutorial |
staff |
|
11:45 - 12:15 |
talk |
Andre van der Kouwe |
|
12:15 - 12:30 |
break |
|
|
12:30 - 13:00 |
Working lunch Optional talk - Combined Gray Matter/White Matter Analysis of the Aging Brain |
talk |
David Salat |
13:00 - 13:30 |
lunch |
|
|
13:30 - 14:15 |
talk |
David Salat |
|
14:15 - 14:45 |
talk |
Doug Greve |
|
14:45 - 15:00 |
break |
|
|
15:00 - 15:45 |
talk |
Doug Greve |
|
15:45 - 16:00 |
QDEC demonstration |
demo |
Doug Greve |
16:00 - 17:00 |
tutorial |
staff |
|
17:00 - 17:45 |
tutorial |
staff |
Friday, February 12th - ROIs / Troubleshooting / Multi-Modal / Q&A
Time |
Title |
Type |
Lecturer |
9:00 - 9:30 |
talk |
David Salat |
|
9:30 - 10:30 |
talk |
Doug Greve |
|
10:30 - 11:00 |
tutorial |
staff |
|
11:00 - 11:30 |
break |
|
|
11:30 - 12:00 |
talk |
Allison Stevens |
|
12:00 - 12:30 |
How to QA a Recon, Troubleshooting Tutorial demonstration |
demo |
Allison |
12:30 - 13:15 |
lunch |
|
|
13:15 - 14:15 |
tutorial |
staff |
|
14:15 - 15:30 |
talk |
Doug Greve |
|
15:30 - 15:45 |
break |
|
|
15:45 - 16:45 |
tutorial |
staff |
|
16:45 - 17:30 |
talk |
Doug Greve |