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:

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


Question / Suggestion Box

During the course, if you have questions or suggestions, 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 here. You can fill it in throughout the remainder of the course but you can't save your answers and finish it later so be sure to submit it before you leave. If you started it but cannot finish it until later, enter any random 4 digit number at the top of the survey and hit submit. When you are at home, fill out a new form (skipping questions you already answered) but put that same 4 digit number in at the top so we can tie your answers together.

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

Introduction to Freesurfer

talk

David Salat

9:30 - 10:30

Analyzing the Individual Subject

talk

Doug Greve

10:30 - 10:45

break

10:45 - 11:15

Tkmedit/Tksurfer demonstration

demo

Doug Greve

11:15 - 11:45

Interaction with Individual Subject Data Tutorial

tutorial

staff

11:45 - 12:15

MRI Acquisition Methods for Morphometry

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

FreeSurfer Applications

talk

David Salat

14:15 - 14:45

Surface-based Smoothing/Surface-based Registration

talk

Doug Greve

14:45 - 15:00

break

15:00 - 15:45

Group Analysis / GLM / Multiple Comparisons

talk

Doug Greve

15:45 - 16:00

QDEC demonstration

demo

Doug Greve

16:00 - 17:00

Group Analysis / Multiple Comparisons - mri_glmfit Tutorial

tutorial

staff

17:00 - 17:45

Group Analysis - qdec Tutorial

tutorial

staff

Friday, February 12th - ROIs / Troubleshooting / Multi-Modal / Q&A

Time

Title

Type

Lecturer

9:00 - 9:30

Accuracy, Reliability and Validation

talk

David Salat

9:30 - 10:30

ROI Analysis

talk

Doug Greve

10:30 - 11:00

ROI Analysis Tutorial

tutorial

staff

11:00 - 11:30

break

11:30 - 12:00

Failure Modes

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

Troubleshooting Tutorial

tutorial

staff

14:15 - 15:30

Multi-Modal Integration

talk

Doug Greve

15:30 - 15:45

break

15:45 - 16:45

Multi-Modal Integration Tutorial

tutorial

staff

16:45 - 17:30

Designing Event-related Experiments for fMRI

talk

Doug Greve

FsTutorial/CapeTown2010CourseSchedule (last edited 2010-02-11 11:43:38 by AllisonStevens)