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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:

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

FreeSurfer Course, July 8th and 9th, 2010

Washington University, St. Louis, Missouri

Thursday, July 8th - Introduction / Single Subject / Group Analysis/ CVS / DTI / Troubleshooting

Time

Title

Type

Lecturer

9:00 - 9:30

Introduction to Freesurfer

talk

Lilla Zollei

9:30 - 10:15

Analyzing the Individual Subject - Part I

talk

Allison Stevens

10:15 - 11:00

Group Analysis / GLM / Multiple Comparisons

talk

Lilla Zollei

11:00 - 11:15

break

11:15 - 12:15

Introduction to Surface-based Registration, Combined Volume and Surface Registration

talk

Lilla Zollei

12:15 - 1:00

Lunch

--

--

1:00 - 1:45

Introduction to Diffusion Processing/Tractography

talk

Lilla Zollei

1:45 - 2:15

Analyzing the Individual Subject - Part II

talk

Allison Stevens

2:15 - 2:45

Data Troubleshooting

talk

Allison Stevens

2:45 - 3:00

break - move to computer room (Becker 601 A/B) for tutorials and demo

3:00 - 3:30

Tkmedit/Tksurfer/Troubleshooting Demos

demo

Allison Stevens

3:30 - 4:15

Interaction with Individual Subject Data Tutorial

tutorial

staff

4:15 - 5:15

Troubleshooting Tutorial

tutorial

staff

Friday, July 9th - Longitudinal / Multi-Modal / ROI / Q&A

Time

Title

Type

Lecturer

8:30 - 9:15

Longitudinal FreeSurfer see also: LongitudinalProcessing

talk

Martin Reuter

9:15 - 10:30

ROI Analysis

talk

Allison Stevens

10:30 - 11:00

Multi-Modal Integration

talk

Lilla Zollei

11:00 - 11:30

break - move to computer room (Becker 601 A/B) for tutorials and demo

11:30 - 11:45

QDEC demonstration

demo

Nick Schmansky

11:45 - 12:45

Lunch

--

--

12:45 - 1:30

Group Analysis / Multiple Comparisons - mri_glmfit Tutorial

tutorial

staff

1:30 - 2:15

Group Analysis - qdec Tutorial

tutorial

staff

2:15 - 3:15

Multi-Modal Integration Tutorial

tutorial

staff

3:15 - 3:30

break

3:30 - 4:00

ROI Analysis Tutorial

tutorial

staff

4:00 -

Question and Answer Session

talk

staff

-

optional - FreeSurfer Installation on Personal Laptops

one-on-one

staff

-

optional - Start Processing Your Own Data

one-on-one

staff

Additional