top

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


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

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 Schedule

FreeSurfer/FS-FAST Course, May 19 and 20, 2011

MGH, Charlestown Navy Yard,

Thursday, May 19th - Introduction / Single Subject / Troubleshooting

Time

Title

Type

Lecturer

2:00 - 2:30

Introduction to Freesurfer

talk

Doug Greve

2:30 - 3:30

Analyzing the Individual Subject

talk

Doug Greve

3:30 - 3:45

Failure Modes

talk

Allison Stevens

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, May 20th - 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 - 10:45

Group Analysis / GLM / Multiple Comparisons

talk

Martin Reuter

10:45 - 11:15

QDEC demonstration

demo

Doug Greve

11:15 - 11:30

break

11:30 - 12:30

Group Analysis / Multiple Comparisons - mri_glmfit

tutorial

staff

12:30 - 1:15

Group Analysis - qdec

tutorial

staff

1:15 - 2:15

lunch

2:15 - 3:30

Basics of fMRI Analysis

talk

Doug Greve

3:30 - 3:45

break

3:45 - 5:00

Functional Analysis with FS-FAST

talk

Doug Greve

5:00 - 6:00

FsFastTutorialV5.1

tutorial

staff

Additional