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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


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 Course, April 4 - 6, 2011

MGH, Charlestown Navy Yard, Building 149, Conference Room A

Monday, April 4th - Introduction / Single Subject / MRI / Longitudinal/ Troubleshooting

Time

Title

Type

Lecturer

8:00 - 8:30

optional - Unix Tutorial for FreeSurfer Users online practice

tutorial

Allison Stevens

8:30 - 9:00

optional - Intro to FreeSurfer Jargon

talk

Allison Stevens

8:30 - 9:00

Course Registration

sign-in

staff

9:00 - 9:30

Introduction to Freesurfer

talk

Bruce Fischl

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

Failure Modes

talk

Bruce Fischl

12:15 - 1:15

Lunch (Suggestions)

--

--

12:45 - 1:15

Optional Lunch Talk- A Non-physicist's Intro to MR SpinBench

talk

Dylan Tisdall

1:15 - 2:15

Troubleshooting Demonstration, Troubleshooting Tutorial

tutorial

staff, Allison

2:15 - 2:45

Surface-based Smoothing/Surface-based Registration

talk

Doug Greve

2:45 - 3:15

FreeSurfer Applications

talk

David Salat

3:15 - 3:30

break

3:30 - 4:15

Registration Methods

talk

Lilla Zollei

4:15 - 4:45

Longitudinal FreeSurfer see also: LongitudinalProcessing

talk

Martin Reuter

4:45 - 5:30

Longitudinal Tutorial

tutorial

staff

5:30 -

optional - FreeSurfer Installation on Personal Laptops

one-on-one

staff

5:30 -

optional - Start Processing Your Own Data

one-on-one

staff

Boston Beer Works location information here and here.
Meet us at 6:25pm at the front of Building 149 (the entrance on the opposite side of the building from where the Course is held).
If you miss us, we are taking the 6:30pm MGH/Navy Yard shuttle to North Station (the next one departs at 6:45pm). From there, you cross the street and go down Canal Street. Boston Beer Works will be on your right.

Tuesday, April 5th - Group Analysis/ ROIs / Registration / Diffusion

Time

Title

Type

Lecturer

9:00 - 10:00

Group Analysis / GLM / Multiple Comparisons

talk

Mert Sabuncu

10:00 - 10:30

QDEC demonstration

demo

Nick Schmansky

10:30 - 10:45

break

10:45 - 11:45

Group Analysis / Multiple Comparisons - mri_glmfit Tutorial

tutorial

staff

10:45 - 11:45

Group Analysis - qdec Tutorial

tutorial

staff

11:45 - 12:45

Lunch

--

--

12:15 - 12:45

Optional Lunch Talk- MRI Acquisition Methods for Morphometry

talk

Andre van der Kouwe

12:45 - 1:45

ROI Analysis

talk

Doug Greve

1:45 - 2:15

ROI Analysis Tutorial

tutorial

staff

2:15 - 3:15

Introduction to Diffusion MRI

talk

Anastasia Yendiki

3:15 - 3:30

break

3:30 - 4:15

Diffusion Processing Tutorial

tutorial

staff

4:15 - 4:45

TRActs Constrained by UnderLying Anatomy (TRACULA)

talk

Anastasia Yendiki

4:45 - 5:30

Tracula Tutorial

tutorial

staff

5:30 - 6:00

optional - Quality Checking a Recon

demo

Allison Stevens

Wednesday, April 6th - Multi-Modal / Future Directions / fMRI / Q&A

9:00 - 10:00

Basics of fMRI Analysis

talk

Doug Greve

10:00 - 10:15

break

10:15 - 11:30

FSFAST

talk

Doug Greve

11:30 - 12:30

FSFAST Tutorial

tutorial

staff

12:30 - 1:30

Lunch

--

--

1:00 - 1:30

Optional Lunch Talk- Motion-compensated neuroanatomical imaging

talk

Dylan Tisdall

1:30 - 2:00

Accuracy, Reliability and Validation

talk

David Salat

2:00 - 2:20

Future Directions: Inferring architectonic boundaries from in-vivo MRI

talk

Bruce Fischl

2:20 - 2:45

break & Evaluation

2:45 - 3:45

Multi-Modal Integration

talk

Doug Greve

3:45 - 4:30

Multi-Modal Integration Tutorial

tutorial

staff

4:30 - 5:00

Question and Answer Session, FsQuiz

talk

staff

Additional