top

FreeSurfer Tutorial and Workshop

Course Policies

Laptop damage policy

Getting the tutorial data

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

Please DO NOT try to download the tutorial data during the course! We have copies of this data stored on servers located in the course room. Attempting to download this data from the public link (this link) during the course presents excessive and unnecessary load on our network, and likely will fail due to this load. Please contact a staff member for help in getting this data.

About the Course

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 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).

Note: During the tutorial sessions, you will be shown a variety of command strings on the tutorial wiki pages. Only those that appear in a box should be copy-and-pasted into the terminal. They will look like this:

command arg1 arg2

Tip for Mac users: The tutorials often refer to keyboard shortcuts (such as Alt+v) which do not work on a Mac. For a list of equivalent keyboard commands on a Mac, please refer to MacCommands.

Online Question Forum

Videos of Lectures

Course Evaluation

Throughout the course, you may post questions here (anonymously or not).

You can find videos of the lectures here.

The course evaluation will be posted here on the last day of the course.

Course Schedule

FreeSurfer Course, May 5-7, 2014

8:00 - 9:30am Registration Desk Open

Monday, May 5th - Introduction / Single Subject Analysis /Troubleshooting

Time

Title

Type

Lecturer

8:30 - 9:00

optional - Unix Tutorial for FreeSurfer Users

tutorial

Ender Konukoglu

9:00 - 9:15

optional - Intro to FreeSurfer Jargon

talk

Ender Konukoglu

9:15 - 9:30

break

9:30 - 10:00

Introduction to Freesurfer

talk

Bruce Fischl

10:00 - 11:00

Analyzing the Individual Subject

talk

Bruce Fischl

11:00 - 11:20

break

11:20 - 12:00

optional - A Non-physicist's Intro to MR SpinBench

talk

Dylan Tisdall

12:00 - 1:00

Lunch (Suggestions for where to eat)

--

--

1:00 - 1:20

Freeview demonstration

demo

Louis Vinke

1:20 - 2:20

Interaction with Individual Subject Data Tutorial

tutorial

staff

2:20 - 2:50

FreeSurfer Troubleshooting

talk

Bruce Fischl

2:50 - 3:10

break

3:10 - 3:50

Quality Checking a Recon

demo

Allison Stevens

3:50 - 4:50

Troubleshooting Tutorial

tutorial

staff

4:50 - 5:00

Question and Answer Session (Answers to online questions here)

talk

staff

Boston Beer Works location information here and here.
Meet us in front of Building 149 to catch the 6:15pm shuttle bus (it leaves on time!).
If you miss us, we are taking the MGH/Navy Yard shuttle to North Station. From there, cross the street to get to Canal Street. Boston Beer Works will be down that street, on your right. (If you miss the 6:15 bus, the next few buses depart at 6:30pm, 6:45pm, 7pm, 7:15pm, and 7:45pm).

Tuesday, May 6th - Group Analysis / ROI Analysis / Multimodal

Time

Title

Type

Lecturer

9:00 - 9:40

Surface-based Analysis: Intersubject Smoothing & Registration

talk

Doug Greve

9:40 - 10:20

Group Analysis

talk

Ender Konukoglu

10:20 - 10:40

break

10:40 - 11:20

Group Analysis Tutorial

tutorial

staff

11:20 - 11:40

Multiple Comparisons

talk

Ender Konukoglu

11:40 - 12:00

QDEC demonstration

demo

Doug Greve

12:00 - 1:00

Lunch

--

--

1:00 - 1:20

Multiple Comparisons Tutorial

tutorial

staff

1:20 - 2:00

QDEC Tutorial

tutorial

staff

2:00 - 2:30

ROI Analysis

talk

Martin Reuter

2:30 - 2:50

break

2:50 - 3:20

ROI Analysis Tutorial

tutorial

staff

3:20 - 3:50

Longitudinal FreeSurfer see also: LongitudinalProcessing

talk

Martin Reuter

3:50 - 4:30

Longitudinal Tutorial

tutorial

staff

4:30 - 5:30

Basics of fMRI Analysis

talk

Jon Polimeni

Wednesday, May 7th - fMRI / Multimodal / Longitudinal / Future Directions / Q&A

Time

Title

Type

Lecturer

9:00 - 9:45

FSFAST

talk

Doug Greve

9:45 - 10:00

break

10:00 - 10:40

FSFAST

talk

Doug Greve

10:40 - 11:40

FSFAST Tutorial

tutorial

staff

11:40 - 12:40

Lunch

--

--

12:40 - 1:40

Multi-Modal Integration

talk

Lilla Zollei

1:40 - 2:55

Multi-Modal Integration Tutorial

tutorial

staff

2:55 - 3:15

break & Evaluation

3:15 - 3:45

Future Directions

talk

TBD

3:45 - 4:15

optional technical talk - MRI Acquisition Methods for Morphometry

talk

Andre van der Kouwe

4:15 - 4:45

optional technical talk - Motion-compensated neuroanatomical imaging

talk

Dylan Tisdall

4:45 - 5:15

optional technical talk - Registration Methods

talk

Lilla Zollei

5:15 - 5:30

Question and Answer Session (Answers to online questions here), FsQuiz

talk

staff

Additional Useful Information

During the Course

After the Course