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FreeSurfer Tutorial and Workshop

Course Policies

Getting the tutorial data

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 if needed outside of the course.

Wifi

You may connect to any of the following wifi networks in the classroom area (all networks use the same password):

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 commands. 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

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

You can find videos of the lectures here.

Course Schedule

FreeSurfer Course, April 3-6

Our awesome FreeSurfer shirts can be purchased here.

8:00 - 9:30am Registration Desk Open

* Indicates an optional technical talk. These talks have great content. They are related to, but not directly about, the FreeSurfer processing stream.
** Indicates an optional talk that covers basic/beginner material.

Monday, April 3rd - Introduction / Single Subject Analysis / ROI Analysis

Time

Title

Type

Lecturer

8:30 - 9:00

** Intro to Linux for FreeSurfer Users

talk/demo

Zeke Kaufman

9:00 - 9:15

** Intro to FreeSurfer Jargon

talk

Emma Boyd & Lilla Zöllei

9:15 - 9:30

break

9:30 - 10:00

Introduction to Freesurfer

talk

Bruce Fischl

10:00 - 11:10

Analyzing the Individual Subject

talk

Doug Greve

11:10 - 11:30

break

11:30 - 11:45

Freeview demonstration

demo

Andrew Hoopes

11:45 - 12:15

Interaction with Individual Subject Data Tutorial

tutorial

staff

12:15 - 1:15

Lunch (Suggestions for where to eat)

--

--

1:15 - 1:30

Interaction with Individual Subject Data Tutorial

tutorial

staff

1:30 - 2:00

Surface-based Analysis: Intersubject Registration & Smoothing

talk

Lilla Zöllei

2:00 - 2:20

break

2:20 - 3:20

ROI Analysis

talk

Doug Greve

3:20 - 4:00

ROI Analysis Tutorial

tutorial

staff

4:00 - 4:30

** A Non-physicist's Intro to MR (SpinBench)

talk

Robert Frost

4:30 - 5:00

* Running FreeSurfer in the cloud with AWS batch

talk

Paul Wighton

Answers to online questions here

Tuesday, April 4th - Group Analysis / Longitudinal Analysis / Troubleshooting

Time

Title

Type

Lecturer

9:00 - 9:50

Group Analysis

talk

Emily Lindemer

9:50 - 10:30

Group Analysis Tutorial

tutorial

staff

10:30 - 10:50

break

10:50 - 11:10

Multiple Comparisons

talk

Doug Greve

11:10 - 11:30

Multiple Comparisons Tutorial

tutorial

staff

11:30 - 11:50

QDEC demonstration

demo

Doug Greve

11:50 - 12:50

Lunch

--

--

12:50 - 1:30

QDEC Tutorial

tutorial

staff

1:30 - 2:00

FreeSurfer Troubleshooting

talk

Bruce Fischl

2:00 - 3:00

Troubleshooting Tutorial

tutorial

staff

3:00 - 3:20

break

3:20 - 4:20

Quality Checking a Recon

demo

Allison Stevens

4:20 - 5:05

Longitudinal FreeSurfer see also: LongitudinalProcessing

talk

Lilla Zöllei

5:05 - 5:35

Longitudinal Tutorial

tutorial

staff

6:30 - ?

Boston Beer Works

social activity

you!

Answers to online questions here

Boston Beer Works location information here and here.
Meet us in front of Building 149 to catch the 6:30pm 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. (Shuttles depart every 15 minutes up until 7:15pm and every half hour after that).

Wednesday, April 5th - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition

Time

Title

Type

Lecturer

9:00 - 9:30

Multi-Modal Integration, Part 1: Registration

talk

Lilla Zöllei

9:30 - 10:00

Multi-Modal Integration Tutorial, Part 1

tutorial

staff

10:00 - 10:15

** A Non-Physicist's Intro to Diffusion MRI Physics

talk

Robert Frost

10:15 - 10:35

break

10:35 - 11:15

Introduction to Diffusion MRI

talk

Anastasia Yendiki

11:15 - 12:00

Diffusion Processing Tutorial

tutorial

staff

12:00 - 1:00

Lunch

--

--

1:00 - 1:50

TRActs Constrained by UnderLying Anatomy (TRACULA)

talk

Anastasia Yendiki

1:50 - 2:50

Tracula Tutorial

tutorial

staff

2:50 - 3:00

Longitudinal TRACULA

talk

Anastasia Yendiki

3:00 - 3:20

break

3:20 - 4:20

Basics of fMRI Analysis

talk

Jon Polimeni

4:20 - 4:50

* MRI Acquisition Methods

talk

André van der Kouwe

Answers to online questions here

Thursday, April 6th - fMRI Analysis / Multimodal Analysis / Future Directions

Time

Title

Type

Lecturer

9:00 - 9:30

FSFAST, Part 1: Preprocessing

talk

Doug Greve

9:30 - 10:00

FSFAST Tutorial, Part 1

tutorial

staff

10:00 - 10:20

break & Evaluation

10:20 - 11:20

FSFAST, Part 2: GLM Analysis

talk

Doug Greve

11:20 - 12:00

FSFAST Tutorial, Part 2

tutorial

staff

12:00 - 1:00

Lunch

--

--

1:00 - 1:30

Multi-Modal Integration, Part 2: Group Analysis

talk

Doug Greve

1:30 - 2:00

Multi-Modal Integration Tutorial, Part 2

tutorial

staff

2:00 - 2:30

* An Overview of Registration Methods

talk

Lilla Zöllei

2:30 - 3:00

Future Directions

talk

Bruce Fischl

Answers to online questions here

* Indicates an optional technical talk. These talks have great content. They are related to, but not directly about, the FreeSurfer processing stream.
** Indicates an optional talk covering basic/beginner material.

Additional Useful Information

During the Course

After the Course

FsTutorial (last edited 2017-04-02 17:20:36 by ZekeKaufman)