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FreeSurfer Tutorial and Workshop

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 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:

  • perform surface reconstructions;
  • generate subcortical segmentations;
  • fix errors encountered during the volume or surface processing;
  • overlay functional data onto surfaces;
  • perform group analysis of structural (e.g. thickness) and functional data.

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!

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.

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 29 - May 1, 2013
MGH, Charlestown Navy Yard, Building 114, Room D1

Fill out the Course evaluation here!!!

Monday, April 29th - Introduction / Single Subject / Registration / Troubleshooting

Time

Title

Type

Lecturer

8:00 - 8:30

optional - Unix Tutorial for FreeSurfer Users

tutorial

Maritza Ebling

8:30 - 9:00

optional - Intro to FreeSurfer Jargon

talk

Melanie Ganz

8:30 - 9:00

Course Registration

sign-in

staff

9:00 - 9:30

Introduction to Freesurfer

talk

Doug Greve

9:30 - 10:30

Analyzing the Individual Subject

talk

Doug Greve

10:30 - 10:50

break

10:50 - 11:10

Freeview/Tksurfer demonstration

demo

Doug Greve

11:10 - 11:40

Interaction with Individual Subject Data Tutorial

tutorial

staff

11:40 - 12:20

Surface-based Analysis: Intersubject Smoothing & Registration

talk

Doug Greve

12:20 - 1:20

Lunch (Suggestions for where to eat)

--

--

12:35 - 1:20

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

talk

Dylan Tisdall

1:20 - 2:00

FreeSurfer Troubleshooting

talk

David Salat

2:00 - 3:00

Quality Checking a Recon

demo

David Salat

3:00 - 3:20

break

3:20 - 3:40

Troubleshooting Demonstration

demo

Louis Vinke

3:40 - 4:40

Troubleshooting Tutorial

tutorial

staff

Tuesday, April 30th - ROIs / Longitudinal / Multimodal / Group Analysis

Time

Title

Type

Lecturer

9:00 - 9:40

ROI Analysis

talk

Doug Greve

9:40 - 10:10

ROI Analysis Tutorial

tutorial

staff

10:10 - 10:30

break

10:30 - 11:30

Group Analysis / GLM / Multiple Comparisons

talk

Melanie Ganz

11:30 - 11:50

QDEC demonstration

demo

Nick Schmansky

11:50 - 12:50

Lunch

--

--

12:20 - 12:50

Optional Lunch Talk- MRI Acquisition Methods for Morphometry

talk

Andre van der Kouwe

12:50 - 1:50

Group Analysis / Multiple Comparisons - mri_glmfit Tutorial

tutorial

staff

12:50 - 1:50

Group Analysis - qdec Tutorial

tutorial

staff

1:50 - 2:20

Longitudinal FreeSurfer see also: LongitudinalProcessing

talk

Martin Reuter

2:20 - 2:40

break

2:40 - 3:40

Longitudinal Tutorial

tutorial

staff

3:40 - 4:40

Multi-Modal Integration

talk

Doug Greve

4:40 - 5:00

Registration Methods

talk

Lilla Zollei

5:00 - 5:45

Multi-Modal Integration Tutorial

tutorial

staff

Boston Beer Works location information here and here.
Meet us at 6:10pm at the front of Building 149 (map to be provided soon).
If you miss us, we are taking the 6:15pm MGH/Navy Yard shuttle to North Station (the next few buses depart at 6:30pm, 6:45pm, 7pm, 7:15pm, and 7:45pm).
From there, you cross the street and go down Canal Street. Boston Beer Works will be on your right.

Wednesday, May 1st - fMRI / Diffusion / Q&A

The Course Evaluation has been posted. Please feel free to start filling it out!

Time

Title

Type

Lecturer

9:00 - 10:00

Basics of fMRI Analysis

talk

Jon Polimeni

10:00 - 10:40

FSFAST

talk

Doug Greve

10:40 - 11:00

break

11:00 - 11:40

FSFAST continued

talk

Doug Greve

11:40 - 12:40

FSFAST Tutorial

tutorial

staff

12:40 - 1:40

Lunch

--

--

1:10 - 1:40

Optional Lunch Talk- Motion-compensated neuroanatomical imaging

talk

Dylan Tisdall

1:40 - 2:20

Introduction to Diffusion MRI

talk

Anastasia Yendiki

2:20 - 2:50

Diffusion Processing Tutorial

tutorial

staff

2:50 - 3:10

break & Evaluation

3:10 - 3:40

TRActs Constrained by UnderLying Anatomy (TRACULA)

talk

Anastasia Yendiki

3:40 - 4:25

Tracula Tutorial

tutorial

staff

4:25 - 5:00

Future Directions - Optical Coherence Tomography

talk

Caroline Magnain

5:00 - 5:30

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

talk

staff

The FreeSurfer Evaluation is here!

Additional Useful Information

FsTutorial (last edited 2022-11-28 14:32:26 by LiamrSennott)