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== Videos of Lectures ==
You can find videos of the lectures [[http://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA|here]].

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FreeSurfer Tutorial and Workshop

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 Evaluation

Please fill out our course evaluation here. You can fill it in throughout the remainder of the course but you can't save your answers and finish it later so be sure to submit it before you leave.

Videos of Lectures

You can find videos of the lectures here.

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


Commands on a Mac

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.

Course Schedule

FreeSurfer Course, November 4 - 6, 2013
MGH, Charlestown Navy Yard, Building 114, Room D1

8:00 - 9:30am Registration Desk Open

Monday, Nov 4th - Introduction / Single Subject Analysis /Troubleshooting

Time

Title

Type

Lecturer

8:30 - 9:00

optional - Unix Tutorial for FreeSurfer Users

tutorial

Maritza Ebling

9:00 - 9:15

optional - Intro to FreeSurfer Jargon

talk

Allison Stevens

9:15 - 9:30

break

9:30 - 10:00

Introduction to Freesurfer

talk

Bruce Fischl

10:00 - 11:00

Analyzing the Individual Subject

talk

Doug Greve

11:00 - 11:20

break

11:20 - 12:05

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

talk

Dylan Tisdall

12:05 - 1:00

Lunch (Suggestions for where to eat)

--

--

1:00 - 1:30

Freeview/Tksurfer demonstration

demo

Doug Greve

1:30 - 2:00

Interaction with Individual Subject Data Tutorial

tutorial

staff

2:00 - 2:30

FreeSurfer Troubleshooting

talk

Bruce Fischl

2:30 - 2:50

break

2:50 - 3:50

Quality Checking a Recon

demo

Allison Stevens

3:50 - 5:00

Troubleshooting Tutorial

tutorial

staff

5:00 - 5:15

Question and Answer Session (Answers to online questions here)

talk

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.

Tuesday, Nov 5th - 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

Eugenio Iglesias

10:20 - 10:40

break

10:40 - 11:20

Group Analysis Tutorial

tutorial

staff

11:20 - 11:40

Multiple Comparisons

talk

Eugenio Iglesias

11:40 - 12:00

QDEC demonstration

demo

Eugenio Iglesias

12:00 - 1:00

Lunch

--

--

1:00 - 1:20

Multiple Comparisons Tutorial

tutorial

staff

1:00 - 2:00

QDEC Tutorial

tutorial

staff

2:00 - 3:00

ROI Analysis

talk

Doug Greve

3:00 - 3:20

break

3:20 - 3:50

ROI Analysis Tutorial

tutorial

staff

3:50 - 4:20

Longitudinal FreeSurfer see also: LongitudinalProcessing

talk

Martin Reuter

4:20 - 5:00

Longitudinal Tutorial

tutorial

staff

5:00 - 5:15

Question and Answer Session (Answers to online questions here)

talk

staff

Wednesday, Nov 6th - Diffusion / Multimodal / Longitudinal / Future Directions / Q&A

Time

Title

Type

Lecturer

9:00 - 9:30

Multi-Modal Integration, Part 1

talk

Doug Greve

9:30 - 10:00

Multi-Modal Integration Tutorial, Part 1

tutorial

staff

10:00 - 10:40

Introduction to Diffusion MRI

talk

Anastasia Yendiki

10:40 - 11:00

break

11:00 - 11:30

Diffusion Processing Tutorial

tutorial

staff

11:30 - 12:00

TRActs Constrained by UnderLying Anatomy (TRACULA)

talk

Anastasia Yendiki

12:00 - 1:00

Lunch

--

--

1:00 - 1:45

Tracula Tutorial

tutorial

staff

1:45 - 2:15

Multi-Modal Integration, Part 2

talk

Doug Greve

2:15 - 3:00

Multi-Modal Integration Tutorial, Part 2

tutorial

staff

3:00 - 3:20

break & Evaluation

3:20 - 3:50

optional technical talk - MRI Acquisition Methods for Morphometry

talk

Andre van der Kouwe

3:50 - 4:20

optional technical talk - Motion-compensated neuroanatomical imaging

talk

Dylan Tisdall

4:20 - 4:45

optional technical talk - Registration Methods

talk

Lilla Zollei

4:45 - 5:15

Future Directions

talk

Bruce Fischl, Lilla Zollei, Ender Konukoglu

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

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