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name:: {{{ nmrclass1_wifi_2.4Ghz nmrclass1_wifi_2.4Ghz nmrclass1_wifi_2.4Ghz nmrclass1_wifi_2.4Ghz }}}

password:: {{{ brain.map }}}

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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

name::  nmrclass1_wifi_2.4Ghz nmrclass1_wifi_2.4Ghz nmrclass1_wifi_2.4Ghz nmrclass1_wifi_2.4Ghz 

password::  brain.map 

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 4-7

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 covering basic/beginner material.

Monday, April 4th - Introduction / Single Subject Analysis / ROI Analysis

Time

Title

Type

Lecturer

8:30 - 9:00

** Intro to Linux for FreeSurfer Users

talk/tutorial

Zeke Kaufman

9:00 - 9:15

** Intro to FreeSurfer Jargon

talk

Allison Stevens & Lilla Zollei

9:15 - 9:45

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

talk

Dylan Tisdall

9:45 - 10:00

break

10:00 - 10:30

Introduction to Freesurfer

talk

Bruce Fischl

10:30 - 11:40

Analyzing the Individual Subject

talk

Doug Greve

11:40 - 12:00

Freeview demonstration

demo

Allison Moreau

12:00 - 1:00

Lunch (Suggestions for where to eat)

--

--

1:00 - 2:00

Interaction with Individual Subject Data Tutorial

tutorial

staff

2:00 - 2:30

* MRI Acquisition Methods

talk

Andre van der Kouwe

2:30 - 2:50

break

2:50 - 3:20

Surface-based Analysis: Intersubject Registration & Smoothing

talk

Doug Greve

3:20 - 3:50

ROI Analysis

talk

Doug Greve

3:50 - 4:40

ROI Analysis Tutorial

tutorial

staff

6:15 - ?

Boston Beer Works

social activity

staff

Answers to online questions here

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. (Shuttles depart every 15 minutes up until 7:15pm and every half hour after that).

Tuesday, April 5th - Group Analysis / Longitudinal Analysis / Multimodal Analysis

Time

Title

Type

Lecturer

9:00 - 9:30

** Basics of Group Analysis

talk

Emily Lindemer

9:30 - 10:10

Group Analysis

talk

Emily Lindemer

10:10 - 10:30

break

10:30 - 11:10

Group Analysis Tutorial

tutorial

staff

11:10 - 11:30

Multiple Comparisons

talk

Emily Lindemer

11:30 - 11:50

Multiple Comparisons Tutorial

tutorial

staff

11:50 - 12:50

Lunch

--

--

12:50 - 1:10

QDEC demonstration

demo

Martin Reuter

1:10 - 1:50

QDEC Tutorial

tutorial

staff

1:50 - 2:35

Longitudinal FreeSurfer see also: LongitudinalProcessing

talk

Martin Reuter

2:35 - 2:55

break

2:55 - 3:35

Longitudinal Tutorial

tutorial

staff

3:35 - 4:05

Multi-Modal Integration, Part 1

talk

Lilla Zollei

4:05 - 4:30

Multi-Modal Integration Tutorial: Multimodal Registration

tutorial

staff

4:30 - 5:10

* An Overview of Registration Methods

talk

Lilla Zollei

Answers to online questions here

Wednesday, April 6th - Diffusion Analysis / fMRI Analysis

Time

Title

Type

Lecturer

9:00 - 9:15

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

talk

Dylan Tisdall

9:15 - 10:00

Introduction to Diffusion MRI

talk

Anastasia Yendiki

10:00 - 10:40

Diffusion Processing Tutorial

tutorial

staff

10:40 - 11:00

break

11:00 - 11:40

TRActs Constrained by UnderLying Anatomy (TRACULA)

talk

Anastasia Yendiki

11:40 - 12:00

Tracula Tutorial

tutorial

staff

12:00 - 1:00

Lunch

--

--

1:00 - 1:30

Tracula Tutorial

tutorial

staff

1:30 - 1:40

Longitudinal TRACULA

talk

Anastasia Yendiki

1:40 - 1:55

break

1:55 - 2:55

Basics of fMRI Analysis

talk

Jon Polimeni

2:55 - 3:35

FSFAST

talk

Doug Greve

3:35 - 3:50

break

3:50 - 4:30

FSFAST

talk

Doug Greve

4:30 - 5:30

FSFAST Tutorial

tutorial

staff

Answers to online questions here

Thursday, April 7th - Multimodal Analysis / Troubleshooting / Future Directions

Time

Title

Type

Lecturer

8:30 - 9:00

* Motion-compensated Neuroanatomical Imaging

talk

Dylan Tisdall

9:00 - 9:30

Multi-Modal Integration, Part 2

talk

Doug Greve

9:30 - 10:00

Multi-Modal Integration Tutorial: fMRI Integration & Surface-based Group fMRI Analysis

tutorial

staff

10:00 - 10:30

FreeSurfer Troubleshooting

talk

Bruce Fischl

10:30 - 11:00

break & Evaluation

11:00 - 12:00

Troubleshooting Tutorial

tutorial

staff

12:00 - 1:00

Lunch

--

--

1:00 - 2:00

Quality Checking a Recon

demo

Allison Moreau

2:00 - 2:50

Future Directions

talk

Bruce Fischl

2:50 - 3:00

Question & Answer session

--

staff

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 2022-11-28 14:32:26 by LiamrSennott)