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Bonus Talks: [[https://www.youtube.com/watch?v=SwsH64PBBZE|Intro to MRI Presentation]],[[http://surfer.nmr.mgh.harvard.edu/pub/docs/IntroMRI.pptx|Intro to MR Slides]], [[https://www.youtube.com/watch?v=aZfy8gsPxZE| MRI Aquisition Techniques for Morphometry]], [[http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurfer_Acquisition_Sep2019.ppt|MRI Acquisition Methods]]
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|| Troubleshooting || [[ https://www.youtube.com/watch?v=gf0BC0xs0tM | YouTube Presentation ]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.apr2019.ppt|FreeSurfer Troubleshooting]] || [[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Tutorial]] || || Troubleshooting || [[ https://www.youtube.com/watch?v=gf0BC0xs0tM | YouTube Presentation ]], [[https://www.youtube.com/watch?v=AR83_Bt04VQ| Demo]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.apr2019.ppt|FreeSurfer Troubleshooting]] || [[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Tutorial]] ||
|| Multiple Comparisons || [[ https://www.youtube.com/watch?v=s87--3yG6mU&t=1114s| YouTube Presentation]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Multiple Comparisons Slides]] || [[FsTutorial/MultipleComparisonsV6.0Perm|Multiple Comparisons Tutorial]] ||
|| Longitudinal Analysis || [[ https://www.youtube.com/watch?v=vxJODPBLd3M&t=147s| YouTube Presentation ]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] || [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]] ||
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=== Day 3: Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition ===

Upcoming FreeSurfer courses

If you would like to be notified about upcoming FreeSurfer courses, sign up for the course mailing list.. We host two Boston courses each year, typically in the first week of April and the last week of September.

Suggested Steps for Conducting an at-home FreeSurfer Course

Step 1: Download FreeSurfer For your Computer

Follow the instructions on this page to get FreeSurfer on your personal computer. We highly recommend downloading the standalone Dev version of Freeview to replace the Freeview application in the FreeSurfer v6.0 download package due to incompatabilites with newer operating systems (especially if you have a mac).

Step 2: Download the tutorial data

Download the tutorial data here (~ 8GB).

Step 3: test your FreeSurfer Install and Tutorial Data

These are some instructions written by Paul Wighton on how to run a script that will test some of the FreeSurfer tutorial commands on your laptop and ensure your install is working well enough to attempt the tutorials for the course.

FreeSurfer 6 can be downloaded from here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
More insallation instructions can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
The tutorial data can be downloaded from here: https://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz

On my machine, I stored the downloaded `tar.gz` files in a directory called `/home/paul/lcn/data/fs-course-20200310`.  After extracting the archives I have the following subdirectories in `/home/paul/lcn/data/fs-course-20200310`
- `freesurfer`
- `tutorial_data_20190918_1558`

Next, edit the file `bashrc` in the `tutorial_data_20190918_1558` directory.  (In my case, the full path of that file is `/home/paul/lcn/data/fs-course-20200310/tutorial_data_20190918_1558/bashrc`) and change lines 16 and 19 to match the location of freesurfer and the tutorial data on your machine.

In my case, I edited the lines to read:
- Line 16: `export TUTORIAL_DATA=/home/paul/lcn/data/fs-course-20200310/tutorial_data_20190918_1558`
- Line 19: `export FREESURFER_HOME=/home/paul/lcn/data/fs-course-20200310/freesurfer`

Next, change into the tutorial data directory:

```
cd /home/paul/lcn/data/fs-course-20200310/tutorial_data_20190918_1558
```

and test the installation by running:
```
source bashrc
test_commands.sh.15
```

This may take a while (30 minutes to an hour) and the script will constantly "steal focus" so you will not be able to use your machine while the tests are running.

If at some point, you see:
```
mean.practice.table (END)
```

Hit `q` so the script can continue (I had to do this twice)

When you see `colortable with 14176 entries read (originally /autofs/cluster/freesurfer/centos7_x86_64/stable6/FreeSurferColorLUT.txt)` you can hit enter and the script will end.

Step 4: Suggested Schedule (5 days)

Day 1: Intro to FreeSurfer and Working with the Individual Subject

Subject

Talk

Slides

Relevant Tutorials

Intro to Linux for FreeSurfer Users

YouTube Presentation

*Slides

Tutorial

Intro to FreeSurfer Jargon

YouTube Presentation

Slides

N/A

Intro to FreeSurfer Software

YouTube Presentation

Slides

N/A

Analyzing the Individual Subject

YouTube Presentation Part 1, YouTube Presentation Part 2

Slides

N/A

Intro to Freeview and the FreeSurfer Output

Freeview demonstration

N/A

Introduction to FreeSurfer Output Tutorial, Practice Working with Data

ROI Analysis

YouTube Presentation

Slides

ROI Analysis Tutorial

Bonus Talks: Intro to MRI Presentation,Intro to MR Slides, MRI Aquisition Techniques for Morphometry, MRI Acquisition Methods

Day 2: Working with Multiple Subjects and Troubleshooting

Surface-based analysis: Intersubject Registration & Smoothing

YouTube Presentation

Slides

N/A

Group Analysis

Video 1, Video 2

Group Analysis

Group Analysis Tutorial

Troubleshooting

YouTube Presentation, Demo

FreeSurfer Troubleshooting

Troubleshooting Tutorial

Multiple Comparisons

YouTube Presentation

Multiple Comparisons Slides

Multiple Comparisons Tutorial

Longitudinal Analysis

YouTube Presentation

Longitudinal FreeSurfer

LongitudinalTutorial

Day 3: Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition

Structural & Functional Data Integration

talk

David Salat

Answers to online questions here

Tuesday, September 24th - Group Analysis / Longitudinal Analysis / Troubleshooting

Time

Title

Type

Lecturer

8:00 - 9:00

*** Morning Help Session

research technicians

9:00 - 9:45

Group Analysis

talk

Viviana Siless

9:45 - 10:25

Group Analysis Tutorial (FSGD Examples)

tutorial

staff

10:25 - 10:45

break

10:45 - 11:30

FreeSurfer Troubleshooting

talk

Bruce Fischl

11:30 - 12:30

Troubleshooting Tutorial

tutorial

staff

12:30 - 1:30

Lunch

1:30 - 2:15

Quality Checking a Recon

talk

Leah Morgan

2:15 - 2:55

Multiple Comparisons

talk

Doug Greve

2:55 - 3:25

Multiple Comparisons Tutorial

tutorial

staff

3:25 - 4:05

break

4:05 - 4:50

Longitudinal FreeSurfer

talk

Malte Hoffmann

4:50 - 5:30

LongitudinalTutorial

tutorial

staff

5:30 - 7:30

Social Night in the atrium of Bldg. 149

Snacks and Beverages Served

Answers to online questions here

Wednesday, September 25th - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition

Time

Title

Type

Lecturer

8:00 - 9:00

*** Morning Help Session

research technicians

9:00 - 9:30

* Intro to MR

talk

Robert Frost

9:30 - 10:00

Multi-Modal Integration, Part 1: Registration

talk

Aina Frau-Pascual

10:00 - 10:30

Multi-Modal Integration Tutorial, Part 1

tutorial

staff

10:30 - 10:50

break

10:50 - 11:05

* Intro to Diffusion MRI Physics

talk

Robert Frost

11:05 - 11:45

Introduction to Diffusion MRI

talk

Anastasia Yendiki

11:45 - 12:30

Diffusion Processing Tutorial

tutorial

staff

12:30 - 1:30

Lunch

--

--

1:30 - 2:20

Tracts Constrained by UnderLying Anatomy (TRACULA)

talk

Anastasia Yendiki

2:20 - 3:20

TRACULA Tutorial

tutorial

staff

3:20 - 3:40

break

3:40 - 3:50

Longitudinal TRACULA

talk

Anastasia Yendiki

3:50 - 4:50

Basics of fMRI Analysis

talk

Jingyuan Chen

4:50 - 5:30

* MRI Acquisition Methods

talk

Andre van der Kouwe

Answers to online questions here

The FreeSurfer Evaluation is here!

Thursday, September 26th - fMRI Analysis / Multimodal Analysis / Future Directions

Youtube Link

Title

Type

Slides

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

* An Overview of Registration Methods

talk

Lilla Zöllei

1:30 - 1:45

Resting State fMRI

talk

Doug Greve

1:45 - 2:15

Multi-Modal Integration, Part 2: Group Analysis

talk

Doug Greve

2:15 - 3:00

Multi-Modal Integration Tutorial, Part 2

tutorial

staff

3:00 - 3:15

break

3:15 - 3:30

* FreeSurfer vs. VBM

talk

Doug Greve

3:30 - 4:30

* Future Directions

talk

FS Development Team

4:30 - 5:00

Question & Answer Session

staff

Getting the Help and Support you need

For questions related to your own data processing and for troubleshooting help, please contact the FreeSurfer mailing list: freesurfer@nmr.mgh.harvard.edu and attach your recon-all.log file to your email.

For tutorial-specific questions, over the next two weeks (March 23 - April 3rd) our FreeSurfer tutorial support team will be extra available to set up video chats or answer your questions over email. Feel free to email the addresses on the list below for help:

mlarrabee1@mgh.harvard.edu, dccordero@mgh.harvard.edu, mvera2@mgh.harvard.edu, lmorgan6@mgh.harvard.edu, brd15@mgh.harvard.edu

TeachYourselfFreeSurfer (last edited 2022-11-28 14:31:16 by LiamrSennott)