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

Upcoming Live Lectures

Intro to Linux for FreeSurfer Users

Talk

*Slides

Tutorial

Monday March 30th 11:00 - 12:00 EST. Watch with Zoom [[|here]]

Intro to FreeSurfer Jargon

Talk

Slides

N/A

Monday March 30th 11:00 - 12:00 EST. Watch with Zoom [[|here]]

Intro to FreeSurfer Software

Talk

Slides

N/A

Monday March 30th 11:00 - 12:00 EST. Watch with Zoom [[|here]]

Analyzing the Individual Subject

Part 1, Part 2

Slides

Introduction to FreeSurfer Output Tutorial

Monday March 30th 11:00 - 12:00 EST. Watch with Zoom [[|here]]

Intro to Freeview and the working with data

Freeview demonstration

N/A

Practice Working with Data

None currently scheduled. Vote [[|here]] for interest

ROI Analysis

Talk

Slides

ROI Analysis Tutorial

Monday March 30th 11:00 - 12:00 EST. Watch with Zoom [[|here]]

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

Day 2: More Structural Processing and Troubleshooting

Subject

Talk

Slides

Relevant Tutorials

Upcoming Live Lectures

Troubleshooting

Talk, Demo

FreeSurfer Troubleshooting

Troubleshooting Tutorial

Tuesday March 31st 11:00 - 12:00 EST. Watch with Zoom [[|here]]

Longitudinal Analysis

Talk

Longitudinal FreeSurfer

LongitudinalTutorial

None currently scheduled. Vote [[|here]] for interest

An Overview of Registration Methods

Talk

An Overview of Registration Methods

N/A

None currently scheduled. Vote [[|here]] for interest

Day 3: Group Analysis and Statistics

Subject

Talk

Slides

Relevant Tutorials

Upcoming Live Lectures

Surface-based analysis: Intersubject Registration & Smoothing

Talk

Slides

N/A

None currently scheduled. Vote [[|here]] for interest

Group Analysis

Part 1, Part 2

Group Analysis

Group Analysis Tutorial

Wednesday April 2nd 11:00 - 12:00 EST. Watch with Zoom [[|here]]

Multiple Comparisons

Talk

Multiple Comparisons Slides

Multiple Comparisons Tutorial

Wednesday April 2nd 11:00 - 12:00 EST. Watch with Zoom [[|here]]

Day 4: Multimodal Analysis / Diffusion Analysis

Subject

Talk

Slides

Relevant Tutorials

Upcoming Live Lectures

Intro to Diffusion

Part 1, Part 2

Introduction to Diffusion MRI

Diffusion Processing Tutorial

None currently scheduled. Vote [[|here]] for interest

Multi-Modal Integration

Part 1, Part 2

Multi-Modal Integration, Part 1: Registration, Multi-Modal Integration, Part 2: Group Analysis

Multi-Modal Integration Tutorial, Part 1 ,Multi-Modal Integration Tutorial, Part 2

None currently scheduled. Vote [[|here]] for interest

Tracts Constrained by Underlying Anatomy (TRACULA)

Part 1, Part 2

Slides

TRACULA Tutorial

None currently scheduled. Vote [[|here]] for interest

Bonus Talks and Slides: Longitudinal TRACULA

Day 5: fMRI Analysis and FSFAST

Subject

Talk

Slides

Relevant Tutorials

Upcoming Live Lectures

Basics of fMRI

Intro to fMRI Talk

Slides

N/A

None currently scheduled. Vote [[|here]] for interest

Resting State fMRI

Resting State fMRI Presentation

Resting State fMRI Slides

N/A

None currently scheduled. Vote [[|here]] for interest

FSFAST

FSFAST Presentation

FSFAST, Part 1: Preprocessing, FSFAST, Part 2: GLM Analysis

FSFAST Tutorial, Part 1, FSFAST Tutorial, Part 2

None currently scheduled. Vote [[|here]] for interest

Bonus Talks and Slides: Structural & Functional Data Integration

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

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.