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.

Comments on Freeview for Mac users:
1) 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 macOS operating systems
2) If you would like to use Freeview 6.0, follow these instructions to install a necessary patch

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: Prepare with the basics

We usually send this page out to students before each course to help them find resources to cover the basics such as: Intro to unix and scripting, intro to neuroanatomy etc.

Step 5: Suggested Schedule (5 days)

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

Subject

Talk

Slides

Relevant Tutorials

Upcoming/Recorded Live Lectures

Intro to FreeSurfer Jargon

Talk

Slides

N/A

Intro to FS Jargon Talk

Intro to Linux for FreeSurfer Users

Talk

Slides

Tutorial

Intro to Linux Talk

Intro to FreeSurfer Software

Talk

Slides

N/A

Introduction to FreeSurfer Talk

Analyzing the Individual Subject

Part 1, Part 2

Slides

Introduction to FreeSurfer Output Tutorial

Analyzing the Individual Subject Talk

Intro to Freeview and the working with data

Freeview demonstration

N/A

Practice Working with Data

FreeView Demo

ROI Analysis

Talk

Slides

ROI Analysis Tutorial

ROI Analysis talk

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

Troubleshooting Talk

Longitudinal Analysis

Talk

Longitudinal FreeSurfer

LongitudinalTutorial

An Overview of Registration Methods

Talk

An Overview of Registration Methods

N/A

Day 3: Group Analysis and Statistics

Subject

Talk

Slides

Relevant Tutorials

Upcoming Live Lectures

Surface-based analysis: Intersubject Registration & Smoothing

Talk

Slides

N/A

Group Analysis

Part 1, Part 2

Group Analysis

Group Analysis Tutorial

Group Analysis Talk

Multiple Comparisons

Talk

Multiple Comparisons Slides

Multiple Comparisons Tutorial

Multiple Comparisons Talk

Day 4: Multimodal Analysis / Diffusion Analysis

Subject

Talk

Slides

Relevant Tutorials

Intro to Diffusion

Part 1, Part 2

Introduction to Diffusion MRI

Diffusion Processing Tutorial

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

Tracts Constrained by Underlying Anatomy (TRACULA)

Part 1, Part 2

Slides

TRACULA Tutorial

Bonus Talks and Slides: Longitudinal TRACULA

Day 5: fMRI Analysis and FSFAST

Subject

Talk

Slides

Relevant Tutorials

Basics of fMRI

Intro to fMRI Talk

Slides

N/A

Resting State fMRI

Resting State fMRI Presentation

Resting State fMRI Slides

N/A

FSFAST

FSFAST Presentation

FSFAST, Part 1 and 2

FSFAST Tutorial, Part 1, FSFAST Tutorial, Part 2

Bonus Talks and Slides: Structural & Functional Data Integration

Getting the Help and Support you need

You can email the FreeSurfer Help mailing list with questions related to your own data processing and troubleshooting. The address to email for all questions is: freesurfer@nmr.mgh.harvard.edu. For troubleshooting your data processing, be sure to attach your recon-all.log file to your email. For questions specifically related to any of the above lectures or tutorials, feel free to email the speaker of the lecture, you can find their emails below.

Lecture Topic

Lecturer

Email Address

Intro to FreeSurfer Jargon

Dev Cordero

dccordero@mgh.harvard.edu

Intro to Linux for Freesurfer Users
ROI Analysis

Matt Larrabee

mlarrabee1@mgh.harvard.edu

Intro to FreeSurfer Software

Matt Vera

mvera2@mgh.harvard.edu

Analyzing the Individual Subject

Bram Diamond

brdiamond@mgh.harvard.edu

Intro to FreeView & Working with Data

Kim Nestor

knestor1@mgh.harvard.edu

Troubleshooting

Leah Morgan

lmorgan6@mgh.harvard.edu

Group Analysis
Multiple Comparisons

Paul Wighton

paul@corticometrics.com

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.

TeachYourselfFreeSurfer (last edited 2020-04-10 11:58:03 by DevaniCordero)