• TeachYourselfFreeSurfer

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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

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

Day 3: Group Analysis and Statistics

Day 4: Multimodal Analysis / Diffusion Analysis

Bonus Talks and Slides: Longitudinal TRACULA

Day 5: fMRI Analysis and FSFAST

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.

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.