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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. 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
Intro to Freeview and the working with data	Freeview demonstration	N/A	Practice Working with Data
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 || None currently scheduled. Vote [[|here]] for interest ||

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.