How to Prepare for the FreeSurfer Course

"Required" Preparation

If you are a beginner to FreeSurfer, the following content is HIGHLY recommended to enhance your enjoyment of the course.

You will have an opportunity to practice using the command line on the first day of the course. Please watch this video which introduces you to interacting with FreeSurfer through the command line: https://youtu.be/6eJMxh7PlOY
Please familiarize yourself with the terms in this glossary: https://docs.google.com/document/d/1x6PsE6tlOXF7zcvkhwTGngD_B8Mslzsvzlo6_alP_28/edit?usp=sharing

Bonus Course Materials

UNIX
If you are unfamiliar with UNIX, it may help to do this online tutorial:
http://www.ee.surrey.ac.uk/Teaching/Unix/

Other good UNIX references are:
http://www.fmrib.ox.ac.uk/fslcourse/unix_intro/
http://docstore.mik.ua/orelly/linux/lnut/index.htm
https://www.codecademy.com/courses/learn-the-command-line

SCRIPTING
Scripting will not be covered during the course, but the following are some good references:
http://www.linuxjournal.com/article/1299
https://supportweb.cs.bham.ac.uk/documentation/tutorials/docsystem/build/tutorials/unixscripting/unixscripting.html

MR
If you are unfamiliar with MR physics, you can read up on it here:
http://www.cis.rit.edu/htbooks/mri/

There will be an optional talk that will go over the basics of MR physics.

FREESURFER RELATED

This document was put together by a member of the FreeSurfer lab, which details some fundamental information and jargon which you may find useful when learning FreeSurfer for the first time. Download and read the following word document: FS_homework_doc.

We have two new videos to help you familiarize yourself with working in FreeSurfer or Freeview:

Quality Checking a Recon: https://www.youtube.com/watch?v=AR83_Bt04VQ
Freeview Demo: https://www.youtube.com/watch?v=Mv-ECowxq2o

In general, feel free to go through any of the slides and tutorials that we'll be covering during the course. They can be found here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial

Not all of the slides are up or updated yet, but feel free to look at what is there.

You can also find videos of the course lectures here:
http://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA

You can read up on the techniques and applications of FreeSurfer here (found under the References section):
https://surfer.nmr.mgh.harvard.edu/fswiki/

You can download FreeSurfer and process your own data. Instructions on installation are here:
https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall