How to Prepare for the FreeSurfer Course
Please note that this course caters for users with no FreeSurfer experience whatsoever. If you are a complete beginner and would like to gain some foundation in working/interacting with FreeSurfer, then these resources can be useful to you but are not necessary to complete before you arrive at the course. However, we strongly recommend attempting to work with Unix before the course so that you feel comfortable with the pace on the first day, even though we will cover an introduction to Unix in the very first talk.
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
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
We have two new videos to help you familiarize yourself with working in FreeSurfer or FreeView:<<BR>> Qaultiy Checking a Recon: https://www.youtube.com/watch?v=AR83_Bt04VQ FreeView Demo: https://www.youtube.com/watch?v=Mv-ECowxq2o
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