The FSL & FreeSurfer Course is a series of lectures and analysis practical exercises which we have presented a number of times to large groups of researchers at various places round the world. However, it is also suitable for use as a self-taught course, particularly if you have already some background knowledge of analysis (for example, we recommend reading The FMRI Book first - several copies sit around FMRIB).
The slides for the lectures and practicals can be found on the main FSL & FreeSurfer Course website.
It is best to run the course on a linux/Apple desktop. Before running a practical, take your own local copy of the practical data:
cd ~/scratch rsync -a /vols/Data/fslcourse/currentCourse/fsl_course_data/ fsl_course_data/
This will give you a complete copy of the course data. This is huge, so delete it when you have finished the course.
Good luck! Note that we welcome feedback on both the lectures and the practicals.