I’m very new to Freesurfer and I’m struggling to setup my project directory for a functional analysis.

I’m running a study with each subject doing two MRI sessions, i.e. before and after they perform a perceptional training at home for three month.

In each session (i.e. before and after training) they do a sensory mapping task and I want to compare mapping pre- and post-training. If possible I’d like to run this analysis contrasting two groups (who performed different kinds of training).

I’m about to setup the project directory structure as depicted here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV4.5. The first issue I stumbled across is if to put data of all pre-training measurements of all subjects in a different „Session“ ( it says "All the data collected in one functional session (or visit) are placed under the folder (the "session directory").). 

As far as I can see the tutorial does neither cover longitudinal within subject comparisons nor between group comparisons (using mri_glmfit). Thus, any help is highly appreciated!

Thank you!

Sincerely, 

Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c