Dear Greg and Alfonso
 
I have a quite similar design (2 groups and for each of them I do have a pre and post (training) scan). I also want to test for main effects (F test).
 
During each scan I have resting and taks periods.
 
First, I am not sure how to set up the design matrix for this 2 x 2 ANOVA
 
Lets say, there are 4 controls and 4 patients. Do I have to choose 8 subjects or 16 in the Setup menu? For example, If have select 8, I could define two groups (2nd level covariates) and two conditions (pre and post). But then I cannot assign separte scans for each of them (Since I have only 1 session). Hence, I could still use 8 subjects in total but have to use 2 sessions for each subject and assign e.g. session 1 as the pre scan and session 2 as the post scan, right? However, the question is whether "pre" and "post" are still listed as Conditions in the 2nd level tab later on?

Alternatively, I could select 16 subjects, and code as controls_pre controls_post patients_pre patients_post (2nd level covariates) and as conditions still pre and post, e.g.
 
controls_pre [1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0], controls post [ 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0] etc.
 
I tested this. And yes, 4 groups and 2 conditions (pre/post) appear in the second level tab. But this is wrong, I think, as I do have only two groups (controls and patients) with repeated measures (pre and post).
 
Again, I wanted to run F-test first (and then t-tests).
 
Which of the Design scenarios is the correct one to choose?
 
Finally, I wanted to compute background connectivity (time bin: 0 inf) and task PPI connectivity. Does this mean I have to simply add some extra conditions, e.g. pre_background (0-inf) and pre_task (e.g. onset 20 40 60, duration 10) to be able to compute both background and PPI connectivity.
 
Thanks
Lars