Alfonso,
 
Thank you for pointing this prior post out to me.  I'm new to CONN. 
 
Just two questions, however, how does one do the following in your instruction below, "define the two subject groups (e.g., patient and controls) as two simple dummy-coded second-level covariates in Setup.Covariates.Second-level"?
 
Also, in the case of repeated measures for patients but a single timepoint scan for controls, how does one do the following in your instruction, "define three second-level covariates in Setup.Conditions defining these three subject groups (e.g., patients-pre, patients-post and controls, dummy coded using 1/0 values identifying the corresponding scans for each group)." How would that dummy coding look for three groups?
 
Thanks again,
Jeff