Thanks Alfonso, this has been extremely helpful. I will go back and rerun everything with my subject-specific tissue masks as well as make the corrections outlined below with regard to the removal of the first 4 volumes.

Re: question (3): I tried to follow the v15 manual instructions but obviously didn't implement correctly - at the second level, I highlighted both patients and controls (by right clicking on both simultaneously) and then entered 1-1 to specify the between-group contrast. I realize now that after entering this it automatically reverted to giving me the main effect across groups instead, i.e., [1 0; 0 1] as you pointed out below. Should I highlight 'all subjects' instead and then enter '1-1' and finally click on the results explorer? I did try this just now, but conn/matlab is crashing - so not sure if this is a related problem or something else entirely.

Also, when I choose 'spm display' to view the contrast in SPM, I don't see the regressors for 'motion' and 'outliers' that I specified as first-level covariates, shouldn't these also be displayed in the contrast manager window design matrix?