I was digging through the FIX source to track down an error, and I noticed one issue in functionmotionconfounds.m ... Specifically, I see:
[grota,grotb]=call_fsl('imtest ...')
followed by:
if grotb==1
Since grotb is the imtest stdout and not the status, it actually contains the string '0' or '1' (followed by a newline), so you need to say something like this instead:
if isequal(str2num(grotb),1))
I don't think this has any real effect other than making it run a few unnecessary commands, but I wanted to bring it to your attention, in case similar issues pop up elsewhere.