You're right -- if each participant has different EV files then you can't
use the GUI to process them all at the same time. I typically script these
things (as you mentioned in your previous email) but that does require at
least a passing familiarity with Unix. I know it's a pain, but if you're
planning to do much fMRI, it's probably well worth your while to invest the
time to learn the scripting. It will save enormous time in the long
run. On the other hand, if this is a one-off study, I'd just bite the
bullet and use the GUI for each participant.
For what it's worth, you can't run the design.fsf file directly, you need
to call it with feat:
% feat design.fsf
Sorry there isn't an easier answer.