Hi, Robin-
A couple of quick comments/questions:
A) You might want to add the following options to your AP command, to be explicit about the values used (there are defaults, but I prefer to state them):
-blur_size SOMETHING
-anat_has_skull YES_OR_NO
B) Are you sure you want this line in there, even though processing task-based data:
-regress_apply_mot_types demean deriv \
I am used to seeing that just in resting state processing, rather than when task-based events timing for stimuli is available. (Specifically, having the extra regressors for the derivatives of motion included.)
C) In your current code, I think you might actually specifically be better of with 3dcopy to a BRIK/HEAD file to start, rather than the shell's cp. This is because of how the header information will propagate in preparation for refitting.
--pt
