Hi, Yasir-

Typically, one puts a set of EPI dsets into a single afni_proc.py command that makes sense to go together.

If you have runs that are very different---particularly task and rest, or unrelated tasks (a categorization which includes task and rest....)---then I would *not* put them all together into a single afni_proc.py command. I don't see what that would mean--- GLTs would be hard to specify for the task part, and typically task and resting FMRI have different processing paths (e.g., one includes the derivatives of motion params in rest often, but not in task).

I don't understand the 2^8 permutation estimate.

You should likely just process each set of similar tasks together in batches. If nothing "goes together", then you would have N afni_proc.py runs.

Cases like this are why we recommend using @SSwarper for skullstripping+nonlinear warping before running afni_proc.py: you only run *that* once, and then pass its results into each afni_proc.py instance. Same goes for running FreeSurfer: you run it on your subject's anatomical once, and then you can use it in each subsequent AP run.

--pt