Hi-
Yes, @SSwarper is a precursor step to afni_proc.py (that's a *good* thing-- if you have to update your processing and re-run, you don't have to redo the somewhat slow alignment). For this step, you reeeeeeeally want to use several cores/threads. This is where you really want OMP_NUM_THREADS set to be >1, if it all possible, and I provided script stuff for using SLURM explicitly in my previous message.
Running afni_proc.py comes next, *using* the results of @SSwarper. Also having some parallelization wtih OMP_NUM_THREADS set to be >1 (if possible) would also benefit your processing here. Note that applying the warps and regridding lots of EPI volumes can/will still take a while. Quality processing takes time!
For processing a group of subjects or something, you really would be better served by using a more powerful desktop or a cluster. 12 hours seems a bit extreme, but total processing time depends on a lot of things: size of volumes, number of EPIs, whether disks are SSD, amount of memory per processor, phase of the Moon, etc.
--pt
