Hi-

Yes, @SSwarper can be run with any FMRI data (task, rest, naturalistic...).

To speed up (or, well, leverage as much speediness as possible), note that:
1) modern versions use the "lite" 3dQwarp processing-- so make sure you are using an uptodate AFNI.

2) It's parallelized with OpenMP, so deeeeeefinitely make use of that-- set OMP_NUM_THREADS on your system to be many threads. I often use 12 or 20.

When running on a cluster and using SLURM to do swarm/batch processing, we typically include this at the top of our tcsh scripts (could be applied to any shell script in other syntax):

# set thread count if we are running SLURM
if ( $?SLURM_CPUS_PER_TASK ) then
  setenv OMP_NUM_THREADS $SLURM_CPUS_PER_TASK
endif

That way, the knowledge about how many processors have been allocated to your task are merrily passed along to the program. You should see some message in the terminal when the warping starts running about how many processors it is using, so you should be able to tell if this effort has been successful.

--pt