Hi David,
What leaps out is using over 8 GB of RAM. How much RAM do you have?
If it cannot support that, your computer would probably start thrashing
(continually reading and writing swap memory), and it could take a very
long time to complete the process.
If you have enough RAM, then Peter's suggestion for CPU use is great.
If you are on the edge of memory, add the -regress_compute_fitts option
to afni_proc.py. That would drop the RAM usage in 3dDeconvolve by
computing that dataset after the fact (using all_runs and errts). So
it might save ~30% of the RAM usage.
Are you working with high-resolution EPI data?
Exactly how much RAM do you have?
Did you use the -volreg_warp_dxyz option?
- rick