Hi, Shankar-

That seems excessively slow to me. I ran @SSwarper on a 1x1x1 mm**3 anatomical the other day using 5 CPUs and it took about an hour, I think.

Something to note-- that version of AFNI is veeery old, and there have been a lot of modifications to @SSwarper since then, as well as important ones to 3dQwarp. In particular, pretty recently Bob made the default 3dQwarp operation both faster and "lighter" memory-wise. I woudl definitely update you binaries. Done via:

@update.afni.binaries -d

... unless you are on a Mac and using the 10.7_local binaries (as evince by running "afni -ver"), in which case you will need to update via:

@update.afni.binaries -d -package macos_10.12_local

because we haven't maintained the Mac 10.7_local binaries for a long time now.

Additionally, it is possible that 48 CPUs might be too many, and leading to thrashing in the parallelization-- the fight threads is costing too much, and slowing things down. What if you tried, say 12-16 CPUs?

Can you also verify that your computer is really using that many? If you run just the followign in your script:

3dQwarp -hview

... it will open up the 3dQwarp help in a GUI text editor, but more importantly it will echo in the terminal the OpenMP thread count that it has, for example as:

++ OpenMP thread count = 1

--pt