Thanks Greg! I currently do not parallize the procedure, but even so 7 hours does sound too long. So far I only used single commands following the UserGuide, for example:

warp -o ffd40.xform --grid-spacing 40 --initial affine.xform  [ref_image] [float_image]

where I got the affine.xform from the command:

registration --initxlate --dofs 6,9 --auto-multi-levels 4 -o affine.xform [ref_image] [float_image]

Did I do anything wrong?  Also, what is the difference between the method in the online tutorial and that in the User guide? What does the flag '-awr' mean? I cannot find an instruction anywhere in the manual.

I found a sample script of "munger.pl" here:
https://github.com/jefferis/AnalysisSuit...
Could I use the script as it is, or should I modify anything based on my computer specs?

Best,
Dan