Hi Matt,
It's good to hear that you are enjoying those programs. I am not
sure how flexible uber_subject.py will become, but with afni_proc.py
you can at least add an 'empty' processing block and a -copy_files
option. You could then modify the trivial 3dTcat command in the
'empty' block to be your B0 correction command (or script).
The down side to that is that you would have to modify the proc
scripts. The up side is that is would be pretty easy (and could
probably be done with a sed or awk command).
Alternatively, if you have already done any tshift or volreg
blocks, you could tell afni_proc.py to skip them, and even import
your motion parameters (via -copy_files and -regress_motion_file)
to still be used in 3dDeconvolve.
- rick