Hi Paul,

Can you verify whether the EPI times series datasets
have the proper timing in them? Use "3dinfo -VERB"
(upper case) to check the "Time-offsets per slice"
line.

It would be best to properly populated the dataset
to begin with. Otherwise, such timing would have to
be altered in 3dTshift via "-tpattern @TIMING_FILE",
which would have to be passed via -tshift_opts_ts,
and which would probably beg for use of -copy_files.

Of course, uber_subject.py does not have a direct
way to set such options, so they would need to go
into the afni_proc.py command. That would be much
easier to do when scripting afni_proc.py directly.

Going back to the beginning, can you verify whether
the original timing files have such information?
If not, maybe just try to add it first. Note that
3dTcat can be used for that, as well as to3d.

- rick