Hi-
Thanks, but what I am looking for firstly here (and in a couple other threads) is the command that starts with "afni_proc.py ...".
What is posted here is the script created by afni_proc.py.
uber_subject.py opens a GUI to help users input dataset and option information to build an afni_proc.py command. Running this afni_proc.py command builds a full processing script, typically named "proc.SUBJ_ID" or similar---this is a several hundred line tcsh script, describing all the actual processing commands. Executing this proc.* script actually does the processing. When this script is executed, we often recommend making a copy of all the text that gets dumped in the terminal into a separate log or output file for storage+asking questions; this is done with a vertical pipe and "tee" command, which we often make examples for with the output name "output.proc.SUBJ_ID"---I think this last output* file is what you have posted here. (Note that afni_proc.py also generates a QC HTML that you can view, to help investigate processing steps; the command typically finishes with a comment about opening this up in the terminal.)
So, could you please post the command that starts with "afni_proc.py".
In this particular run case, it looks like the EPI-anatomical alignment hasn't gone well, which we can try to help troubleshoot, but we need to see the afni_proc.py command itself as a starting point.
--pt
