Hi Jessica,
As Peter points out, you have some trouble with
the backslash characters.
Note the the stored command at the end of the proc
script shows it ending with the -copy_anat option.
Looking at your command, there is no '\' after that
option, so the command ends.
Also, the # command lines are okay, but they need
backslash continuation characters (if appropriate),
too. That applies to the "Puts the brain into MNI"
line, for example, and others.
Run your afni_proc.py command script through
"file_tool -show_bad_backslash" for additional
suggestions.
- rick