Howdy-

Well, uber_subject.py is a GUI interface to help build afni_proc.py commands for full single subject processing. However, it is fairly old and doesn't allow the user to have the full flexibility of afni_proc.py options, which are pretty wide-ranging. What we recommend people to do to set up processing is to start by looking at one of the several afni_proc.py examples, which exist for both task and rest:
[afni.nimh.nih.gov]
... and to adapt those scripts (and also to ask questions from here). For example, Ex. 11 and 11b are good places to start for resting state processing. Having the code examples as starting points also makes it easier to send your processing back-and-forth for questions here.

This removes the need for PyQt4 or PyQt5 stuff, so that is why PyQt4 is no longer required in the setup instructions.

Also, from your afni_system_check.py, if you run each of the following commands in a terminal:

afni
suma

do the GUIs open? You have a note about needing to set an env variable in your AFNI setup. Perhaps, could you please redo this part of the setup by copy+pasting this in a terminal:

touch ~/.cshrc
echo 'if ( $?DYLD_LIBRARY_PATH ) then' >> ~/.cshrc
echo '  setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace' >> ~/.cshrc
echo 'else' >> ~/.cshrc
echo '  setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace' >> ~/.cshrc
echo 'endif' >> ~/.cshrc

touch ~/.bashrc
echo 'export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace' >> ~/.bashrc

... and then opening a new terminal, run "afni_system_check.py -check_all" again, and see if the " consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace " line at the bottom of the system check output disappears?

--pt