Hi, Chuck-

OK, from the error message in Part 1, it seems your OS is missing an AFNI dependency, listed here:
[afni.nimh.nih.gov]

Could you please run:

sudo yum update

and then you might as well run all of these, to make sure that nothing else is missing:

sudo yum install -y epel-release
sudo yum install -y tcsh libXp openmotif gsl xorg-x11-fonts-misc       \
                    PyQt4 R-devel netpbm-progs gnome-tweak-tool ed     \
                    libpng12 xorg-x11-server-Xvfb firefox
sudo yum update -y

(You have Red Hat v6 there, hopefully these all work.) Though, I am *guessing* given the PATH that you might be running on an administered system? If so, it would be nice to run that set of dependencies, but if someone balks at all of those, I would try the smaller set here:

sudo yum install -y  netpbm-progs libpng12 xorg-x11-server-Xvfb

You can try that test @chauffeur_afni command again, and that should work.

In the meantime, I note that that Xvfb error message is "just" about making the automatic QC images; if you still want to run the code without an error message before the Xvfb dependencies get fixed, you can add this option to your command "-no_qc_image", but then you just have to verify that things have gone right in the GUI yourself.

Also, from the bottom section of the afni_system_check output, you can/should probably also run the following (none of which requires sudo/admin privileges, so you should be able to run them OK yourself on any system):

cp /gpfs/group/dml129/default/sw/afni/20.1.13/bin/AFNI.afnirc ~/.afnirc
suma -update_env
apsearch -update_all_afni_help

--pt