And not to muddy the conversation here, but to interject on an earlier point: Indeed, that earlier version of AFNI probably doesn't have the gtkyd_check.py in it. We have also made some useful recent updates to it.
We have some more updates coming to afni_proc.py's QC HTML coming in near future, in time for the upcoming Bootcamp, so it might be worth pinging the HPC folks about updating AFNI there. Also, you can always have a local copy of AFNI binaries that you control, using the same package flavor of the HPC, so all the dependencies are present, and then you can put your version at the start of your $PATH, and update it as you wish (which would probably be more regularly than the HPC-moderated version).
-pt