Hi Sam,
The ubuntu_16 package will not be appropriate for
an Ubuntu 12-15 system.
In any case, it sounds like your PATH is messed up,
hopefully for just the current terminal window.
Open a new window, and see whether commands like ls
and @update.afni.binaries work:
ls -l
@update.afni.binaries -help
If so, it is probably appropriate for you to use
the linux_openmp_64 package, so get that with:
@update.afni.binaries -package linux_openmp_64
Avoid running any sudo commands when your PATH
may be messed up.
- rick