Emily,

NITRC-CE uses NeuroDebian releases for much of its software, including AFNI, and as a result the CE software versions can lag slightly behind the latest releases.  It also appears that the update script isn't installed as part of the NeuroDebian package.

I would recommend installing the latest version of AFNI using the steps described on the AFNI web site (https://afni.nimh.nih.gov/pub/dist/doc/h...); root access can be gained on a CE instance by calling sudo as user ubuntu (the default user).  You might want to start with a NITRC-CE LITE instance, which has fewer packages preinstalled and will have less chance of conflict when installing AFNI.

We are looking into ways to make the latest versions of software available on CE, but that will come in the future.  Hopefully this will help you get your script working immediately.