Hi Ottar,
What are you looking to do with JIST? That will help us point you in the right direction.

You most likely will need to download this version of JIST http://www.nitrc.org/frs/download.php/7248/JIST-2014Dec12-03-34PM.jar, which is the version 3.2 release, and install it into MIPAV following http://www.nitrc.org/plugins/mwiki/index.php/jist:Install. 

JIST typically needs to be installed in MIPAV to run, but what it sounds like you want is the command line interface (http://www.nitrc.org/plugins/mwiki/index...). This is also wrapped nicely in PyJIST (http://www.nitrc.org/plugins/mwiki/index...).

Hope that helps!
Andrew