Hi Sebastian,

I would recommend giving JIST's command line interface (CLI) a try:
http://www.nitrc.org/plugins/mwiki/index...

It should be just what you're looking for.  A tricky part is making sure that everything
is on java's classpath.  If Lesion-TOADS is installed as a mipav plugin, then your
set-up will be very similar to that given in the "Aliasing" section of that wiki page.

Definitely post again here if you have any trouble, or if the wiki page is unclear (or if you have success!)

Good luck!
John

PS While it should be possible to do what you are asking by using the mipav script adapter,
I think that JIST's CLI will be a bit easier in the end.