Dear LesionToads-Experts,

Since in our lab most of the pipelining is done via bash scripts-could you suggest a way to start LT from inside a shell script? It seems that mipav script recording does not work with LT. Could this possibly be done by manually writing a mipav script with a call to the corresponding MedicAlgorithmLesionToads( with the right parameters )? If the answer is yes- what are the right parameters and in which order will they appear inside the brackets?

Many thanks!
Best regards,
Sebastian

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.

Hi John,

Thanks so much for your advice! This seems to perfectly fit my purpose.
However, I am not sure what to do about the Java vm. There is no /jre/bin/java
in my mipav installation directory. So what will I have to do...Should I use the vm
that is installed on my Mac and change the paths given in the Aliasing section's box
accordingly?

Thanks again!
Best,
Sebastian

Sebastian,

You're correct - I believe that mipav uses the Mac's JVM, and so you should
be able to create an alias in the same way but pointing to *that * jvm as you suggest.

Once you have the java alias set up, you can test it by running: It should be exactly the mipav that you usually run.

Good luck!
John

Yes, on a mac mipav uses the system jvm, so that is the java you will want to point to, since mipav has added a few jars to the system classpath that are useful for its operation.

-Justin