You should also look into OpenDX for 3D plotting and it’s image format, which I was once told will replace dicom. Here is an interesting starter that links to this practical use page that will jump start scripted use. OpenDX does surface plots and 3D data clouds.

Dicom is a tricky “extensible standard” which vendors violate at will, so you will have problems with it. There is purpose built free software like Aeskulap, which also works with pacs. I’ve also been told that ImageJ can deal with dicom, but I have not tried it. Aeskulap was unable to see the images that come from the scanners I have to work with.

You should also check out Debian Medical, where all sorts of medical software is being packaged for Debian. The people running it are great.

I never got sucked into matlab because it was non free and expensive at the time I found it. The main draw to it is not the language, it’s the community that makes useful examples. There are similar communities around other non free visualization tools, but I think people are better off with the even larger community using free tools. The more you look, the more you find.