Hi Daniel -
I've implemented and tested a mechanism to "drive" the dijkstra process from a script file. This file contains a set of instructions that are sent, one after the other to a "back-end" process that performs the actual search.
It's a pseudo client/server model. The server is 'dijkstra_p1' that operates on FreeSurfer surfaces. The main client is 'dijk_dscript.py' that parses instructions either from a separate file, or passed directly on the command line. This python script handles the handshaking and synchronisation with the server.
You don't really have to worry about any of that. I've appended a bash script to this email that generates a set of 'dijkstra_p1' instructions, saves them to a file, and calls 'dijk_dscript' on this file - as we spoke about yesterday. This bash script generates several different scripts set about different seed vertices.
Take a look at the file. Most of the code up to line 180 is fluff. The "meat" is between lines 182 and 221. I'm sure you'd be able to adapt / expand this to suit your needs.
If you want to try all this out, let me know and I'll help you set up the prerequisites. I'm occupied with something for the rest of this afternoon, so we can get together tomorrow if you feel like it.
Cheers --R