Sure, no problem, I'm happy to help.
Yes, you can simply define the 1-vs-2 classifier using the -trainlables file and you don't need to label the sub-bricks belonging to the other classes with 9999s to exclude them from being used to compute the 1-vs-2 classifier. However, the computation time will be much longer if you include all classes, since 3dsvm will train classifiers for all possible class combinations defined in the -trainlabels file. If you are mainly interested in the 1-vs-2 classifier and are trying to figure things out, it will be more time efficient to only train one classifier. I would also look at the -censor option. Here, you can provide a .1D file and include sub-bricks by putting a '1' and exclude by putting a '0' on the corresponding line.
Jonathan
