Hiya-

Yep, that is all quite possible to do in AFNI.

Terminological preface: when tracking in AFNI (using 3dTrackID), all targets are created equal, and tracts are found using whole brain tractography and keeping those which pass through any pairs of them (for probabilistic tracking-- i.e., AND logic) so there's no difference between a 'seed' and 'target'. All ROIs in your input network map are 'targets'. A network is defined as a set of ROIs in a single brick, with each ROI defined as a set of voxels with a particular integer value. Thus, target ROI-1 is defined as all voxels with value 1; ROI-2 is the set of all voxels with value 2, etc. If you want, you can input several networks simultaneously, with each defined in a separate brick of a multibrick file.

Back to your question of inflating the targets: yep, you can use 3dROIMaker to do this. The option in question is called '-inflate NN', where NN is the number of voxels you want to pad the region by. Additionally, there are also options to help you not pad the region 'too much' in some places. This is because you probably just want to pad the target *until* it hits WM for tracking, but to too much further. Assuming you are tracking with the standard WM proxy condition of where FA>0.2, then you can load in the FA map, and stop the local target inflation when it has reached where FA>0.2 (but other parts of the target keep inflating to your set value, if possible).

Let's say you wanted to inflate targets by 2 voxels, and limit it in places as described above. This could be done using:
$ 3dROIMaker -inflate 2 -wm_skel DT_FA+orig -skel_thr 0.2 -skel_stop -inset TARGETMAPS -prefix OUTPUTMAPS
If you want both targets inflated, you can put them into a single brick and do this; assuming your targets don't overlap/touch initially (which sounds like a safe assumption for your data), this will also assign unique integers to each, and ensure that they don't overlap when inflating. If you only want one inflated, then you can do this on your separate file and then combine them into a single brick.

--pt