Hi--

There are various ways to put ROIs together in a single volume. Each target for tracking is the set of voxels with a given integer value, so you will want each target unique target to have a different integer value.

If you have just 2 in the same volume space (in your case, 'thalamus.nii' and 'mpfc.nii'), and you are sure that they do not overlap spatially, then you can do the following:

$ 3dcalc -a thalamus.nii -b mpfc.nii -expr 'step(a) + 2*step(b)' -prefix OUTPUT.nii.gz

I used 'step' above because I wasn't sure if you had already made masks of your ROI files or not. The nonzero voxels from the 'thalamus' file will have integer values of 1, and those of the 'mpfc' file will have values of 2. After this, you can use OUTPUT.nii.gz as your -netrois file.

Then, if you wanted to do mini-probabilistic tracking to find the connections between these targets, then you could do the following (adapting several names from your input example above):

$ 3dTrackID -mode MINIP -dti_in DT -mini_num 7 -uncert UNCERT_UNI+orig <some details..> -netrois OUTPUT.nii.gz -logic AND -prefix o.TM -do_trk_out

And I'll note that lots of tracking/visualization help can be found in the online documentation:
[afni.nimh.nih.gov]

--pt