You can also specify the second ROI as a termination mask, to stop propagation once the curves reach that ROI. That will produce a map of connection probabilities from ROI A to B, which will not necessarily be the same as the connection probabilities when seeding from B and targeting to A. You can use the "multiple masks" mode in probtrackx to overcome this, as both A and B will be used as seeds and targets. 

Hope that helps,

Stam