In DTI-Query, you can create VOI's (as they are called there) on the two regions. Then save the resulting fibers as volumes. The value at each voxel is the number of fibers that pass through that voxel. DTI-Query precompute GUI and command versions also allow for VOIs to be seed or target masks (one or the other depending on the build date). Mike Beauchamp and Tim Ellmore have some utilities for handling VOIs with AFNI and DTI-Query here that you may find useful too:
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