Probabilistic tractography can be performed with FSL's BEDPOSTX via seeding from the ROI's in the brainstem atlas and capturing tracts which pass through the ROI.

Deterministic tractography can be performed with 3D Slicer (http://dmri.slicer.org), it automatically applies a housemade atlas though I'm not sure brainstem tracts are included and fiber tracts

for those ROI may have to be clustered by hand (this is a pretty insignificant extra step).

Or you could generate the tractography using MRtrix3 and then use mrcalc to calculate the parameters you are interested in e.g. number of fibers, length of fibers, density of fibers, FA etc.

You could also consider using FATCAT: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/FATCAT/main_toc.html