Hi,
I think I fixed that bug in the registration_CC branch in this repo. Could you try if this solves your issue? Please note that this is still developmental code, please let us know if you into any issues!
git clone https://github.com/MRtrix3/mrtrix3.git mrtrix3_cc
cd mrtrix3_cc
git checkout registration_CC
./configure
[EDIT] fixed git clone command