Hi Jinglei,
Apologies, my git command requires ssh key access, you can use the HTTPS version of the git clone command. -nl_metric ncc is not implemented in master so the correct procedure should be:
git clone https://github.com/MRtrix3/mrtrix3.git mrtrix3_cc
cd mrtrix3_cc
git checkout registration_CC
./configure
./build
Then you should be able to use the CC metric via ~/mrtrix3_cc/bin/population_template and ~/mrtrix3_cc/bin/mrregister. I’d recommend not using this code for anything else as other commands might be outdated compared to the master branch.
Rob wrote instructions on using custom branches in the wiki
Testing different code branches. Just make sure to build all commands as shown above.