I think I solved my difficulties.  Posting here in case it helps others.

The version of niftyreg on sourceforge is outdated, and has bugs that won't compile on recent systems.  And their release depends on shared libraries which the run_mri_reface.sh script makes difficult to set up.  Instead, the recent version is on github (https://github.com/KCL-BMEIS/niftyreg).  If compiled with defaults, this doesn't use shared libraries and it bypasses the issue.

I also ran into a library issue with Matlab vs ANTS, with errors like: ...matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by ANTS)

While LD_LIBRARY_PATH is already reset in the script, I guess it's reverted to USER_LD_LIBRARY_PATH before calling ANTS.  And since I called this script from Matlab, it had this matlab library conflict.  The fix is therefore to again clear LD_LIBRARY_PATH in Matlab before calling run_mri_reface.sh.