The registration is working by specifying '--class-ref label --class-flt label' in the command line. However, to use munger I also need to specify the interpolation method of reformatx to be '--nn' (nearest neighbor). In the munger manual, it says '-2 [option] additional options for reformatx'. But when I added -2 '--nn' to the munger command, it output an error message:
Unknown option: 2
Unknown option: -
Unknown option: n
Unknown option: n

Anyone knows if I have some misunderstanding of this '-2' option? Full command is like this:
"$MUNGERDIR/munger" -b "$REGBINDIR" -i -a -w -r 0102 -T 22 -l af -X 16 -C 4 -G 32 -R 3 -A '--exploration 16 --accuracy 0.8 --class-ref label --class-flt label' -W '--accuracy 0.8 --energy-weight 5e-1 --class-ref label --class-flt label' -2 '--nn' -s refbrain/"${REFBRAIN}".nrrd images


Thanks! 
Zhilei