We used the following command lines to run munger.pl for both brains and VNCs:

munger.pl -b /path/to/cmtk/binaries -vawr 010203 -T 4 -X 26 -C 8 -G 80 -R 4 \
-A '--accuracy 0.4' -W '--accuracy 0.4' -s "refbrain/IS2.PIC" "images"
# identical except for reference image
munger.pl -b /path/to/cmtk/binaries -awr 010203 -T 4 -X 26 -C 8 -G 80 -R 4 \
-A '--accuracy 0.4' -W '--accuracy 0.4' -s "refbrain/VNCIS1.PIC" "images"

This assumes that munger is called from inside a registration folder with the following structure

• RegistrationFolder (or whatever name you choose)
  • images (contains images to register in nrrd (preferred) or PIC format)
  • refbrain (contains reference brain)

Note that /path/to/cmtk/binaries should only required if they are installed in a directory that is not in your path. On a mac, the default CMTK install will put them in /opt/local/bin/.

For the registration GUI, we would just need the following options as the others are set interactively through dialog boxes:

-awr 010203 -T 4 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4'

See custom_command_lines_for_munger.pl and registration_parameters for further details.