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

<code>
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"
</code>
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:

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

See [[warping_manual:custom_command_lines_for_munger.pl]] and [[warping_manual:registration_parameters]] for further details.