#File  clitkGammaIndex.ggo
package "clitkGammaIndex"
version "1.1"
purpose "Compute the gamma index map for target dose map vs reference dose map. If verbose is given, the ratio of gamma>1 pixels of the total pixel in the image is computed. Absolute dose margin has priority over relative dose margin. The relative dose margin is relative to the maximum dose in the reference image.\n\nclitkGammaIndex -v -i ref.mhd -j disp.mhd -o gamma.mhd -s 3 -r 0.04\nthis will compute the 3mm 4% gamma index between ref and disp."

option "verbose"     v 	"Verbose"		          flag	   off

option "reference" i 	"Reference dose map"	  string   yes
option "target"	   j 	"Target dose map"	  string   yes
option "output"    o 	"Output image filename"	  string   yes

option "spatial-margin"   s 	"Spatial margin [mm]"	  double   yes
option "relative-dose-margin"   r 	"Dose margin relative to max dose in reference [%]"	  double   no
option "absolute-dose-margin"   d 	"Absolute dose margin [Gray]"	  double   no
option "translation-x"   x 	"Target relative position x [mm]"	  double   default="0" no
option "translation-y"   y 	"Target relative position y [mm]"	  double   default="0" no
option "translation-z"   z 	"Target relative position z [mm]"	  double   default="0" no