option "reference" r "Input reference 3D image (float)" string yes
option "target" t "Input target 2D image (float)" string yes
-option "referenceMask" m "Mask to placed over the reference image" string no
+option "referenceMask" m "Mask or labels to placed over the reference image" string no
option "targetMask" - "Mask to placed over the target image" string no
section "Output"
option "vf" - "Result DVF" string yes
option "coeff" - "Result coefficient images" string no
+option "coeffEveryN" - "Result coefficient images at every N iterations (requires --coeff and --verbose)" int no default="20"
option "output" o "Deformed target image" string yes
option "before" - "Difference image before (but after rigid transform)" string no
option "after" - "Difference image after " string no