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"
section "Registration"
-option "levels" - "Number of resolution levels" int no default="1"
+option "levels" - "Number of resolution levels" int no default="1"
+option "skipLastPyramidLevel" - "Skip full resolution pyramid level" flag off
option "intermediate" - "Write the coefficient image of the intermediate levels (provide levels filenames)" string no multiple
+