option "input" i "Input Dicom file" string yes
option "image" j "Used to read image info (spacing, origin)" string yes
option "output" o "Output image base filename (roi number and extension will be append)" string yes
+option "tolerance" t "Tolerance for slice position" double no default="0"
-defgroup "ROIoption" groupdesc="an option of this group is required"
-groupoption "roi" r "ROI to binarize (if -1 = all roi)" int no default="-1" group="ROIoption"
-groupoption "roiName" n "ROI name to binarize (be wary of spaces in ROI names; if blank, use given 'roi' value)" string no default="" group="ROIoption"
-groupoption "roiNameSubstr" s "Substring of ROI name to binarize (reuturns all matches; if blank, use given 'roiName' value)" string no default="" group="ROIoption"
-
+text "\nOutput options - the default output format is mhd"
option "crop" c "Crop binary mask" flag off
option "mha" - "Write the RTStruct as a mha image to avoid special character problems" flag off
+option "nii" - "Write the RTStruct as a nii image" flag off
+option "niigz" - "Write the RTStruct as a gzipped nii image" flag off
option "vtk" - "Write the vtk Mesh as a vtk file" flag off
+defgroup "ROI option" groupdesc="an option of this group is required"
+groupoption "roi" r "ROI number to binarize (if -1 = all roi)" int no default="-1" group="ROI option"
+groupoption "roiName" n "ROI name to binarize (be wary of spaces in ROI names; if blank, use given 'roi' value)" string no default="" group="ROI option"
+groupoption "roiNameSubstr" s "Substring of ROI name to binarize (returns all matches; if blank, use given 'roiName' value)" string no default="" group="ROI option"