option "input" i "Input CT image filename" string yes
option "patient" p "Input patient mask filename" string yes
-option "patientBG" - "Patient Background" int default="0" no
+option "patientBG" - "Patient Background" int default="0" no
option "output" o "Output lungs mask filename" string yes
option "outputTrachea" t "Output trachea mask filename" string no
section "Step 2 : find trachea"
+option "skipslices" - "Number of slices to skip before searching seed" int no default="0"
option "upperThresholdForTrachea" - "Initial upper threshold for trachea" double no default="-900"
option "multiplierForTrachea" - "Multiplier for the region growing" double no default="5"
option "thresholdStepSizeForTrachea" - "Threshold step size" int no default="64"
option "firstKeep3" - "First label to keep" int no default="1"
option "lastKeep3" - "Last label to keep" int no default="2"
+section "Step 5 : openclose"
+option "openclose" - "Final OpenClose" flag off
+option "opencloseRadius" - "Final OpenClose radius" int no default="1"