section "I/O"
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 "afdb" a "Output Anatomical Feature DB (Carina position)" string no
option "output" o "Output lungs mask filename" string yes
option "outputTrachea" t "Output trachea mask filename" string no
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"
+section "Step 5 : [optional] openclose"
+option "openclose" - "Perform an OpenClose operation" flag off
+option "opencloseRadius" - "OpenClose radius" int no default="1"
+
+section "Step 6 : fill holes"
+option "doNotFillHoles" - "Do not fill holes if set" flag on
+option "dir" d "Directions (axes) to perform filling (defaults to 2,1,0)" int multiple no
+