section "I/O"
option "input" i "Input CT image filename" string yes
-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 "afdb" a "Output Anatomical Feature DB (Carina position)" string no default="default.afdb"
+option "output" o "Output lungs mask filename" string no default="lung.mhd"
+option "outputTrachea" t "Output trachea mask filename" string no default="trachea.mhd"
section "Step 1 : Air remove"
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 "seed" - "Index of the trachea seed point (in pixel, not in mm)" int no multiple
-option "doNotCheckTracheaVolume" - "If set, do not check the trachea volume" flag off
-option "verboseRG" - "Verbose RegionGrowing" flag off
+option "type" - "trachea finding algorithm (0: original; 1: LOLA11)" int no default="0"
+option "skipslices" - "0: Number of slices to skip before searching seed" int no default="0"
+option "upperThresholdForTrachea" - "0: Initial upper threshold for trachea" double no default="-900"
+option "multiplierForTrachea" - "0: Multiplier for the region growing" double no default="5"
+option "thresholdStepSizeForTrachea" - "0: Threshold step size" int no default="64"
+option "seed" - "0,1: Index of the trachea seed point (in mm NOT IN PIXELS)" float no multiple
+option "doNotCheckTracheaVolume" - "0,1: If set, do not check the trachea volume" flag off
+option "verboseRG" - "0,1: Verbose RegionGrowing" flag off
+option "maxElongation" - "1: Maximum allowed elongation of candidate regions for the trachea" float no default="0.5"
+option "numSlices" - "1: Number of slices to search for trachea" int no default="50"
+option "seedPreProcessingThreshold" - "1: Threshold for the pre-processing step of the algorithm" int no default="-400"
section "Step 3 : auto extract lung"
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
+#option "dir" d "Directions (axes) to perform filling (defaults to 2,1,0)" int multiple no
+section "Step 7 : lung separation (labelling)"
+option "doNotSeparateLungs" - "Do not separate lungs if set" flag off
+option "removeSmallLabel" - "Remove small label (stomach?) before separation" flag on
+option "noAutoCrop" - "If set : do no crop final mask to BoundingBox" flag off