option "config" - "Config file" string no
option "imagetypes" - "Display allowed image types" flag off
+
option "verbose" v "Verbose" flag off
option "verboseStep" - "Verbose each step" flag off
option "writeStep" w "Write image at each step" flag off
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"
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" int no multiple
+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 "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 "noAutoCrop" - "If set : do no crop final mask to BoundingBox" flag off