1 #File clitkExtractLungs.ggo
2 package "clitkExtractLungs"
4 purpose "Segment lungs in CT image. Need 'patient' mask."
6 option "config" - "Config file" string no
7 option "imagetypes" - "Display allowed image types" flag off
9 option "verbose" v "Verbose" flag off
10 option "verboseStep" - "Verbose each step" flag off
11 option "writeStep" w "Write image at each step" flag off
12 option "verboseOption" - "Display options values" flag off
13 option "verboseWarningOff" - "Do not display warning" flag off
14 option "verboseMemory" - "Display memory usage" flag off
18 option "input" i "Input CT image filename" string yes
19 option "afdb" a "Output Anatomical Feature DB (Carina position)" string no default="default.afdb"
20 option "output" o "Output lungs mask filename" string no default="lung.mhd"
21 option "outputTrachea" t "Output trachea mask filename" string no default="trachea.mhd"
23 section "Step 1 : Air remove"
25 option "lower" - "Initial lower threshold" int no
26 option "upper" - "Initial upper threshold" int no default="-300"
27 option "minSize" - "Minimum component size in voxels" int no default="100"
28 #option "remove1" - "Labels not to keep in air mask (lungs)" int no multiple default="2"
29 #option "firstKeep1" - "First label to keep" int no default="1"
30 #option "lastKeep1" - "Last label to keep" int no
32 section "Step 2 : find trachea"
34 option "skipslices" - "Number of slices to skip before searching seed" int no default="0"
35 option "upperThresholdForTrachea" - "Initial upper threshold for trachea" double no default="-900"
36 option "multiplierForTrachea" - "Multiplier for the region growing" double no default="5"
37 option "thresholdStepSizeForTrachea" - "Threshold step size" int no default="64"
38 option "seed" - "Index of the trachea seed point (in pixel, not in mm)" int no multiple
39 option "doNotCheckTracheaVolume" - "If set, do not check the trachea volume" flag off
40 option "verboseRG" - "Verbose RegionGrowing" flag off
42 section "Step 3 : auto extract lung"
44 option "bins" - "Number of bins to use for the Otsu thresholding" int no default="500"
45 # option "remove2" - "Labels not to keep in air mask (gas)" int no multiple
46 # option "firstKeep2" - "First label to keep" int no default="1"
47 # option "lastKeep2" - "Last label to keep" int no
49 section "Step 4 : remove trachea"
51 option "radius" - "Radius for dilation" int no default="1"
52 # option "remove3" - "Labels not to keep in lungs mask (trachea)" int no multiple
53 # option "firstKeep3" - "First label to keep" int no default="1"
54 # option "lastKeep3" - "Last label to keep" int no default="2"
56 section "Step 5 : [optional] openclose"
57 option "openclose" - "Perform an OpenClose operation" flag off
58 option "opencloseRadius" - "OpenClose radius" int no default="1"
60 section "Step 6 : fill holes"
61 option "doNotFillHoles" - "Do not fill holes if set" flag on
62 option "dir" d "Directions (axes) to perform filling (defaults to 2,1,0)" int multiple no