1 #File clitkExtractPatient.ggo
2 package "clitkExtractPatient"
4 purpose "Input is binarized using initial thresholds, connected components are labeled (firstLabel). The air label (1) is removed. The remaining is binarized and relabeled, patient should now be the principal label (secondLabel). Two mechanismes are provided to influence the label images. Crop to reduce connectivity (image is restored to original size), eg for SBF. Decomposition through erosion and reconstruction through dilation (slow), eg for Pulmo bellows. Choose which labels to keep from second Label image. Final mask is cleaned by opening and closing.
5 The image is padded first with air. If lungs are touching the border (so the air), set openingRadius to 1 in order to have lungs segmented inside the patient"
7 option "config" - "Config file" string no
8 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 image filename" string yes
19 option "afdb" a "Output Anatomical Feature in a DB" string no
20 option "output" o "Output image filename" string yes
24 option "lower" - "Initial lower threshold" double no
25 option "upper" - "Initial upper threshold" double no default="-300"
26 option "openingRadius" - "Radius for opening after threshold" int no default="0"
28 section "First Label Image (air=1)"
30 option "erode1" - "Decompose through erosion" flag off
31 option "radius1" - "Radius for erosion and dilation" int multiple no default="1"
32 option "new1" - "Number of new labels" int no default="1"
33 option "max1" - "Max number of labels to consider" int no default="2"
35 section "Second Label Image (air=1)"
37 option "erode2" - "Decompose through erosion" flag off
38 option "radius2" - "Radius for erosion and dilation" int multiple no default="1"
39 option "new2" - "Number of new labels" int no default="1"
40 option "max2" - "Max number of labels to consider" int no default="2"
41 # option "crop" - "Crop the first label image" flag off
42 # option "boundingBox" b "Bounding box of the crop region (minX,maxX,...)" int no multiple
43 # option "lowerS" - "Size of the lower crop region" int no multiple
44 # option "upperS" - "Size of the upper crop region" int no multiple
46 section "Labels to keep (air=1)"
48 option "firstKeep" - "First label to keep" int no default="1"
49 option "lastKeep" - "Last label to keep" int no default="1"
50 option "remove" - "Labels to remove" int no multiple
54 option "openClose" - "Perform morphological opening and closing with unit radius" flag off
55 option "noAutoCrop" - "If set : do no crop final mask to BoundingBox" flag off