#File clitkExtractPatient.ggo
package "clitkExtractPatient"
version "1.0"
-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 ersion 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."
+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.
+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"
option "config" - "Config file" string no
option "imagetypes" - "Display allowed image types" flag off
option "writeStep" w "Write image at each step" flag off
option "verboseOption" - "Display options values" flag off
option "verboseWarningOff" - "Do not display warning" flag off
+option "verboseMemory" - "Display memory usage" flag off
section "I/O"
option "lower" - "Initial lower threshold" double no
option "upper" - "Initial upper threshold" double no default="-300"
+option "openingRadius" - "Radius for opening after threshold" int no default="0"
section "First Label Image (air=1)"
section "Clean-up"
option "openClose" - "Perform morphological opening and closing with unit radius" flag off
-option "noAutoCrop" - "If set : do no crop final mask to BoundingBox" flag on
+option "noAutoCrop" - "If set : do no crop final mask to BoundingBox" flag off