#File clitkExtractPatient.ggo
package "clitkExtractPatient"
version "1.0"
-purpose "Prefer high resolution input and resample (NN) output at the end (like). 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 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."
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 "input" i "Input image filename" string yes
-option "output" o "Output image filename" string yes
+option "input" i "Input image filename" string yes
+option "afdb" a "Output Anatomical Feature in a DB" string no
+option "output" o "Output image filename" string yes
section "Binarize"
section "Clean-up"
-option "openClose" - "Perform morphological opening and closing with unit radius" flag on
-option "autoCrop" - "Crop final mask to BoundingBox" flag off
+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