Update explanation about clitkExtractPatient

diff --git a/segmentation/clitkExtractPatient.ggo b/segmentation/clitkExtractPatient.ggo
index f4944409a1b10e6286a9930b1046b659a2301ece..5b695aef4e7b3449eb1095fec2e47cfa81d4e40c 100644 (file)
--- a/segmentation/clitkExtractPatient.ggo
+++ b/segmentation/clitkExtractPatient.ggo
@@ -1,7 +1,8 @@
 #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

diff --git a/segmentation/clitkExtractPatientFilter.txx b/segmentation/clitkExtractPatientFilter.txx
index fedf853c82590918849ddc8df2e9e58ec06a7f9e..97f79c5e9050bdcf1b5b4d2275ad0a32e73c60f8 100644 (file)
--- a/segmentation/clitkExtractPatientFilter.txx
+++ b/segmentation/clitkExtractPatientFilter.txx
@@ -117,6 +117,7 @@ GenerateOutputInformation() {
   StartNewStep("Find low densities areas");
 
   // Pad images with air to prevent patient touching the image border
+  // But the lungs can touch the outside air. In such case, use primaryOpeningRadius with 1 kernel
   typedef itk::ConstantPadImageFilter<InputImageType, InputImageType> PadFilterType;
   typename PadFilterType::Pointer padFilter = PadFilterType::New();
   padFilter->SetInput(input);