Hi Suzanne,
I understand that you are facing issue while trying to apply volume masks to a ‘DICOM-RT’ structure.
Please know that issues like these arise when the ROI contour of the structure is incorrectly determined. Once an incorrect ROI is generated then the following operations too result in an unintended output.
The ROI of the hole in the DICOM structure can be obtained and excluded from the ROI before masking. Masking the structure after having a consolidated ROI will cause proper analysis of the DICOM structure and subsequent masking.
Another workaround can be to orthogonally rotate the DICOM structure such that the hole can be detected similarly as it was getting detected in other orientation of the figure where hollow figure’s volume was correctly determined.
You can check the following sample code snippet for reference:
% Extract the contour for the hole
holeContour = contour{contourIndex};
% Create a binary mask with the hole
rtMask = false(size(referenceInfo.XWorldLimits, 2), size(referenceInfo.YWorldLimits, 2), size(referenceInfo.ZWorldLimits, 2));
for i = 1:size(holeContour, 1)
x = holeContour(i, :, 1);
y = holeContour(i, :, 2);
z = holeContour(i, :, 3);
maskSlice = poly2mask(x, y, size(rtMask, 1), size(rtMask, 2));
rtMask(:, :, z) = rtMask(:, :, z) | maskSlice;
end
figure(2), volshow(rtMask)
figure(3), imshow(rtMask(:, :, 76))
I hope this helps.
