creating DICOM RT structure after using contour in Matlab

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Zohreh Khazraei Manesh 2016-5-17

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https://ww2.mathworks.cn/matlabcentral/answers/284590-creating-dicom-rt-structure-after-using-contour-in-matlab

编辑： Zohreh Khazraei Manesh 2016-5-17

Hi everyone!

I need to change (with a matlab code) the boundaries of a tumor structure, imported in DICOM format which should be in the same format after manipulation.

After modifying the structure, I have a 3D matrix containing densities. I used the matlab function "contour" to find the contours at each plane and then I saved the information in the info struct (the dICOM header). Finally, I used dicomwrite to create a DICOM image out of the modified info struct.

When I try to open my DICOM in work stations, I receive the error: "non-closed contours are not supported" and "Misalignments are taking place!". When I plot the contours in MATLAB there are no visible openings, but in some planes there are two or more different islands of the structure (see the figure below). I wonder if that can be the problem, considering that the contour points are saved in DICOM format in the order x1;y1;z1;x2;y2;z2;… .

I would be grateful if anyone can help me with some ideas about what the problem is and how I can solve it. Here is some relevant parts of the code:

a = dicomread('RTSS.dcm'); %RTSS is the structure set file
info = dicominfo('RTSS.dcm'); %dicom header
… %implement the changes on the tumor
for i=1:slices
[c,h]=contour(Infiltrated(:,:,i),1); 
        contourData=[];
        field=['Item_',int2str(i)];
        for j=1:size(c,2)
            contourData=[contourData; c(1,j); c(2,j); i]; 
%points are given x;y;z;x;y;z…
          end
  end    info.ROIContourSequence.Item_3.ContourSequence.(field).ContourData=contourData;
…
dicomwrite(a,'ZoneA.dcm',info, 'CreateMode', 'copy')