How to convert xml file to RT Struct

Dear Expert,

I have xml file (xml folder) that I done contouring on that file. The original file also I have as attached. Both file can get here: https://drive.google.com/drive/folders/1GkDmQO9M5vZlQ4WIGsvpZoPlo1taRmTJ?usp=sharing or as attached.

Anyone can help me to convert xml file to RT Struct.

Please help me

Answer 1

[Deepak]

Hi @mohd akmal masud,

I understand that you are looking to convert contour data from an XML file (exported by HybridViewer) into a DICOM RT Structure Set (RT Struct) using MATLAB. The XML file contains multiple VOIs (structures), each with 2D contours defined at specific Z-slices. You can extract these contours in MATLAB using "xmlread", and match the Z-values with the slices in the reference DICOM image using metadata from "dicominfo".

Below is a sample MATLAB code to achieve the same:

info = dicominfo('original_file.dcm');               % Load DICOM metadata
doc = xmlread('contours.xml');                       % Read the XML
cont = dicomContours(info);                          % Create contour container

vois = doc.getElementsByTagName('voi');
for i = 0:vois.getLength-1
    voi = vois.item(i);
    name = char(voi.getElementsByTagName('title').item(0).getTextContent());
    rois = voi.getElementsByTagName('roi');
    for j = 0:rois.getLength-1
        coords = rois.item(j).getElementsByTagName('coordinate');
        pts = zeros(coords.getLength, 3);
        for k = 0:coords.getLength-1
            c = coords.item(k);
            pts(k+1,1) = str2double(c.getElementsByTagName('x').item(0).getTextContent());
            pts(k+1,2) = str2double(c.getElementsByTagName('y').item(0).getTextContent());
            pts(k+1,3) = str2double(c.getElementsByTagName('z').item(0).getTextContent());
        end
        cont = addContour(cont, i+1, name, pts, 'CLOSED_PLANAR', [255;0;0]);
    end
end

infoRT = convertToInfo(cont);                        % Create RT Struct metadata
dicomwrite([], 'RTSTRUCT.dcm', infoRT, 'CreateMode','copy');

This will generate a valid RTSTRUCT.dcm file, compatible with radiotherapy planning systems, from your XML and DICOM inputs.

Please find attached documentation of functions used for reference:

dicominfo: www.mathworks.com/help/images/ref/dicominfo.html

xmlread: www.mathworks.com/help/matlab/ref/xmlread.html

dicomContours: www.mathworks.com/help/images/ref/dicomcontours.html

convertToInfo: www.mathworks.com/help/images/ref/dicomcontours.converttoinfo.html

I hope this helps.

[mohd akmal masud]

Dear @Deepak,

The error pop up when for this line:

>> cont = dicomContours(info);                          % Create contour container
Error using dicomContours>validateMetadata (line 201)
Invalid SOPClassUID for DICOM-RT Structure Set.

Error in dicomContours (line 17)
validateMetadata(metadata, obj.Dictionary);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^