How to read DICOM RT Structure?

I have a DICOM RT STRUCTURE file (attached) with 1 structure set. I tried dicomread(filename) but it returned an empty array. Are there any scripts to read DICOM RT STRUCTURE file with Matlab?

Answer 1

[Thomas]

Might want to try https://github.com/ulrikls/dicomrt2matlab

or try

RSInfo=dicominfo('RS.ZZ_YUNINN_.dcm');

dicomwrite(1, 'RSDicomOut.dcm', RSInfo, 'CreateMode', 'Copy');

Then read

 X=dicomread('RSDicomOut.dcm');

[Yun Inn]

Hi Thomas,

I tried the code and it returned a single number?

Yun

[Thomas]

hmmm. here is why-

 RSInfo
RSInfo = 
                              Filename: [1x55 char]
                           FileModDate: '04-Mar-2014 05:50:52'
                              FileSize: 1899490
                                Format: 'DICOM'
                         FormatVersion: 3
                                 Width: []
                                Height: []
                              BitDepth: []

The image you attached is not being read correctly by matlab.. no width , height or bit depth..

are you sure your Dicom RT file is valid..

I have another dicom-rt image and this is how the output of dicominfo looks like..

 info1=dicominfo('image_0.dcm')
info1 = 
                          Filename: [1x52 char]
                       FileModDate: '11-Jan-2012 07:42:44'
                          FileSize: 525444
                            Format: 'DICOM'
                     FormatVersion: 3
                             Width: 512
                            Height: 512
                          BitDepth: 16
                         ColorType: 'grayscale'

[Yun Inn]

Hi Thomas,

Finally figured out what was wrong. The RTStructure.dcm file does not have any width, height, or bit depth information. The information is contained in the CTimage.dcm file. The GitHub link with codes provided by Ulrik is very helpful. Thank you very much!

[Yun Inn]

Hi Zahra,

The RTstructure.dcm is related to the set of CTimage.dcm files. Without the CTimage.dcm, the RTstructure.dcm will be meaningless.

In order for the correct readout of the structures, the RTstructure.dcm and the whole set of CTimage.dcm (all axial slices) must be in the same folder. Subsequently, you can use the codes provided by Ulrik on Github (https://github.com/ulrikls/dicomrt2matlab) to read and convert the structure into binary image in matlab. To display the outline of structure, you can try using the bwtraceboundary function.

If you have more than 1 structures, you can browse the structure from the output under: contours(?,?).Segmentation;

Hope you can see this reply and it would be helpful to you.

[zahra]

Dear Yun,

Thank you for your help and guides. I gather all of the CT images with the structure file in one folder and run the following function: >> dicomrt2matlab('RTSTRUCT_NAGHDI MAHBANOO_S1_C1')

but finally get these errors, I don't know what is the header and what should I do to fix this error, Do you have any idea?

error: Reading image headers... Converting RT structures... ??? Reference to non-existent element of a cell array.

Error in ==> getAffineXfm at 7 dr = headers{1}.PixelSpacing(1);

Error in ==> readRTstructures at 4 xfm = getAffineXfm(imgheaders);

Error in ==> dicomrt2matlab at 26 contours = readRTstructures(rtssheader, imageheaders); %#ok<NASGU>

Bests

[Yun Inn]

Hi Zahra,

Check that you have these functions from the Github download: (1) scanDir.m (2) dicomrt2matlab.m (3) loadDicomImageInfo.m (4) readRTstructures.m (5) getAffinexfm.m

Then put all the dicom files (RTstructure.dcm and all CTimage.dcm) in one folder (e.g. FolderA), and just run these 2 lines:

% Specify the path of the folder

directory='/Users/xxxx/Desktop/FolderA;

% Output into the same folder

files_out = scanDir(directory);

You should see the .mat file saved in the same folder. It could take a few minutes to get the output depending on the number of CT slices and structures.

Hope it works for you!

[zahra]

Hi,

Thank you very much. I do your suggestions but finally get this:

Converting C:\Users\zahra si\Documents\MATLAB\brachy\patient2\RTSTRUCT_NAGHDI MAHBANOO_S1_C1.dcm

and the files_out is just: files_out =

     {}

I really don't know what is the problem!

Bests,

[zahra]

Excuse me, I mean that no .mat file was created.

Bests, Zahra

[zahra]

Dear Yun,

Finally I can have a .mat file in that folder after running the codes, but can you see your structures on the CTs? If yes would you please let me know how? I can't do it by imshow.

Bests, Zahra

[Yun Inn]

Hi Zahra,

I haven't tried that but you should be able to. If you are seeing all black on the CT image, then its the windowing. You can set the window limits.

imshow(Im, [LowLim UpLim])

To display the structure, you have to specify which structure first. Example:

Str1=contours(1,1).Segmentation; % (1,1) is just an example.

Choose your own structure of interest. Then

   imshow(Str1)

If you want only the outline, you have to trace the boundary first, bwtraceboundary. To superimpose, use 'hold on'.

[Thomas]

Hello Zahra, Can you describe how you solved the problem with

files_out =

       {}         ?

Any help is much appreciated, Tom

[manuela]

Hello Zahra, I have the same problem as Thomas, Please let me know how you solved the problem files_out = {} Thank you very much, Manuela

[zahra]

Hi Thomas, Excuse me I see your question now. I just did what Yun said put all of my CTs and structures to a single folder and run the code as : % Specify the path of the folder

directory='/Users/xxxx/Desktop/FolderA;

% Output into the same folder

files_out = scanDir(directory); Bests.

Answer 2

[SimonD]

This is now solved with a new MATLAB function:

https://uk.mathworks.com/help/images/ref/dicomcontours.html

Answer 3

[MARIA LIZONDO]

Hi all,

I have tried to use this code but I have problems to view the structure...

imshow(Str1)

Error using images.internal.imageDisplayValidateParams>validateCData (line 115)
Multi-plane image inputs must be RGB images of size MxNx3.

Error in images.internal.imageDisplayValidateParams (line 27)
common_args.CData = validateCData(common_args.CData,image_type);

Error in images.internal.imageDisplayParseInputs (line 78)
common_args = images.internal.imageDisplayValidateParams(common_args);

Error in imshow (line 222)
      images.internal.imageDisplayParseInputs({'Parent','Border','Reduce'},preparsed_varargin{:});

Thanks in advance!

Maria

[Mengxiao Wang]

Hi Maria, Can you solve the problem to view the structure？ Thank you very much. Megan

[Walter Roberson]

What shows up for size(Str1) and class(Str1) ?