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Segmentation not working on Dicom images

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Warid Islam
Warid Islam on 22 Nov 2022
Commented: Warid Islam on 29 Nov 2022
This is related to a previous question I asked before.
I want to manually segment tumors from Dicom images. I tried the code below but I get a greyish image.
I=dicomread('IMG-0012-00219.dcm');
metadata = dicominfo('IMG-0012-00219.dcm');
WC = metadata.WindowCenter; % original [40; 40]
WW = metadata.WindowWidth;
figure, imshow(I,[WC(1)-WW(1), WC(1)+WW(1)]);
h = drawfreehand; %draw something
M = ~h.createMask();
I(M) = 0;
imshow(I,[WC(1)-WW(1), WC(1)+WW(1)]);
imwrite(im2double(I),'Image3.png','mode','loseless')
The segmentation works fine, but the image is greyish which is not desirable. Any suggestions would be appreciated.
  5 Comments
DGM
DGM on 28 Nov 2022
You either have to shift/rescale all the image data, or you simply don't use zero for the fill color. It depends if you want to preserve the relative scale and value of the image data.
If you don't care about the absolute scale of the data and all you want is an image for visualization purposes, you might be able to just do something like this:
% ...
h = drawfreehand; %draw something
M = ~h.createMask();
% create a copy and normalize it WRT the window metadata
outpict = mat2gray(I,[WC(1)-WW(1), WC(1)+WW(1)]); % unit-scale double
outpict(M) = 0; % fill background region with black
% display and write
imshow(outpict);
imwrite(outpict,'Image3.png','mode','loseless')
Warid Islam
Warid Islam on 29 Nov 2022
Hi @DGM,
It worked. Thank you very much.

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Answers (1)

Image Analyst
Image Analyst on 22 Nov 2022
I'm not sure what you mean by the image looks greyish. It looks like the masked blob in the middle has the full dynamic range. Do you just want to make the gray background be black? Like (untested)
grayMask = grayImage == grayImage(1,1);
grayMask = bwareafilt(grayMask, 1);
grayImage(grayMask) = 0;
imshow(grayImage, []);
  2 Comments
Warid Islam
Warid Islam on 28 Nov 2022
I tried the above code. But I am getting the following image.
The resulting image should look something like below. The reason I am not using the result below because that is the result of segmenting the original image which was converted to png file and then segmentation was performed. What I want now is to apply the segmentation on the original dicom file and obtaining the segmentation result as below.
Image Analyst
Image Analyst on 28 Nov 2022
Please attach the original gray scale image and the segmented (binary) image (the mask image).

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