difference open image with pydicom or sitk

Beginner Questions
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1

Hello everybody,
I tried to open a DICOM image with sitk.ReadImage. I don’t have any error message, so I can see the image with plt.imshow, but all the pixels of the image are equal to 0.

If I try to open the same image with pydicom, I don’t have any problem to visualize the image, and the pixel values are different from 0.

I don’t know why I can’t read this image with sitk.ReadImage.

Have you ever experienced this problem? Do you have a solution, so I can read my DICOM image with sitk. ReadImage ?

Thank you in advance for your answers.

2

It is hard to give any advice without the image in question, or at least its description (key tags). The exact code snippet you used for reading would be helpful too.

3

PT000073.dcm (314.7 KB)

You can find attach my image and the code below:

SITK:
filename1=‘PT000073.dcm’
image = sitk.ReadImage(filename1)
image_cast = sitk.Cast(image[:,:,0], sitk.sitkInt32)
img_arr = sitk.GetArrayFromImage(image_cast)
plt.imshow(img_arr)

pydicom:
filename=‘PT000073.dcm’
ds = dcm.read_file(filename)
img_arr = ds.pixel_array[100:300,100:300]
plt.imshow(img_arr)

4

Having looked at your image the result is not surprising. The original image is floating point (float64) with values in [0,1]. You cast it to int32, so all pixel values go to zero.

Try it without the cast (I’d also set the visualization colormap to gray as the default is viridis):

image = sitk.ReadImage(filename1) 
img_arr = sitk.GetArrayFromImage(image[:,:,0]) 
plt.imshow(img_arr)
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