pydicom-seg
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Segmentation shape is not the same as the original image shape
This is what I'm trying:
# read individual segments from dicom file via pydicom_seg
dcm = pydicom.dcmread(dicom_filename)
print(dcm.pixel_array.shape)
# Use a SegmentReader to iterate through all the segments
reader = pydicom_seg.SegmentReader()
result = reader.read(dcm)
segmentations = []
for segment_number in result.available_segments:
print(segment_number)
image_data = result.segment_data(segment_number) # directly available
image = result.segment_image(segment_number) # lazy construction
print(sitk.GetArrayFromImage(image).shape)
segmentations.append(image)
The original dicom image pixel array's shape is (440, 512, 512).
However the individual segment shapes are (114, 512, 512); strange.
Is there a way to read the segments where the shape of the original image is preserved?
I need this because I'm trying to combine all the segments back to a numpy array, and save it in a different format like .nii.gz, where I need the dimensions of the combined output to be the same as the original dicom input.