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Spacing in file header #14
Description
Hi,
I would like to report a possible problem with the "spacing" value in the header of the nifti files produced by DiffTumor.
I am using the HuggingFace version of DiffTumor. I executed it and it produced correct segmentation outputs. However, the value of spacing in the output nifti files for liver do not seem correct.
Code:
import nibabel as nib
organ='case00001/predictions/liver.nii.gz'
tumor='case00001/predictions/liver_tumor.nii.gz'
ct='case00001.nii.gz'
spacing1=nib.load(organ).header.get_zooms()
spacing2=nib.load(tumor).header.get_zooms()
spacing3=nib.load(ct).header.get_zooms()
print('Spacing organ:',spacing1)
print('Spacing tumor:',spacing2)
print('Spacing ct:',spacing3)
v1=nib.load(organ).get_fdata().shape
v2=nib.load(tumor).get_fdata().shape
v3=nib.load(ct).get_fdata().shape
print()
print('Voxels organ:',v1)
print('Voxels tumor:',v2)
print('Voxels ct:',v3)Output:
Spacing organ: (1.5, 1.5, 1.5)
Spacing tumor: (0.703125, 0.703125, 1.25)
Spacing ct: (0.703125, 0.703125, 1.25)
Voxels organ: (512, 512, 347)
Voxels tumor: (512, 512, 347)
Voxels ct: (512, 512, 347)
Expected output: the organ spacing should match the CT spacing
Spacing organ: (0.703125, 0.703125, 1.25)
Spacing tumor: (0.703125, 0.703125, 1.25)
Spacing ct: (0.703125, 0.703125, 1.25)
Voxels organ: (512, 512, 347)
Voxels tumor: (512, 512, 347)
Voxels ct: (512, 512, 347)
Could you please verify if you can reproduce this bug? And if other organs are affected by it?
Thanks!
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