Fix ITK direction for nnU-Net

change_itk_direction.py

# Set ITK direction from image1 to image2
#
# Usage:
#	python change_itk_orientation.py <image1> <image2>
# Example:
#	python change_itk_orientation.py sub-001_T1w.nii.gz sub-001_T1w_seg.nii.gz
#
# Jan Valosek
#

import sys
import SimpleITK as sitk

# Read images
image1  = sitk.ReadImage(sys.argv[1])
image2 = sitk.ReadImage(sys.argv[2])

print(f'image1 direction:\n{image1.GetDirection()}')
print(f'image2 direction:\n{image2.GetDirection()}')

# Change image2 direction
print('changing image2 direction...')
image2.SetDirection(image1.GetDirection())
# Save updated image2
sitk.WriteImage(image2, sys.argv[2].replace('.nii.gz', '_updated_dir.nii.gz'))

read_itk.py

# Read ITK origin, spacing, direction, and size
# Details: https://simpleitk.readthedocs.io/en/master/fundamentalConcepts.html
#
# Usage:
#	python read_itk.py <image1> <image2>
# Example:
#	python read_itk.py sub-001_T1w.nii.gz sub-001_T1w_seg.nii.gz
#
# Jan Valosek
#

import sys
import SimpleITK as sitk

# Read images
image1  = sitk.ReadImage(sys.argv[1])
image2 = sitk.ReadImage(sys.argv[2])

ori1, spacing1, direction1, size1 = image1.GetOrigin(), image1.GetSpacing(), image1.GetDirection(), image1.GetSize()
ori2, spacing2, direction2, size2 = image2.GetOrigin(), image2.GetSpacing(), image2.GetDirection(), image2.GetSize()

print("origin:")
print(ori1)
print(ori2)

print("spacing:")
print(spacing1)
print(spacing2)

print("direction:")
print(direction1)
print(direction2)

print("size:")
print(size1)
print(size2)