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sarthakpati/read_and_write_nifti_using_simpleitk.py

Last active May 20, 2021 15:17
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read_and_write_nifti_using_simpleitk.py
import SimpleITK as sitk
# read image
inputImage = sitk.ReadImage('/path/to/input.nii.gz')
# get result in the form of a numpy array
npa_res = my_algorithm(sitk.GetArrayFromImage(inputImage)) # my_algorithm does something fancy
# Converting back to SimpleITK (assumes we didn't move the image in space as we copy the information from the original)
result_image = sitk.GetImageFromArray(npa_res)
result_image.CopyInformation(inputImage)
# write the image
sitk.WriteImage(result_image, '/path/to/result.nii.gz')
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