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')