load, create and save nifti image with nibabel

nibabel_basic_operations.py

from nibabel import load, save, Nifti1Image

# load main image
nii_path = path_to_nii_file
zmap = load(nii_path)
img_data = zmap.get_data()

# load anothor image to mask
mask_path = path_to_mask
mask = load(mask_path)
mask_data = mask.get_data()

# do masking 
masked_file = mask_data * img_data
# binarize it
masked_file = np.where(masked_file > 0 , 1, 0)

#save the new file out 
out = Nifti1Image(masked_file, header=zmap.header, affine=zmap.affine)
save(out, 'path_to/mask.nii.gz')