Make affine matrix of a nifti file identity matrix.

nii_fix_affine.py

"Make affine matrix of a nifti file identity matrix."

import os
import nibabel as nb
import numpy as np

NII = "/path/to/tile.nii.gz"

nii = nb.load(NII)
data = np.asarray(nii.dataobj)

hdr = nii.header
hdr.set_sform(hdr.get_qform())
aff = hdr.get_qform()

img = nb.Nifti1Image(data, affine=aff, header=hdr)
basename, ext = nii.get_filename().split(os.extsep, 1)
out_name = '{}_{}.{}'.format(basename, "fixed", ext)
nb.save(img, out_name)

print("Finished.")