

def save_3D_nparray_nifti(np_matrix_3d, output_image, fname_atlas):
    img = nib.Nifti1Image(np_matrix_3d, np.eye(4))
    affine = img.get_affine()
    np_matrix_3d_nii = nib.Nifti1Image(np_matrix_3d, output_image)
    nib.save(np_matrix_3d_nii, output_image)
    sct.run(((('fslcpgeom ' + fname_atlas) + ' ') + output_image), verbose=0)

dataset/ETHPy150Open neuropoly/spinalcordtoolbox/dev/atlas/create_atlas/create_masks_csf_and_gm.py save_3D_nparray_nifti/VarMisuse@46/88 `affine`->`output_image`