nifti file header and image

save_new_nii.py

# https://bic-berkeley.github.io/psych-214-fall-2016/saving_images.html

def array_to_nii(array_3d, scan, output_path):
    '''
    Same affine and same header
    convert mask only contains 0 and 1, so convert data type to uint8
    :param array_3d:
    :param scan:
    :param output_path:
    :return:
    '''
    data_type = np.uint8
    array_3d = array_3d.astype(data_type)
    nii_img = nib.Nifti1Image(array_3d, affine=scan.affine, header=scan.header)
    nii_img.set_data_dtype(dtype=data_type)
    nib.save(nii_img, output_path)