An example script to convert Nifit segmentation from value range (0, 1, 2) to (0, 2) by dropping label 1.

convert_to_tumor_only.py

from argparse import ArgumentParser

import numpy as np
import nibabel as nib

def convert(src, dst):
    seg = nib.load(src)
    
    seg_data = np.asanyarray(seg.dataobj)
    seg_data = np.where(seg_data == 2, 1, 0).astype(np.uint8)
    
    out = nib.Nifti1Image(seg_data, seg.affine)
    nib.save(out, dst)
    
if __name__ == "__main__":
    parser = ArgumentParser()
    parser.add_argument("--src", "-s", type=str, help="Source Nifti segmentation file.")
    parser.add_argument("--dst", "-d", type=str, help="Output Nifti file.")
    
    args = parser.parse_args()
    convert(args.src, args.dst)