mha2niix.py

#!/usr/bin/python3.10
from pathlib import Path
import argparse
import SimpleITK as sitk

def main(folder: str, output: str | None):
    input_path = Path(folder)
    output_path = input_path if output is None else Path(output)
    output_path.mkdir(parents=True, exist_ok=True)
    for file in input_path.iterdir():
        img = sitk.ReadImage(file)
        sitk.WriteImage(img, output_path.joinpath(file.stem + '.nii.gz'), useCompression=True)
        print(f'[success] converted {file.name} to nii')

if __name__ == "__main__":
    parser = argparse.ArgumentParser('mha2nixi')
    parser.add_argument('folder', type=str)
    parser.add_argument('output', default=None, type=str)
    args = parser.parse_args()
    main(args.folder, args.output)