Convert mha file format to NIfTI

mha_to_nii.py

#/usr/bin/env python
# -*- coding: utf-8 -*-
"""
nii_to_tif

convert all mha files in a directory to nifti

Author: Jacob Reinhold (jacob.reinhold@jhu.edu)
"""

import argparse
from glob import glob
import os
import sys

import itk


def arg_parser():
    parser = argparse.ArgumentParser(description='convert all mha images in a directory to nifti')
    parser.add_argument('img_dir', type=str)
    parser.add_argument('out_dir', type=str)
    return parser


def split_filename(filepath):
    path = os.path.dirname(filepath)
    filename = os.path.basename(filepath)
    base, ext = os.path.splitext(filename)
    if ext == '.gz':
        base, ext2 = os.path.splitext(base)
        ext = ext2 + ext
    return path, base, ext


def main():
    try:
        args = arg_parser().parse_args()
        fns = glob(os.path.join(args.img_dir, '*.mha'))
        if len(fns) == 0:
            raise Exception(f'Could not find .mha files in {args.img_dir}')
        for fn in fns:
            print(f'Converting image: {fn}')
            img = itk.imread(fn)
            _, base, _ = split_filename(fn)
            out_fn = os.path.join(args.out_dir, base + '.nii.gz')
            itk.imwrite(img, out_fn)
            print(f'Saved to: {out_fn}')
        return 0
    except Exception as e:
        print(e)
        return 1


if __name__ == "__main__":
    sys.exit(main())

I get this error:

"File "mha_to_nii.py", line 41
    raise Exception(f'Could not find .mha files in {args.img_dir}')
                                                                 ^
SyntaxError: invalid syntax"

do u know what could have gone wrong?

@shahrzad-shapoori This script requires python 3.6+. You are probably receiving the error because of the f-string. Either change that to a .format or whatever or update your python version. If you still receive the error, please report back with your python version number and the exact error message if it is different.

Thanks! I upgraded my Python and it worked :-)