sitk_nrrd_nii.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Aug 14 11:13:32 2020

@author: wangmeiqi
"""


import os
import nrrd
import nibabel as nib
import numpy as np
import SimpleITK as sitk 


#where you want to save ouput files
save_route = '/Users/wangmeiqi/code_and_data/HCC/ntuh/hcc_ntuh_niigz_1012'

#where are your input files
main_route = '/Users/wangmeiqi/code_and_data/HCC/ntuh/HCC_labeled'

filename = 'temp'

route = os.path.join(main_route, filename)

dir_ = []

path = []


for root, dirs, files in os.walk(route):

    for file in files:
        
        if file != '.DS_Store':
            
            filename = os.path.join(root, file)
            
            read_img = sitk.ReadImage(filename)
            
            name = root.split("/")
            
            output_path = os.path.join(save_route, file[:-5] + '_' + name[-1] + '.nii.gz')
            
            sitk.WriteImage(read_img,  output_path)
            
            print("fininshing: " + output_path)