Reading and converting DICOM images using SimpleITK

dicom_conversion.py

import os
import SimpleITK as sitk

input_dicom = '/path/to/input/dicom'
output_dicom_dir = '/path/to/output'
# create the folder output_dicom_dir
series_IDs = sitk.ImageSeriesReader.GetGDCMSeriesIDs(input_dicom)
if not series_IDs:
  print("ERROR: given directory \"" + input_dicom + "\" does not contain a valid DICOM series.")
  sys.exit(1)

if len(series_IDs) > 1:
  print(f"WARNING: more than 1 DICOM series was found in the folder: {input_dicom}")

itk_images = []
for i in range(0,len(series_IDs)):
  series_file_names = sitk.ImageSeriesReader.GetGDCMSeriesFileNames(input_dicom, series_IDs[i])
  series_reader = sitk.ImageSeriesReader()
  series_reader.SetFileNames(series_file_names)
  series_reader.MetaDataDictionaryArrayUpdateOn()
  series_reader.LoadPrivateTagsOn()
  image_dicom = series_reader.Execute()
  
  itk_images.append(image_dicom)
  sitk.WriteImage(image_dicom, os.path.join(output_dicom_dir, series_IDs[i] + ".nii.gz"))

## do fancy processing with itk_images