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I am using the sliver07 dataset and my task is to convert.mhd format images to .nii format. Following the answer of Medical Imaging Data - how to convert .raw/mhd to Nifti/nii, I was able to convert it for 1 image but now as I apply it for multiple images, it is not converting.

File module structure is this way:

  • scan
    • file1.mhd
    • file2.mhd

My code:

import glob
my_path='/content/drive/MyDrive/Datasets/sliver07/sliver07-training-scans/scan/'
files=glob.glob(my_path+'*.mhd')

# Scan from train
import SimpleITK as sitk
out = '/content/drive/MyDrive/Datasets/sliver07/sliver07-training-scans/trial/'

for i in range(len(files)):
        img = sitk.ReadImage(files[i]) 
        sitk.WriteImage(img, out + files[i] + '.nii')

But the code is executing without error but conversion is not done yet. What must be wrong?

AMANDEEP KAUR
  • 23
  • 8

1 Answers1

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Got it! The path was wrong

# Scan from train
  import SimpleITK as sitk
   out = '/content/drive/MyDrive/Datasets/sliver07/sliver07-training-scans/trial/'

  for i in range(len(files)):
       img = sitk.ReadImage(files[i]) 
       sitk.WriteImage(img,  files[i].replace('.mhd','.nii'))
AMANDEEP KAUR
  • 23
  • 8