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:
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?
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'))