How to convert Multiple png or Jpeg images into one nifti image by python3?

Question

I have 191 different png images.

How can I convert them into one 3d nifti image?

Answer 1

Here's a SimpleITK python script that can read in a stack of PNG images and output a 3d Nifti image:

import SimpleITK as sitk
import glob

file_names = glob.glob('*.png')
reader = sitk.ImageSeriesReader()
reader.SetFileNames(file_names)
vol = reader.Execute()
sitk.WriteImage(vol, 'volume.nii.gz')

The script assumes that the glob gets the file names in the proper order. Also the 3-d volume created will have uniform spacing in X, Y, and Z. If the Z spacing is not the same as X and Y, you can call vol.SetSpacing with whatever the spacing values should be.