Convert nrrd to nii.gz

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Hello there!

For a special use case, I need all my data in nii.gz format. Right now, I have 200+ CT-Volumes plus segmentations both stores in .nrrd data format. I could open each of those volumes/segmentations in 3D slicer manually and store them as nii.gz, but I am looking for a way to script that problem, so I don’t have to do it 200 times.

Since I am a newbie to that topic, I do not know where to start and I was wondering if you have any good ideas/known libraries/ways to script that problem within 3D slicer or outside 3D slicer.

Thanks in advance!

2

These scripts were written for diffusion images but should work for other volumes.

dcm2niix should also work.

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3

Really easy to do in Python with SimpleITK.

import SimpleITK as sitk

img = sitk.ReadImage("your_image.nrrd")
sitk.WriteImage(img, "your_image.nii.gz")

fin

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