stl - Python: how to save individual slices from segmented .nii.gz file

Question

I am performing a vertebrae segmentation task and I've output multiple segmentation.nii.gz files. Each of the segmented niftis files contains different segments (segment 1,2,3...), corresponding different vertebraes labelled in the file.

My question is how to save the individual slices from each segmented nii.gz file? So the desired output should be look like following (which is generated by 3DSlicer)

desired output of each individual slices from the segmentation niftis file

Input: one segmented niftis file including slices for each vertebrae (nii.gz)

Desired output: individual '.stl'/'obj'/'nii'/'nrrd' files for each of the slices

I have tried the 3DSlicer python transcripts, it is too complex to either install and operate so it is not desired to deliver. I am not sure whether SimpleITK could work in this.

Thank you in advance for your time and effort.

question from:https://stackoverflow.com/questions/65913683/python-how-to-save-individual-slices-from-segmented-nii-gz-file

Answer 1

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