NRRD segmentation to Nifti using Slicer Python API

nrrd2nifti.py

"""

Usage:
Slicer --python-script nrrd2nifti.py --no-splash --no-main-window -- Segmentation.seg.nrrd

"""
import os
import sys

if len(sys.argv) == 1:
    print("Usage: nrrd2nifti.py <nrrd file (.nrrd)>")
    sys.exit(1)

if len(sys.argv) == 2 and not sys.argv[1].endswith(".nrrd"):
    print("Usage: nrrd2nifti.py <nrrd file (.nrrd)>")
    sys.exit(1)

segmentation_filename = os.path.abspath(sys.argv[1])
segmentationNode = slicer.util.loadSegmentation(segmentation_filename)
labelmapNode = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(labelmapNode)

slicer.modules.segmentations.logic().ExportAllSegmentsToLabelmapNode(
    segmentationNode, labelmapNode, slicer.vtkSegmentation.EXTENT_REFERENCE_GEOMETRY
)

output_file = segmentation_filename.replace('.nrrd', '.nii.gz')
slicer.util.saveNode(labelmapNode, output_file)

print('Segmentation saved to', output_file)

sys.exit(0)