@tueboesen Yes, exporting the Segmentations to Labelmap volume nodes is a good way to work with them from numpy, but keeping track of the mapping between label numbers and segment IDs requires some care.
A good way to address this is to always use a color node to specify the mapping when going back and forth. You’ve probably been looking already, but the script repository has a lot of good examples, and if you search for color you’ll see how they are used for this purpose.
https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#segmentations
Also for this operation you can say to just mrml, vtk, numpy, and the segmentation logic. Mixing in sitk and qt may just make it harder to tell what’s going on.
hope that helps,
Steve