Thanks for the pointers Mike. So it sounds like there is no way to preserve the pixel identities (with gaps/jumps between pixel values) when I convert from segments back to labelmaps? Can you confirm that it just rebuilds the pixels from the list, starting at the top as 1, and counting up 1 pixel per group. I think this is how it’s behaving but it would help to be certain, so I can relabel in python as you suggest. I am managing 75 labels, so my process is prone to error.
Maybe a whole different problem: but at some point I want to convert back to 8 bit, and suspect there will be low-depth rounding errors that merge the pixel classes. Can I create an 8 bit labelmap file?
Still, does anyone know of a way within slicer to convert from segments to labelmaps and preserve the gaps in assigned pixel values?
I feel like this discussion is related: