I am a little bit confused about how labelmap indices are determined after the segmentation->Label map conversions. I was under the impression that it was the order of the segments. Am I mistaken? Because in the screenshot below for both converted volumes the skull segment is the first in the segmentation, but it got index number of 1 in the one labelmap and the 2 in the other.
I am using the right-click convert visible Segments to labelmaps option in the data module. Is there another way to make sure label indices match the order.