Thanks ever so much all of you.
Apologies, I m not getting this right.
In segment editor , I add a segment, then with scissors I mark my area of interest and select the option fill outside. Then I add s mask to mask the filled segment. Then I try to register the unmasked bit of the volume with elastix. But this registers the whole volume that’s been masked too, not only the unmasked bit.
Second option I tried was again, went to segment editor, Add segment button then use scissors with the erase outside option. Nothing happened. But if I use the fill outside option it fills.
If I do this to an already created segment/ stl scissors can delete part of the segment.