Reference geometry is not defined for a new segmentation, only if you edit a segment in Segment Editor with a master volume specified. In that case the resolution will be 1x1x1mm^3.
In the current version the only way to specify the geometry in such a case is like this:
- Make the closed surface the master representation. You can do that in the Representations section in the Segmentations module
- Long-click the Create button in the row of Binary labelmap
- Click the only path in the top half of the popup window
- Click the “Set geometry from volume” button in the bottom half, in the row of Reference image geometry
- Set the volume you want the geometry to come from
We should really rework the reference geometry part of the user interface, but it has never reached the top of the priority list up to this point. At the least probably we should allow selecting a reference volume in the Advanced section of the Export/import panel when we import models. Currently it’s only enabled when exporting labelmaps. @kayarre and @lassoan what do you think?