Correct registration in Slicer output to Freesurfer

Hi all, for this project here, I am inputting into Slicer a brain image made in Freesurfer, namely the orig.mgz. Then I am managing manual segmentations done in Slicer using Segment Editor. Then I click on Export visible segments to binary labelmap and click on the resulting new labelmap export to file, and save as a .mgz file. When I use the freesurfer command:

tkmedit 1 orig.mgz -segmentation Slicerlabel.mgz, the Slicerlabel.mgz does not correct overlay with the orig.mgz.

(I know tkmedit is somewhat deprecated, but I think it wouldn’t overlay in freeview either)

Does anyone have any pointers on where to go?

If you haven’t already, you should try to use the SlicerFreeSurfer extension: