Troubleshooting: Imported segmentations appear in a wrong location

Dear 3D Slicer Community,

I am currently facing problems with my segmentations. After exporting them as a Labelmap (-label) and reimporting they appear a few slices lower than expected (comparison of original and reimport as images attached)

Has anyone faced the same problem? Many thanks in advance for your help.


It seems that you have highly anisotropic volume (large space between slices) and the volume axes are not aligned with default slice view axes (because before recent Slicer-4.13 versions, by default slice view axes were aligned to anatomical axes and not to the volume axes).

You can either hit “Rotate to volume plane” button in the slice view controller or use latest Slicer Preview Release (because that aligns slice views with volume axes by default).