If your image is highly anisotropic then it means that you won’t be able to fully utilize the high resolution information within the image slice, because you just miss so much information between the slices.
You can find more information here: How can I import in the same volume 3 DICOM files of the same volume - #2 by lassoan
If your goal is not to reproduce the missing information (which is impossible), and it is OK to have sharp edges along two axes, while smooth interpolation along the third one, then you can use morphological interpolation to fill in the gaps. To achieve this, resample the input volume to be isotropic as @muratmaga suggested above, but then only segment at the middle of the original slices. To do that, you can choose your original sparse volume as background volume and use Scissors effect to fill a thin slice (Operation: Fill inside; Slice cut: symmetric 0.1mm or whatever the resolution along the high-resolution axis). You will end up with thin slices with large gaps between them. When you are finished with your segmentation, use Fill between slices effect to fill in the gaps.
Before “Fill between slices”:
After “Fill between slices”:
