Hello @a10227,
This has to do with the non-isotropic pixel spacing in your data. This is very common in medical imaging and microscopy. ITK-SNAP accounts for this during display. In your display you just retrieved the pixels without taking spacing into account. This is discussed in the Fundamental Concepts page and in this Jupyter notebook. The latter includes a function make_isotropic which you can use to enable correct display of your images in a notebook.