Landmark registration malfunction


I am using the Landmark Registration module to perform registration of a post mortem ex vivo hemisphere on MRI on a normal brain MRI atlas to correct for the distortion that occurs due to absence of the skull in post mortem ex vivo scanning. As I am using brains with Alzheimer’s disease, the brains show a lot of atrophy and a lot of distortion.

After performing the landmark registration, it looks like this:

To save the transformed hemisphere, I need to use the Harden transform button. However, when I click it the transformation changes and the registration becomes totally inaccurate.

Could you explain what the Harden transform button does exactly? Any ideas how to avoid this change of transformation?