Thank you for introducing me to this amazing tool! I do have a few issues I am experiencing with registration in MADI3D that I was hoping you could identify.

1. When the brain I want to align needs to be Z-flipped to match the reference brain, I will Z-flip in Fiji and run CMTK registration that way. However the output is always heavily skewed when I do this, is there a reason why?

2. When alignment is successful I do get large voids in the earlier and later stack layers. Is there any way to remedy this issue. I have attached an example of what I am talking about below.

3. Finally I would like to mention that after running alignment to the reference brain the top part of the brain is not being pulled out to match the reference brain. Our brains have been slightly squised because of the slides so I was wondering if this is an issue that CMTK registration can fix or not.

Thank you once again!