Hi Thorsten,

Thank you for the quick and helpful reply. I had a closer look at my data with your comments in mind, in most of channel the registration is almost perfect. There are a few bits where the registration isn't though. If i then look at these bits in the affine registered data I noticed that in these cases the structures where quite far apart. So it would appear that the warping isn't able to bridge the gap and register all the way.

As you guessed correctly I am using the munger. To loosen the warping should I be changing the values for Jacobian constraint and rigidity weight then ? It would be great if Greg ( or anyone else) could give some advice on how to adapt the munger. 

Best,

Pieter