For my application, I want to interpolate between two images(CT to PET). Therefore I map between them like that:
[X,Y,Z] = ndgrid(linspace(1,size(imagedata_
I'll let to someone else answering the question, but I think that you're asking the wrong one. I lack context of course, but at first glance Matlab isn't the right tool for the job.
After you've done that registration step, you could export the resulting images (now of identical size and spacing), and continue with your interpolation in Matlab if you wish (or with the same tools).