Looking again at your description, it appears that you might be trying to resample one slice with another slice. This is generally a bad idea because sampling a 2D surface in a 3D space often causes the sampling to miss. A better approach is to create a single slice, transform it to the location of the other slice(s), and then resample the original volume in the place of the new slice.
I describe that in more detail here: plot difference between two slices