[dvanvoorst]

I'm assuming that you mean that part of the target box is missing in the image...
Do you have your light source close to the camera? (it should be) Ideally you'd use an LED light ring around the camera. That should provide a very clean reflected image of the target.
Are you using the NI Vision Assistant to capture and test the image and various filters? It makes it very easy to capture images and test out different filters.