Responding to my own question, it's not possible to analyze the images within outputing them, because the main activity used by the ARToolkit inherits from AndARActivity, that inherits from activity, so they need a layout.
The solution that I'm using is:
-I implement 2 apps, the first one take images from the camera and make the necessary analyse and the second one use the data from the first one
-I implement a osc transmission for sharing data between apps
-I force the first app to keep runing, soo it keep getting the camera data while the second starts
I think it's not the best option, but I need results and that way it works.