Arguably understanding how the cortex operates is one of the biggest challenges that faces science, but what is being done to advance our understanding? Although we have started gathering a vast amount of detailed information about the components that make up the cortex, one of the next challenges is to place all of this information back into the context of the behaving animal: For it is how the vast interconnected circuits of the cortex are used by the animal that will ultimately lead to the greatest understanding of brain function. Motivation underlies the performance of self-determined behavior and is fundamental to decision making, especially with regard to seeking food, mates, and avoiding peril. As many decision making based behaviors in rodents involve a combination of head movements, eye movements, vestibular driven neuronal activity and active sensing of the environment to guide the behavior, studying the freely moving animal is of advantage. This lecture will be broken down into three topics that we are currently working on: Multiphoton calcium imaging of neuronal populations in the freely moving rodent and the accurate extraction of spikes, head and eye tracking during decision making tasks in the freely moving mammal, and finally how spike timing dependent plasticity rules can change the spiking of visual cortex neurons. I will present results from our lab showing how different freely moving mammals have distinct eye movement strategies that are of major evolutionary benefit.