"The area of the brain initially identified as being affected was the brain stem, the part that controls balance, coordination, vital functions  like breathing & heart rate, consciousness, and many nerves controlling eye and facial muscles movements and sensation. As that part showed improvement, we (the Veterinarians at A&M) were able to identify other areas that had been affected.  This primarily was the cerebral cortex or forebrain, the large part of the brain that processes information from all areas of the body, controls conscious/voluntary movements, arousal level and consciousness, impulse control, and cognition (thinking, personality, etc.) This explains why we can now recognize things like the cortical blindness, the deafness, the abnormal mentation (mental activity) and activity patterns, the licking/teeth grinding, etc. This is also the part of the brain that causes seizures, so the earlier seizures told us we had damage in the forebrain. Other parts of the brain were probably also affected, such as the limbic system, and amygdala, which controls emotions like fear, anxiety, aggression, and the hypothalamus, which controls temperature, as well as appetite and thirst centers. So each day may find us dealing with new problems. The fact that the brainstem has shown significant improvement gives us hope that each of these other parts of the brain will show similar improvement.  Like we discussed, this may very well take several weeks to months for a full recovery, and she may always have some residual problems. Basically, we are waiting for the brain to rewire itself around the damaged areas. Because we probably all don't use even a portion of our brain capacity, the brain is capable of recruiting and reconnecting neurons (brain cells) to do the jobs lost by the  hypoxia."