This 2014 rodent study showed one aspect of how stress changed the amygdala. Stress didn’t allow normal matching of neuronal activity to increased blood flow:

“Chronic stress — which is a contributing factor for many diseases — impairs neurovascular coupling in the amygdala..

Neurovascular coupling (is) the process that matches neuronal activity with increased local blood flow.”

http://www.pnas.org/content/111/20/7462.full “Stress-induced glucocorticoid signaling remodels neurovascular coupling through impairment of cerebrovascular inwardly rectifying K+ channel function”