Our neuro-pathways are reinforced by our thoughts. For example if you talk about the same problems again and again, only those experiences are reinforced and strengthened. Our neuro-pathways shape perception of everything. To any event, our first reaction may be of a two year child, then our reaction is tempered by our beliefs, experience and conditioning. So doing meditation, focusing on all pleasant feelings, focusing on beauty, inclusiveness etc. simply strengthens those pathways and allows us to feel them more deeply. Constant self-doubt strengthens that pathway etc. Any thought we indulge and involve ourselves in strengthens that pathway. The neural pathways maybe what we call Karma. When its on autopilot, its a self created system that has taken over. We need to deconstruct our real self one by one from this universe of neural pathways which is what is done in meditation.
The amygdala has highway pathways to the cortex, however the cortex has only sinewy lines going back to the amygdala. Similarly most of our gut brain in used for digestion and extraction of nutrients.