TMS can be combined with various forms of brain imaging. Studies like this have not only allowed us to map brain function but also brain circuitry--and not only in the cortex--but deep inside the brain as well.
The part of the brain responsible for the antidepressant effects of TMS is the left dorsolateral prefrontal cortex. This is a small but important area concerned with executive function.
This part of the cortex is involved with high level organization and planning. You're using this part of your cortex right now to focus your attention and to hold new information in your working memory while you process it and incorporate it into what you already know. This is the same part of your brain that allows you to watch what you're doing so you don't make a fool of yourself in public.
The dorsolateral prefrontal cortex has extensive connections throughout the cortex as well as with deep, sub-cortical nuclei. And by modulating the circuits connecting them, TMS alleviates the symptoms of major depression.
One way to think about it is like this: antidepressants work their way up the ladder of the central nervous system. By altering neurotransmitter levels at the synaptic cleft, they alter communication between individual neurons, which changes the firing pattern in larger circuits, which, in turn, modulates the activity of entire networks.
In TMS, the therapeutic sequence moves in the opposite direction--from network...to circuit...to neuron...to synapse.
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