Nerves do not use electricity as such to communicate. The signals is transferred within the cell as charged ions and between the cells as chemicals. In addition EMP charges have a hard time entering under the skin so your nerves will be relatively protected. However the danger of EMP towards the human body is more with regards to burns caused by sparks. These sparks may cause some damage to your nervous system but mostly to the longer nerves in your spine and extremities and not the ones in your brain. We know from people who have survived big EMP blasts at very close ranges that the brain is generally unaffected by it.
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