Nefesh is the lower level of Light in the body but is the most important to sustain the life of a person. The Liver is the control center of the Nefesh in the body.
Ruach is higher and comes from Zeir Anpin. We achieve this additional light in this world by following the ways of the Torah with the general rule “Do good and avoid bad”. The Heart is the center for the Ruach.
Neshama is the highest level of Light that can be achieved in this world. Righteous people that already have the level of Ruach and act selflessly for the benefit of others, can achieve the level of Neshama. Since it’s the highest level, it connects to the brain.
The higher-level of the soul controls the level below it. Neshamah and Ruach can leave the person if he loses the righteous path. The level of Nefesh is removed only at the time of death, meaning when the heart stops and there is no blood circulation in the body.