Nefesh HaChayim, Reb Itzele's Long Annotation

For that reason their combination in people is in three vessels: the brain, the heart and the liver. And they [emphatic] are the vessels of the soul-Neffesh, soul-Ruakh, and soul-Neshama in a person. And in each of the three vessels the three mothers (alef, mem and shin) express physically to demonstrate their powers in a variety of observable ways. Namely, in the vessel of the brain the combination of elements is recognized via thought. And as is made known in the Zohar, that according to how the four elements are combined in the vessel of the brain, that’s how the intellect will be revealed within it.