Already by 1835, the reasons for calling the Salish people in Montana, Flathead, and for calling the Ni-Mii-Puu, Nez Perce, had been forgotten. At least Samuel Parker could not discern the reasons during his travels.
I was disappointed to see nothing peculiar in the shape of the Flathead Indians, to give them their name. Who gave them this name, or for what reason, is not known. Some suppose it was given them in derision for not flattening their heads, as the Chenooks and some other nations do, near the shores of the Pacific. It may be so, but how will those, who indulge this imagination, account for the Nez Perces being so called, since they do not pierce their noses. That those names are given by white men, without any known reason, is evident from the fact, that they do not call each other by the names which signify either flat head or pierced nose.Many years ago, when I was a graduate student, my friend Otis Halfmoon told a class that I was teaching that the name Nez Perce probably stems from the Ni-Mii-Puu sign language term for themselves in which they pointed from right to left across their face to indicate that they had crossed over between those mountains. He speculated that someone thought they were piercing their noses with the gesture, adding that he is glad they did not think it was an act of cleaning their noses.
Samuel Parker, Journal of an Exploring Tour Beyond the Rocky Mountains (1838), 76.