BEDFORD, Mass. — In a small room banked by refrigerators of preserved brains, a pathologist held a specimen up to the light in frank admiration. Then it was time to cut — once in half and then a thick slice from the back, the tissue dense and gray-pink, teeming with folds and swirls.

It was the brain of a professional running back.

“There,” said Dr. Ann McKee, the chief of neuropathology at the V.A. Boston Healthcare System and a professor of neurology and pathology at Boston University’s medical school, pointing to a key area that had an abnormal separation. “That’s one thing we look for right away.”

Over the past several years, Dr. McKee’s lab, housed in a pair of two-story brick buildings in suburban Boston, has repeatedly made headlines by revealing that deceased athletes, including at least 90 former N.F.L. players, were found to have had a degenerative brain disease called chronic traumatic encephalopathy, or C.T.E., that is believed to cause debilitating memory and mood problems. This month, after years of denying or playing down a connection, a top N.F.L. official acknowledged at a hearing in Washington that playing football and having C.T.E. were “certainly” linked.

His statement effectively ended a very public dispute over whether head blows sustained while playing football are associated with the disorder. But it will not resolve a quieter debate among scientists about how much risk each football player has of developing it, or answer questions about why some players seem far more vulnerable to it than others.