The windowless, cinder block room is quiet and cold at the VA-BU-CLF Brain Bank in Jamaica Plain.

Dr. Ann McKee gently lifts the brain of a former NFL player who died in his 40s onto the stainless steel operating table.

“This is a seriously small brain for a very large man,’’ she said. Then with a long knife and a steady hand, she slices into the tissue and soon finds gaps that shouldn’t be there.

These are all signs of chronic traumatic encephalopathy (CTE), a progressive degenerative disease of the brain caused by repeated blows to the head.

Although tau protein tests will be taken to confirm this, McKee, chief of neuropathology at the VA Boston Healthcare System and director of BU’s CTE Center, is confident this player has CTE.

“First of all, it’s very damaged,’’ she said. In fact, the odds are overwhelming that she’s right.

Of the deceased NFL players who donated their brains for research, 99 percent were diagnosed with CTE, according to a study she co-authored and was published in the Journal of the American Medical Association on July 25. That’s 110 out of 111 former NFL players. Researchers acknowledge that those numbers are biased because families have donated brains of those who were already displaying signs of CTE.

The distinguished scientist has spent decades examining brain tissue of former football, hockey, and soccer players, as well as war victims of bombings. She’s trying to solve the mysteries of CTE, for which there is no cure or treatment. Currently CTE cannot be diagnosed until after death. It’s especially upsetting when she meets future donors.

“I feel like Dr. Death. I do,’’ she said. “I just feel so helpless.’’ She admits it is very stressful. She has trouble sleeping at night.

McKee, 63, grew up outside Green Bay, Wis., the youngest of five children. She and her family loved football. Her father and four brothers played college football. She played in touch football games with them. Her brothers would block for her and urge her to somersault over them. “I never got hurt,’’ she said.

She watched football every weekend. She was a Cheesehead. Her heroes were Bart Starr, Paul Hornung, and Ray Nitschke, then Brett Favre and Aaron Rodgers. She attended a few games at an icy Lambeau Field in high school.

“It was a temple,’’ McKee said.

But after years of documenting damaged brains, the joy of watching football faded.

“I can’t say I love football anymore, ’’ she said. This year was the first time McKee didn’t watch the Super Bowl.

“I’ll tell you the reason I stopped. It was September of this [past] year. We got the brain of this kid, 13 years old. He was playing football and he just had this massive traumatic brain injury.

“He had the kind of injury you would have if you got into a motor vehicle accident. If a truck hit you. It just sort of speaks to the severity of the injury. It looks like they are shielded from it. They’ve got these helmets and these pads and look larger than life — even these little kids — but the brain is fragile. You get hit the wrong way and it can end your life.

“And I thought, I just can’t do this anymore. I just can’t.’’

So she stopped watching football.

“For a long time, you compartmentalize, you watch football, you get sucked in, it’s fun,’’ McKee said. “You can forget the research, but the kids are the hard part, the really hard part, because you know they just had everything in front of them. Everything. And now that mother is just devastated.’’

Her job is time-consuming and emotionally taxing. It wears her down.

“I think it’s definitely taken a toll on my family,’’ said McKee, who has three adult children. “It’s taken a toll on me. I can’t do half the stuff I used to like to do.

“I used to garden. I used to be a lot more active. I used to take care of my house. I gave all that up. I gave up cooking . . . I used to do a lot of things I can’t do anymore because I don’t have time.’’

Even when she takes a vacation, she’s working on a paper. She doesn’t get to see friends much.

“Like if they’re having a party or something, I’m mostly there, but there’s a part of me that’s not there,’’ she said. “That’s got to go back to work. I’ve just got so much work to do, I’ve just got to keep going.’’

McKee, who started out as an art major at the University of Wisconsin, still makes time for painting. “That’s the one thing that helps me,’’ she said. “I do really enjoy that.’’

The tau protein patterns that show when a brain has CTE look like art, she said.

Her painting is only an occasional release, however. Soon, she’ll be back at work, examining brains and perhaps having to connect a slide to a grieving family.

Such was the case of Patrick Risha, a former high school football star and Dartmouth linebacker who took his own life in 2014. Risha’s family donated his brain to the VA-BU-CLF Brain Bank, and McKee diagnosed CTE. Karen Zegel, Risha’s mother, started the Patrick Risha CTE Awareness Foundation to help prevent CTE in young athletes and military members.

“Dr. McKee shows a lot of compassion for those families who have lost loved ones to CTE,’’ Zegel wrote in an e-mail. “She has made it her life’s work to discover how the disease is caused and more importantly try to prevent it, especially in children. She is raising the alarm for precaution in kids, against huge forces to discredit her work. She is a true crusader with quiet dignity and resolve to do the right thing.’’

McKee has learned to deal with those “huge forces.’’ Her research has made enemies. “Sports leagues, doctors who work for sports leagues, scientists who don’t believe the work,’’ she said. “You name it. There are a lot of them.’’

What’s especially difficult, McKee said, is interacting with the players.

“I just feel so bad,’’ she said. “I wish there was something I could say. I wish there were some optimistic path that we could follow. I wish the stats weren’t the stats. I mean, I am wishing these guys would live really healthy lives, and it really bothers me.’’

McKee became friends with former New England Patriots and Philadelphia Eagles fullback Kevin Turner, who agreed to donate his brain in 2010 and died in 2016 of ALS, triggered by acute CTE.

“Just the salt of the earth,’’ McKee said. “One of the nicest guys on the earth.’’ He also was diagnosed with one of the worst cases of CTE she has seen.

She remembers Turner asking her if his two sons should play football.

“I’m thinking, are you kidding?’’ she said. “Why are you asking this? It’s obvious. Here you are in your 40s and you have this motor neuron disease and it’s robbing you of your life and you’re asking me this question? Then six months later I hear that his kids are playing football. His kid plays for Clemson; I guess he’s a very good player . . . I just don’t get it.’’

Nolan Turner is a redshirt freshman safety this season for Clemson, the defending national champion.

What’s needed, McKee said, is increased education strategies and solutions.

“You need to keep your head out of the game,’’ she said. But even that might not be enough, she warned.

“The truth is, even if you don’t use your head when you play you’re still getting these tremendous blows,’’ she said. “Back and forth, even quarterbacks when they get sacked are getting tremendous blows because it’s just a lot acceleration, deceleration.’’

She sympathizes with Giselle Bundchen, who recently said that her husband Tom Brady has suffered concussions.

“Tom achieved everything he could have ever achieved in football. I can see her point,’’ McKee said. “Why take any more risk? I see that and think that makes sense.’’

Her advice is simple.

“It’s a dose exposure,’’ McKee said. “The sooner he quits, the better. The good thing about Tom is he started playing late. I think his father said he didn’t start to play until he was in high school. That’s good.

“He loves the game, right? They all say that. They love the game. I think they have a sense that they are invincible. And look, they’re pretty amazing. They’re incredibly fit, they do amazing physical things, so there’s a sense that they’re special . . . but the problem is we’ve just seen so many players with it.’’

She also called on Patriots owner Robert Kraft to do more.

“He could embrace this research,’’ McKee said. “He’s a billionaire. He could do a lot to help his players.’’

McKee doesn’t want football to be banned.

“No, I don’t think banning things is the way to address this,’’ she said. “What I really want is for people to come together collectively and try to solve this problem . . . so we don’t have kids being cut down with the ramifications of this disease.’’

But if McKee had young children, she wouldn’t let them play football. “That would be the choice I would make,’’ she said. “But I don’t want to make that choice for everyone. If football is your passion in life and you would rather play football for 20 years and have a shortened life span, that’s your choice.’’

McKee doesn’t think youth tackle football is a good idea, either. “Frankly, I think it should be no football until you’re physically mature,’’ she said. “Until you’re big, strong, and your muscles have developed.’’

She began her research in the field in 2003 on the brain of a war veteran. After that, she got the brain of a boxer, and then John Grimsley, a former NFL linebacker. It was a revelation.

“I saw this brain and it was like, ‘Oh, my God.’ It was shocking,’’ she said. “Now looking back naively, we thought we’ve got to tell the NFL because they’ll be so concerned, they’ll want to get to the bottom of this.’’

McKee laughs and shakes her head.

“Well, yeah, it was naive,’’ she said. “But it’s like you discover a problem and you think you’ve got to alert the authorities.’’

The NFL invited her to league headquarters in New York on May 19, 2009, to present her work to their Mild Traumatic Brain Injury Committee, formed in the mid-1990s at the request of then-commissioner Paul Tagliabue.

“I was nervous. I didn’t want to go. I was intimidated,’’ McKee said. “They were like, ‘What is she doing here? Is there a doctor in this room, because I don’t know what she’s doing?’ It was really sexist. You could feel it. I feel like if they had tomatoes, they would’ve thrown them.’’

But the NFL eventually did donate $1 million to fund CTE research and recently issue a statement praising the researchers’ new study. The league also agreed to pay $1 billion to an estimated 20,000 players in a settlement.

Recently, the NHL unsuccessfully went to court to get records for the BU CTE Center for its defense in a lawsuit by former players.

McKee said it would take 13 years to honor that request. A US District judge in Minnesota ruled that it was “ an overwhelming burden.’’

Despite the overwhelming task and the stress, McKee isn’t quitting.

“I won’t ever get to stop working on this until I die,’’ she said. “I’m sure of it.’’

Stan Grossfeld can be reached at stan.grossfeld@globe.com.