The NFL, which spent years criticizing researchers who warned about the dangers of football-related head trauma, has backed out of one of the most ambitious studies yet on the relationship between football and brain disease, sources familiar with the project told Outside the Lines.

The seven-year, $16 million initiative was to be funded out of a $30 million research grant the NFL gave the National Institutes of Health in 2012. The NFL has said repeatedly that it has no control over how that money is spent, but the league balked at this study, sources said, because the NIH awarded the project to a group led by Dr. Robert Stern, a prominent Boston University researcher who has been critical of the league.

In a news release announcing the study Tuesday morning, Boston University said the NIH would pay for the project but made no mention of the NFL. The study seeks to capture what has been described as the holy grail of concussion research: the ability to diagnose chronic traumatic encephalopathy, or CTE, in living patients.

Asked why the NFL did not want to fund the study, NFL spokesman Brian McCarthy on Monday referred questions to the NIH, writing in an email: "The NIH makes its own funding decisions." He did not respond to follow up questions. On Tuesday, McCarthy tweeted that the story was wrong.

The NFL's decision not to fund the Boston University CTE study delayed its announcement for months, and the issue ultimately reached the office of NIH director Dr. Francis S. Collins, according to sources. As late as this week, some officials held out hope the league would change its mind, but the NIH remained committed to funding the project regardless.

The Foundation for the NIH, a non-profit organization that partnered with the NFL to administer the grant, released a statement late Tuesday morning that "the NFL was willing to contribute to the Boston University CTE study headed by Dr. Stern." The statement did not specify under what conditions the NFL was willing to participate, and a spokeswoman did not respond to immediate follow up inquiries.

But sources told Outside the Lines that after Stern and Boston University passed a "scientific merit review" and received approval from an NIH advisory council of high-level experts last spring, the NFL raised objections to the selection. Dr. Walter Koroshetz, director of the NIH's National Institute for Neurological Disorders and Stroke, told Outside the Lines this week that he had asked the FNIH over a period of several months if the NFL would be providing funding for the study but never received a definitive response. He said he attempted to expand the study over the summer to include other researchers -- a proposal that might have satisfied the league. But the NIH ultimately decided to fund the study on its own.

The FNIH statement said the NFL's overall funding commitment "remains intact." The NIH, according to the statement, will seek applications for an another study on CTE next year using NFL funding, which "will double the support for research in this area."

When the NFL's "unrestricted" $30 million gift was announced in 2012, the NIH said the money came "with no strings attached"; however, an NIH official clarified the gift terms two years later, telling Outside the Lines that, in fact, the league retained veto power over projects that it funds. Koroshetz affirmed that this week.

Sources told Outside the Lines that the league exercised that power when it learned that Stern, a professor of neurology and neurosurgery at Boston University, would be the project's lead researcher. The league, sources said, raised concerns about Stern's objectivity, despite the merit review and a separate evaluation by a dozen high-level experts assembled by the NIH.

Stern, the director of clinical research for Boston University's Alzheimer's Disease and CTE centers, has a complicated history with the league. He once said NFL commissioner Roger Goodell inherited a "cover-up" from his predecessor, Paul Tagliabue. In October 2014, he filed a 61-page declaration opposing the NFL's settlement of a lawsuit in which thousands of former players accused the league of hiding the link between football and brain damage. Stern wrote that the settlement would deny compensation to many deserving players, including some of the most severely disabled.

Robert Stern, director of clinical research for Boston University's Alzheimer's Disease and CTE centers, has a complicated history with the NFL. Stephan Savoia/AP Images

Former San Francisco 49ers linebacker Chris Borland said a phone consultation with Stern in March sealed his decision to retire after his rookie season because of concerns about getting brain disease. Stern warned Borland that he might already have brain damage but also cautioned that the science was still in its infancy.

"I am a scientist, first and foremost," said Stern, who referred all questions about the project's funding to the NIH. "And as a scientist I have always and will always conduct research with complete impartiality. If I say things about the NFL or others that may sound negative, that has nothing to do with the impartiality of my science."

Dr. Ann McKee, a neuropathologist affiliated with Boston University and the U.S. Department of Veterans Affairs, recently received a $6 million grant that came through the NFL's 2012 donation to the NIH. McKee, like Stern, at times has criticized the league and has warned that the number of players with CTE is likely to be high.

Why the NFL, which has faced long-standing questions about its involvement in the science of concussions, would fund a project headed by McKee -- and not one led by Stern -- was not clear.

From 2003 to 2009, the NFL published its own research denying that football players get brain damage; much of that research was later discredited. But since then, the NFL has poured tens of millions of dollars into concussion research, allowing the league to maintain a powerful role on an issue that directly threatens its future.

Some neuroscientists believe the league uses its money and influence to reward researchers who focus primarily on issues such as safety, equipment and proper tackling.

"Up until now they have controlled every dollar that they have spent on this issue," said Eric Nauman, a professor of mechanical and biomedical engineering at Purdue University. Research -- published without the NFL's support -- by Nauman and his colleague, Thomas Talavage, a professor of electrical and computer engineering and of biomedical engineering at Purdue, has shown that repetitive head trauma from football leads to dramatic changes in brain chemistry.

"There was no way they were going to just give that money to the NIH and say, 'Do whatever you want,'" Nauman said.

The Boston University-led study involves 50 researchers at 17 institutions and hundreds of former NFL and college players who will participate as subjects. The study seeks to detect, define and measure the progression of CTE, which can only be diagnosed after death and has been found in 87 former NFL players over the last 10 years.

Ultimately, a test for living patients could go a long way to answering one of the most fundamental -- and yet elusive -- questions: What percentage of players are likely to get brain disease from playing football?

"We view this study as the primary study in the world, as far as we know, specifically addressing methods of diagnosing CTE during life," Stern said.

The NFL's $30 million grant -- its largest single donation -- is administered by the Foundation for the NIH (FNIH), a nonprofit organization that solicits donations for NIH research. Koroshetz said he had asked FNIH since May whether the NFL would fund the project but never received a commitment. There has been no indication that the league is walking away from its original donation.

Koroshetz said he was never told directly that the NFL was refusing to support the CTE study. "No one has ever said that to me: 'The NFL said no,'" he said. "They're their own organization. They have committed $30 million; I am hopeful they stick to their commitment. If they don't, then I'll be upset."

On "60 Minutes" last month, commissioner Goodell was asked if NFL-funded research may be "sowing the seeds of your own destruction."

"No, we want facts," Goodell replied. "The facts will help us develop better solutions. And that's why we're advancing medical research. That's why we're funding directly to Boston University on some of this research."

The funding issue coincides with the release this week of a new film, "Concussion," starring Will Smith, about the NFL's attempts to silence Dr. Bennet Omalu, who discovered the first case of brain damage in a former NFL player while working as a Pittsburgh coroner in 2005.

The Boston University study announced Tuesday originated with a July 2014 NIH request for applications, or RFA. It advised applicants that any publication of the results would require acknowledgement of the Sports Health Research Program, which the FNIH website describes as an "innovative partnership among the National Football League, the NIH and FNIH" launched in 2012.

In the spring, the NIH notified Stern and Boston University that their research group had won the research grant following a "scientific merit review" and a separate review by an NIH advisory council. The other principal investigators are Dr. Jeffrey Cummings, director of the Cleveland Clinic's Lou Ruvo Center for Brain Health; Dr. Eric Reiman, executive director of the Banner Alzheimer's Institute in Phoenix; and Martha Shenton, a Harvard University professor of psychiatry and radiology and director of the Psychiatry Neuroimaging Laboratory at Brigham & Women's Hospital.

"There really is an urgent need to get more information about the clinical features and clinical course of CTE," Reiman told Outside the Lines. He added that the information is needed not only to help "affected players or the at-risk players who are vulnerable. It's everybody -- every parent, every child. We can't get that information fast enough."

Shenton agreed. "We don't know enough, and if we want to be able to prevent a further cascade of progressive changes, we need to know what's going on now and need to understand who's more at risk," she said.