MARY LOUISE KELLY, host:

The military center that's supposed to lead the effort to diagnose and treat traumatic brain injuries and post traumatic stress disorder is having a hard time carrying out its mission. That's what the Government Accountability Office concludes in a new report. NPR's Danny Zwerdling has the story.

DANNY ZWERDLING: Think back to 2007. Hundreds of thousands of troops had already come home from Iraq and Afghanistan with PTSD. Many also had brain injuries from explosions. And Congress told the Pentagon: We want you to set up a national center to deal with these terrible injuries.

So, the Pentagon created the Defense Centers of Excellence for Psychological Health and Traumatic Brain Injury. The Defense Centers were supposed to lead a ground-breaking campaign to figure out the best ways to fight brain injuries and PTSD. Except, the new investigation has found that the Defense Centers' program is in trouble.�

Ms. DENIS FANTONE (Government Accountability Office): I would have to describe this organization as an organization that is struggling.

ZWERDLING: That's Denise Fantone at the GAO, the Government Accountability Office. She helped supervised the investigation to find out what's going on at the Defense Centers of Excellence?�

Ms. FANTONE: We have considerable concern about what it is that it's actually accomplishing?

ZWERDLING: The GAO put out the first part of this study a few months ago. The new one completes it. To do it, they dissected Pentagon budget figures. They analyzed confidential documents. They interviewed the officials who run the Defense Centers of Excellence, or DCOE, as they call it.

Fantone says those officials could not explain: What are their goals? How will they achieve them? How much money will they have to spend? How will they measure whether their programs are working?�

Ms. FANTONE: I can't say with any certainty that I know what DCOE does and I think that's a concern.

ZWERDLING: We wanted to talk about all this with top officials at the Pentagon, but a spokeswoman said they weren't available in time for our deadline. The spokeswoman did send us a statement, quote, "We appreciate GAO's thorough review and overall, the department concurred with the report's findings. There is still substantial work to be done." unquote. The spokeswoman said the Pentagon is conducting its own study now, to figure out how to make the Defense Centers better.�

Sources in the military tell NPR and ProPublica that from the beginning, a lot of top officials did not want to set up the Defense Centers for Psychological Health and Traumatic Brain Injury. Some of them didn't believe the injuries are a big problem, some still don't.

Others are annoyed that a new kid on the block is getting budget money that they want to get, instead. In fact, one of the most interesting findings in the new GAO report is a two-sentence footnote.

The GAO found that the members of the Pentagon committee that were assigned to plan the Defense Centers were so worried about their mission that they had a nickname. They called themselves The Red Cell. That's the name generals sometimes give to the enemy.

Daniel Zwerdling, NPR News.

KELLY: And our story was co-reported by T. Christian Miller of ProPublica.

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