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The family of Justina Pelletier, the 15-year-old girl at the center of a battle spanning two states and two prestigious hospitals, is devastated but defiant after a Massachusetts judge gave permanent custody of the girl to the state's Department of Children and Families.

Speaking a day after Massachusetts juvenile court Judge Joseph Johnston issued a four-page ruling blasting Pelletier’s parents for being verbally abusive and complicating efforts to bring the West Hartford, Conn., family together, Lou Pelletier told Fox News Channel the Bay State bureaucracy has been aligned against his family from the beginning.

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"You keep hoping for the best, as any human being would do, but with everything that's happened with this judge for the last 13-and-a-half months, it's like, nothing surprises you," Pelletier said. "And this decision yesterday, in my mind, was not a surprise at all."

The Massachusetts Department of Children and Families took emergency custody of Justina on Valentine’s Day 2013 after doctors at Tufts Medical Center, which had been treating her for a rare condition, and doctors as Boston Children’s Hospital, clashed over the cause of her medical problems, which included difficulty eating and walking.

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    At Tufts, Justina had been treated for mitochondrial disease, a group of rare genetic disorders affecting cellular energy production. When Justina began experiencing some gastrointestinal problems, the Tufts doctor treating her, Dr. Mark Korson, wanted the girl to visit Dr. Alejandro Flores at Boston Children's Hospital, according to the family's attorney, Phil Moran. Flores had treated Justina in the past, Moran said, and Korson thought it beneficial for the teen to see a gastroenterologist.

    What happened next was a "tragic nightmare" for Justina and her family, Moran told FoxNews.com.

    Justina was taken by ambulance to Boston Children's Hospital because she was in a wheelchair at the time and a heavy snow storm was blanketing the region. Because she arrived by ambulance, she was taken directly into the hospital's emergency room, where a "resident refused to send her to Dr. Flores" and, "declared this was his case," according to Moran. He said the unnamed resident then called upon a psychologist who diagnosed Justina with somatoform disorder -- a mental condition in which a patient experiences symptoms that are real but have no physical or biological explanation. Justina was diagnosed with the disorder "within 25 minutes," Moran claims.

    The Pelletier family rejected the new psychiatric diagnosis and wanted to bring Justina back to Tufts, Moran said. He claims the hospital tried to force the girl's parents to sign papers preventing them from seeking another opinion.

    After tempers flared between the Pelletiers and staff at Boston Children's, the hospital notified the state that it suspected the parents of medical child abuse.

    The girl was kept at Boston Children’s psychiatric ward for nearly a year, but was then slated to be transferred to another state facility. Johnston said the family, which vented its anger in various media interviews, hampered efforts to have her placed as near them as possible. She is currently being held at the Wayside Youth and Family Support Network facility in Framingham, Mass.

    Lou Pelletier told Fox News it shouldn't surprise anyone that he was left angry after seeing his child taken away.

    "There's never been a complaint about the Pelletier family regarding our daughter, our family, prior to Boston Children's Hospital getting involved," Pelletier said. "The complaints have been when DCF decided we didn't smile rightly at them or do whatever."

    He said Johnson ignored the testimony of his daughter's original doctors, who stand by the diagnosis of mitochondrial disease. In the more than a year since the ordeal began, the Pelletiers have only been allowed hourly visits each week with their daughter, whose condition, they say, has deteriorated. She has not attended school or church since the family lost custody of her, he said.

    "Tufts was working fine with her, diagnosed medically, going to school, ice skating and doing all those things," Lou Pelletier said. "Look at her then and look at her now."

    Justina's older sister, Jennifer, told Fox News her parents are loving and supportive. Watching her sister's condition worsen in the hands of Massachusetts officials has been frightening, she said.

    "If something happens to my sister under their care, she's not just going to be another number in the system," Jennifer said. "It's insane."

    Johnston's ruling leaves it up to the state Department of Children and Families to decide whether or when Justina should be returned to her family, and leaves open the possibility the girl will be in state care until she turns 18. The judge is expected revisit the decision to award permanent custody in a follow-up court hearing on May 25.

    In the meantime, Lou Pelletier said his family is appealing a decision in which Johnston backed the Boston Children's doctors, and said the family's attorneys have filed a writ of habeus corpus against Massachusetts for wrongful imprisonment.

    FoxNews.com's Cristina Corbin contributed to this report.