Marsha Small used ground-penetrating radar to survey beneath the cemetery on the Chemawa Indian School campus near Salem, Oregon. As she worked, she prayed to the children, even though her Northern Cheyenne language would sound foreign to them because the children buried in this earth had been brought to the school from reservations and tribal lands throughout the western United States.

Small, 56, conducted the survey using ground penetrating radar as part of her master's thesis research at Montana State University.

In the school's historical records, she had found autograph books from the 1890s in which children wrote private messages to each other.

"Please remember me when I'm in the grave," one boy who was re-named Danny Boone by the school staff, had written to a friend.

As she soon discovered, the tragic death of childhood friends was likely more common for Chemawa students that previously believed.

Buried at Chemawa Indian Boarding School

In her thesis, "A Voice for the Children of Chemawa Cemetery", which she completed this fall, Small reports that her surveys indicate there are possibly hundreds of unmarked burial sites at Chemawa, which is one of the last operating government run Indian Boarding Schools.

Government and church-run boarding schools were created under the infamous "Kill the Indian, save the man" approach. Captain Richard H Pratt, a US army veteran of the Indian wars, opened the first boarding school in 1879, saying: "Transfer the savage-born infant to the surroundings of civilisation, and he will grow to possess a civilised language and habit." His intention was the forced assimilation of the Native American population through the elimination of their language, customs, and culture. By 1926 government officials estimated more than 86 percent of Native children were attending the schools.

Many of the children were forcibly separated from their families and ancestral lands and many suffered brutal physical, sexual and emotional abuse at the schools where they were converted to Christianity and coerced into abandoning their indigenous cultures.

"Our homelands are the places where we're taught everything, where we go to feel full and heal as indigenous people," Small said. "For these children to be buried in an unknown land with an unknown prayer, I can't think of a more horrific fate."

'Cultural genocide'

Small's research was published just a few months before the Canadian Truth and Reconciliation Commission released its final report on December 15, the conclusion of a seven-year examination of that country's parallel system of residential schools.

The commission declared that the practise constituted "cultural genocide". Its research elucidated an often untold dark chapter of Canadian history and provided recommended steps for healing and recovery, to include reparations for residential school survivors and a revamped state history curricula that tell the stories of indigenous people.

Small's work is a stark reminder of how far behind the US lags in addressing and even committing to fully documenting its own boarding school history, which remains relatively unknown to the general public.

Government records indicate that epidemics of tuberculosis, trachoma and influenza often swept through overcrowded dormitories at the boarding schools, where children were often malnourished and exposed to germ-infested conditions due to inadequate funding.

While it was common boarding school practise to send near death children home before they died, most schools did and still do have cemeteries.

There are more than 200 documented graves at the Chemawa cemetery, and Small came to her conclusions by comparing the shapes and sizes of unidentified electronic signatures in her GPR data to the areas of known burials.

Effects of abuse on Native communities

"It's remarkable what she's found. So many children were shipped away, and parents never were able to see them again," said Denise Lajimodiere, president of the National Native American Boarding School Healing Coalition and an assistant professor in educational leadership at North Dakota State University.

"There is a great deal of unresolved grieving in our communities from what we lost to the boarding schools," Lajimodiere explained.

Lajimodiere has been interviewing boarding school survivors since 2008, and she is among the Native leaders, researchers and elders who believe the boarding school effects reverberate in their communities to this day.

The challenges many tribes face, from high rates of substance abuse disorders to the loss of language, can be at least partially connected to boarding schools, Lajimodiere said.

"Loneliness, the feeling of abandonment, and then many of the kids were malnourished and abused, sexually and mentally. Our research is indicating there can be an intergenerational basis for disease disparities from this trauma," said Lajimodiere, whose own father attended Chemawa.

"But it's America's best kept secret," Lijamodiere said. "It's not in the history books. Sometimes we don't know about it in our own families."

In her dissertation, Small refers to the boarding school effect as "soul wounds," and urges the federal government to create state Tribal Advisory Boards to oversee boarding school cemeteries and provide funds for ceremonial protocols to be conducted.

READ MORE: Canada accused of 'cultural genocide'

Bureau of Indian Education

In contrast, the Canadian courts allocated more than $60 million to the commission which conducted a seven year investigation. These included many truth telling events throughout the nation that more than 9,000 residential school survivors attended. The commission will also create a research centre that will safe keep residential school documents and foster continued scholarship.

Native American law experts say one reason a similar process has yet to happen in the United States is due to an idiosyncrasy of the law - relatively short statute of limitations for civil suits involving abuse cases.

In Canada, said Don Wharton, senior attorney for the Native American Relief Fund, no such limitation existed on residential school victims, and the lawsuits seeking damages were starting to gum up the legal system.

This forced the courts to deal with the issue, leading to the Indian Residential School Settlement Agreement that established the commission.

The office of the Senate Committee on Indian Affairs declined to comment for this story, but Charles Roessel, Director of the US Bureau of Indian Education (BIE), said that even without a federal truth and reconciliation process, federal Indian schools are seeking to address the past by establishing schools for Indian students that build culture, language learning and tribal sovereignty into the curriculums.

Of the $130 million proposed for the BIE's 2016 budget, Roessel said there would be a significant increase for tribal language programs.

READ MORE: Canada's dark history of abuse at residential schools

"Indian education has a dark history, but now is not the time to dwell on it because it's an exciting time," he said.

"We're redefining what education is and what success means for Indian students. We're ensuring the Indian voice is heard, and that the culture and history is taught and respected," Roessel insisted.

For Small, her fight for the children of Chemawa is also inextricably tied to the modern struggles of Native people.

An Oregon Department of Transportation plan to build a cloverleaf exchange at an Interstate 5 exit would be less than a football field from the cemetery and could potentially disturb the remains of the Chemawa children, she said.

"There needs to be a voice for a children, they need to have the prayers and ceremony to go to the next camp," Small said. "But people act like the cultural genocide never happened, but as long as this get swept under the rug, it will continue."