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According to the autopsy report (PDF), Habibullah was not injured when he first arrived at the Bagram detention facility:
MEDICAL RECORD REVIEW: Copies of the inprocessing evaluation are reviewed in full. The clinical portion documents the decedent as "appearing well", without injuries and offering "moderate resistance to inprocessing". The decedent was "dead on arrival" per the Medical Treatment Facility (MTF) Emergency Room record which was otherwise non-contributory.
On autopsy, however, Habibullah's body bore the stigmata of torture (Graphic content warning):
Head and Neck: Multiple abrasions and contusions and evidence of ligature or other instrument applied to the neck:
On the right side of the neck there are two parallel, faint, linear abraded contusions. each averaging 1 1/4 x 1/4 inches with 1/2 inch separation between the two. They average approximately 10 inches below the top of the head and three inches to the right of the anterior midline. Just to the left of these is a similar, fainter, patchy abraded contusion in
approximately the same dimensions.
Torso: Multiple contusions and abrasions including "brush burn" injuries consistent with being dragged on the ground.
Extremities: Multiple contusions and abrasions, including injuries around the wrists consistent with shackling. On the thighs were linear contusions likely made from being struck with blunt objects. The patterns in the skin of the left calf revealed the likely source of the injuries- combat boots:
On the back of the left knee and calf is a 11 x 7 1/2 inch red-dark purple contusion which extends upwards above the back of the knee in a linear fashion. On internal examination, confluent hemorrhage extends deep within the muscle which is focally necrotic. On the left calf, centrally located, is a patterned abrasion consisting of multiple parallel horizontal linear abrasions the largest averaging 1 1/2 x 1/4 inches, these are closely spaced.
The Autopsy listed the cause of death as "Pulmonary embolism due to blunt force injuries", and the manner of death as homicide