1. A method to measure bone density and structure of the proximal femur of the hip of an individual subject from images acquired with a three-dimensional (3-D) X-ray imaging device, the method comprising: providing 3-D images acquired from a 3-D X-ray imaging device to a computer programmed with image processing software; automatically identifying the pelvis and the left hip and the right hip including a volume of bone that includes the femoral head and lesser trochanter of each hip; automatically identifying the femoral head of at least one hip as an anatomical marker of the at least one hip; automatically determining a 3-D center of the femoral head of the at least one hip by applying the Hough Transform in at least one plane by the computer executing the software to analyze voxels of the 3-D images without operator interaction; automatically finding the lesser trochanter of the at least one hip by computing the cross-sectional areas of bone along a femoral shaft; automatically computing an anatomical center of the femoral neck by iteratively reformatting the images and computing cross-sectional bone areas along the femoral neck to converge on the anatomical center; automatically positioning a neck region of interest (ROI) at the anatomical center of the femoral neck; automatically positioning a hip ROI bounded by the neck ROI and the lesser trochanter; and automatically determining bone density and bone structure measures of the regions by the computer executing the software.