1. A method for multiple bone segmentation for three-dimensional computed tomography, the method comprising: receiving computed tomography (CT) data representing first and second bones of a patient; separately segmenting, by a processor, the first and second bones; refining, by the processor, just the segmenting of the first bone using a first confidence map of the segmenting, the first confidence map being a first spatial distribution over voxels; refining, by the processor, just the segmenting of the second bone using a second confidence map of the segmenting, the second confidence map being a second spatial distribution over the voxels; then, adjusting, by the processor, results of the segmenting of the first and second bones jointly using the first and second confidence maps; and outputting an image showing the first and second bones with the adjusted results of the segmenting.