A method is disclosed for spinal anatomy segmentation. In one example, the method includes combining a fully convolutional network with a residual neural network. The method also includes training the combined fully convolutional network with the residual neural network from end to end. The method also includes receiving at least one medical image of a spinal anatomy. The method also includes applying the fully convolutional network with the residual neural network to at least one medical image and segmenting at least one vertebral body from the at least one medical image of the spinal anatomy.