Current noninvasive evaluation of bone marrow proliferation in leukemia treatment is limited to manually examining marrow tissue in multiple regions of interest (ROIs). The statistics extracted from these ROIs often fail to provide an accurate global characterization of the patient's marrow. We propose an automatic framework for segmenting spinal marrow compartments to characterize the bone marrow from full-body joint PET/CT scans acquired subsequent to bone marrow transplantation. We first apply a graph-cut algorithm to the CT volume to obtain a 3D full-body bone map. We then isolate the spinal column in a single sagittal plane where connected components labeling and iterative thresholding are used to segment the vertebral bodies. This fully automated approach achieves an average accuracy of 91.7% and a worst case accuracy of 80.4% in testing on 51 scans of 17 patients. Finally, we outline a method for rejecting the cortical bone in transverse planes that can be combined with the sagittally segmented vertebral bodies to obtain a 3D map of the vertebral body medullary cavities for the entire spine.