In most finite element (FE) studies of vertebral bodies, axial compression is the loading mode of choice to investigate structural properties, but this might not adequately reflect the various loads to which the spine is subjected during daily activities or the increased fracture risk associated with shearing or bending loads. This work aims at proposing a patient-specific computer tomography (CT)-based methodology, using the currently most advanced, clinically applicable finite element approach to perform a structural investigation of the vertebral body by calculation of its full six dimensional (6D) stiffness matrix. FE models were created from voxel images after smoothing of the peripheral voxels and extrusion of a cortical shell, with material laws describing heterogeneous, anisotropic elasticity for trabecular bone, isotropic elasticity for the cortex based on experimental data. Validated against experimental axial stiffness, these models were loaded in the six canonical modes and their 6D stiffness matrix calculated. Results show that, on average, the major vertebral rigidities correlated well or excellently with the axial rigidity but that weaker correlations were observed for the minor coupling rigidities and for the image-based density measurements. This suggests that axial rigidity is representative of the overall stiffness of the vertebral body and that finite element analysis brings more insight in vertebral fragility than densitometric approaches. Finally, this extended patient-specific FE methodology provides a more complete quantification of structural properties for clinical studies at the spine.