Sounds like you have second moment of area and moment of inertia confused.
Second moment of area is calculated from 2D cross-sections and (assuming that the neutral plane of bending = principal axis) relates to resistance of the member to bending. Use BoneJ's Slice Geometry plugin, which can take as input a 2D image or image stack (3D - series of 2D images).
Moment of inertia is calculated from 3D pixel data and relates to the acceleration of a freely floating body under an applied torque. It's mostly helpful in a bone morphology context to examine the distribution of bone mass around a bone's centroid, and to align bones' principal axes to the image axes. Use BoneJ's Moments of Inertia plugin to do this.