To create subtraction images you can use Subtract Scalar Volume module that is pre-built inside 3D Slicer. Alternatively, you can use Python and perform simple subtraction between two volumes. Relevant thread: Scalar subtraction
However, if you are calculating difference between two segmentations (bone segmented on image 1 - bone segmented on image 2), you don’t need to subtract them, just segment both and calculate their respective volumes with Segment Statistics module.