I just did some code digging, and indeed, reformatx --jacobian should do the trick. If you want the nonrigid component only, add the --jacobian-correct-global flag also. That should divide the Jacobian determinant by the global scaling factor of the affine transformation component. (But note that this is based only on the affine transformation that was used to seed the nonrigid registration. It does not, say, fit an affine transformation to the deformation field.)