Hello, I'm going back and running the jacobian analyses (using v4 recon-all) so that I can look at distortion arising from the spherical registration.
Couple questions about what is going on "under the hood":
1) When using the -jacobian_white flag, the command executed is: mris_jacobian ?h.white ?h.sphere.reg ?h.jacobian_white
Why the use of ?h.white rather than ?h.sphere as the "original surface"?
2) When using the -jacobian_dist0 flag (which appears to be analogous to the old -jacobian flag in the recon-all from v3) the input surface used is ?h.sphere.reg. If I understand correctly, this means that the resulting ?h.jacobian_dist0 file reflects the ADDITIONAL distortion that ensues when registering the already partially registered ?h.sphere.reg to the average convexity of the target atlas with the distance constraints turned offf. Is that concept of "additional" distortion the correct way to think about the ?h.jacobian_dist0 data?
3) In terms of Eq (5) from Fischl et al 1999 ("High-Resolution Intersubject Averaging..."): J = J_p + A*J_a + D*J_d Are BOTH constants A and D set to zero by the -dist0 flag in mris_register (or is it just D that is set to zero)?
thanks, Mike H.