A followup on issue (2):
If I'm understanding you correctly, the -jacobian_dist0 flag and
associated ?h.jacobian_dist0 file are supposed to get at the TOTAL
distortion, starting at ?h.white, when you morph without any distance
constraints.
If that is the intent, then I'm confused about the syntax of
'mris_register. Namely, the "input surface" used currently as part of
the -jacobian_dist0 flag is ?h.sphere.reg, whereas it would seem that
you would want to use ?h.white as the input surface if you are trying to
capture the TOTAL distortion.
e.g., here is the actual command used (with the part of my confusion
changed to CAPS):
[EMAIL PROTECTED] Jacobian dist0 lh Thu Dec 20 13:43:15 CST 2007
/disk/conte_raid1/freesurfer/conte_mprage/010921_6038/scripts
mris_register -curv -norot -jacobian ../surf/lh.jacobian_dist0 -dist
0 ../SURF/LH.SPHERE.REG /pkg/brainmap/freesurfer-
v4.0.1/average/lh.average.curvature.filled.buckner40.tif
../surf/lh.sphere.dist0.jacobian.reg
thanks for clarifying,
Mike
On Fri, 2007-12-21 at 13:46 -0500, Bruce Fischl wrote:
> Hi Mike,
>
> 1. This will include distortions in the spherical mapping as well as the
> spherical registration (note that global area scaling is taken out,
> unless you specify -n). I think this is probably what you want, since
> otherwise the spherical transformation could wash out interesting things
> or introduce artifactual ones.
>
> 2. Here the thought was that you don't want to look at the residual
> distortion, but all of it, by morphing without any metric constraints (just
> topology).
>
> 3. Just the D is set to 0. A is actually a topology preserving term and
> won't change the distortion much (it only affects negative definite or very
> close to singular areas)
>
> cheers,
> Bruce
>
>
> On Fri, 21 Dec 2007, Michael Harms wrote:
>
> >
> > 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.
> >
> >
> >
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