Hi Bruce,

Just to make sure I understand:  When you say "the subject's ?h.sphere.reg file contains the list of locations on the sphere of each subject", does that mean that the subject's sphere is a sphere centered at the origin (and of fixed radius for all subjects), and that the coordinate triple for a vertex in ?h.sphere.reg are the x,y,z coordinates for the location of that vertex on that sphere?  (So that the sum of the squares of the coordinates in ?h.sphere.reg should be the same for all vertices?)

Thanks,
David


On Thu, Aug 29, 2013 at 10:14 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi David

the subject's ?h.sphere.reg file contains the list of locations on the sphere of each subject. Mapping to another subject would involve looking up the closest set of vertices on the target subject for each source subject vertex. mri_surf2surf can do this I believe.

cheers
Bruce

On Thu, 29 Aug 2013, David Romano wrote:

Hi everyone,

I'm new to FreeSurfer (so sorry in advance for any failures to make sense!),
and have read through Bruce Fischl's '99 papers on how FreeSurfer maps the
yellow (white?) surface onto a template sphere (equipped with convexity
information), and have tried to go through the introductory material on the
wiki, but I can't seem to figure out an answer to my question.

Ideally, given subjects A and B, I'd like to be able to find a one-to-one
map between the white surface of A given in A's native volume space, and the
white surface of B, given in B's native volume space.  

My (vague) understanding from the '99 HBM paper is that the transformation
of the white surface proceeds in two steps: first the mesh in native space
is "spherized" in a way that minimizes metric distortion, and then the
resulting mesh is warped to optimize a match between the convexity at each
mesh vertex and the convexity at the point of the spherical convexity
template that the vertex is mapped to (by "spherizing" followed by warping).

>From this, I assume that a vertex in native space may be mapped to a
non-vertex in the spherical convexity template, which could make impossible
to have a sensible one-to-one map from the white surface mesh of subject A
to the white surface mesh of subject B (via maps back and forth to the
template).  But does the corresponding map between the full white surface of
subject A to the full white surface of subject B exists?  And if so, are
there FreeSurfer commands could I use to extract this map explicitly, or
might it only exists in form of calculations that aren't stored?

I hope this makes some sense, or at least that if it doesn't, someone might
be able to point me to the right resources that could clear up my confusion.

Thanks in advance for your help and your patience!

Best regards,
David Romano

P.S.  I have the same question about the pial surface, but this seems like
it would be an order of magnitude more complicated.




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