exactly On Thu, 29 Aug 2013, David Romano wrote:

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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