Hi Jidan,
It sounds to me that what you're asking is whether it is possible to
invert the "mapping" from {lh,rh}.white to {lh,rh}.sphere, but apply
that inversion to {lh,rh}.sphere.reg, thus generating a putative
"{lh,rh}.white.reg" surface. I'm not sure that operation is possible,
or if the resulting surface would even be meaningful.
cheers,
-Mike H.
On Fri, 2009-07-24 at 10:20 +0800, Zhong Jidan wrote:
> Hi Bruce,
>
> For my 2nd point, I mean, after we get the lh.sphere.reg as the
> deformed subject, it should have similar sulco-gyral pattern as the
> template. I want to compute the distance between the deformed subject
> and the template, to see how close they are after the registration. In
> other words, I want to check the distance error. But the distance
> based on the sphere doesn't include the geometry information. I want
> to get the real distance in their white surface, which is between
> lh.reg.white and template.white. Also if I have lh.reg.white, it would
> be interesting to compute the real distance between the subject.white
> and lh.reg.white to see how far it moves.
>
> But from the method you told me, "You can use the mapping to paint the
> geometry of one subject onto another folded surface if you want to
> visualize the geometric mapping (e.g. the curv of one subject on the
> white surface of another)." If "paint" means set a value for
> the vertex for visulization, (just like paint the functional
> information on a surface ) this would not make me get the real
> geometry of the .reg.white, right? When you paint the curvature
> information of the lh.sphere.reg and template.sphere to another white
> surface, you can only see the curvature difference on the
> corresponding point but can not see the real geometry of the two.
> I'm not sure whether I understand your surggestion correctly...This
> what I'm confused.
>
> Thanks,
> Jidan
>
>
> On Thu, Jul 23, 2009 at 8:12 PM, Bruce Fischl
> <fis...@nmr.mgh.harvard.edu> wrote:
> Hi Jidan,
>
> we construct fsaverage by mapping the icosahedron vertices to
> a set of subjects, then assigning that vertex to the position
> that is the average of the tal coords of those vertices.
> Sorry, I don't understand the 2nd point. Maybe you can
> explain what you are trying to accomplish?
>
> cheers,
> Bruce
>
>
>
>
> On Thu, 23 Jul 2009, Zhong Jidan wrote:
>
> Hi Bruce,
>
> Thanks for your reply. I'm not clear about two points
> you mentioned.
>
> ->To represent a folded surface we either (1) map to
> an individual subject,
> or (2) use a volume transform such as tal and the
> vertex correspondence from
> the sphere.reg to find the average coordinate of a
> vertex. This is how we
> build the fsaverage and average7 surfaces.
>
> For the (2) point, what do you exactly mean? I?m
> confused. I thought your
> fsaverage is derived by averaging 40 subjects' volume
> image and then
> reconstruct the surface based on that. How can I use a
> volume transform such
> as tal and the vertex correspondence from the
> sphere.reg to find the average
> coordinate of a vertex? I'm totally lost with this
> sentence..
>
>
> ->You can use the mapping to paint the geometry of one
> subject onto another
> folded surface if you want to visualize the geometric
> mapping (e.g. the curv
> of one subject on the white surface of another).
>
> For this one, I think you mean that, I can use one
> white surface as a base.
> Then paint the curvature information on the white
> surface to see the
> geometry. But this is not I want... To be specific, if
> I have a lh.sphere,
> lh.sphere.reg, they share the curvature information,
> and the only difference
> is the spherical coordinates. Then it is non sense to
> paint the curvature
> information to another white surface to see the
> geometry because there is
> only one .curv file. Another problem is, this
> lh.sphere may have different
> number of points with the white surface. ... Not sure
> whether I understand
> it correctly, hope for your suggestion.
>
> Thanks,
>
> Jidan
>
>
>
>
> On Tue, Jul 21, 2009 at 8:26 PM, Bruce Fischl
> <fis...@nmr.mgh.harvard.edu>wrote:
>
> Hi Jidan,
>
> the atlas only exists in spherical coords. To
> represent a folded surface we
> either (1) map to an individual subject, or
> (2) use a volume transform such
> as tal and the vertex correspondence from the
> sphere.reg to find the average
> coordinate of a vertex. This is how we build
> the fsaverage and average7
> surfaces (we know this is a hack, but it's
> easy and a good visualization
> tool).
>
> You can use the mapping to paint the geometry
> of one subject onto another
> folded surface if you want to visualize the
> geometric mapping (e.g. the curv
> of one subject on the white surface of
> another).
>
>
> cheers,
> Bruce
>
>
>
> On Tue, 21 Jul 2009, Zhong Jidan wrote:
>
> Hi Freesurfer experts,
>
> I asked this question previously, but
> I found it problematic when
> displayed
> in your mailist. I'm sorry that the
> question still not solved and I feel
> sorry to trouble you again.
>
> In your sphere registration in
> freesurfer, the procedure is like:
> creating
> the template.tif by
> mris_make_template. The template you
> use in
> Freesurferis created by iterative
> registration of 40 subjects,
>
> according to
> "High-resolution inter-subject
> averaging and a coordinate system for
> the
> cortical surface, Fischl, B., Sereno,
> M.I., Tootell, R.B.H., and Dale,
> A.M.,
> (1999). Human Brain Mapping, 8:272-284
> (1999)".
> So, after the template generation
> process, you will get a .tif file
> which
> include the necessary infomation (like
> the means and variances of curv,
> sul
> from the aligned spheres). But,do you
> have the other information of this
> final template, such as the sphere
> representation, folded surface
> representation of this template? I
> know that under
> */subjects/fsaverage/surf, there are
> some surface representations of the
> average of the 40 subjects, but to my
> knowledge, they are just used for
> visulazation and are not the surface
> representation of the template.tif
> you
> used, am I right?
>
> 2, subjects' sphere registration to
> the template sphere
> In this process, we can get the
> deformed subjects spheres( *.reg ),
> which
> have a one-to-one correspondance to
> the original subject surfaces. Except
> the .reg sphere with the cuvature
> information, do you have any other
> form
> of
> representation of the deformed
> sphere? You know that there are other
> kinds
> of surface mapping methods, like
> Miller's Large Defformation
> deffeomrphic
> surface mapping, they just do surface
> mapping using the folded surfaces.
> After surface mapping, they will get
> the deformed folded surface which
> would
> be aligned with the template folded
> surface. With the deformed subject
> and
> template folded surfaces, they can
> tell directly which sulcus or gyrus is
> aligned well. So, for your mapping,
> when I get the deformed sphere, do
> you
> have any command or method to put the
> sphere back to the folded surface so
> I
> can see the suci and gyri directly?
> If you also have the surface
> representation of the template, then i
> can superimpose them to see how
> good
> the alignment is.
>
> If you think I didn't state this
> problem clearly, please refer to an
> example
> in the following:
>
> I found one reference using your
> sphere registration method.
> "Simpliÿÿed
> Intersubject Averaging on the Cortical
> Surface Using SUMA"Brenna D.
> Argall,
> Ziad S. Saad,and Michael S.
> Beauchamp"Human Brain Mapping 27:14
> ÿÿ27(2006)"
> You may see the attachment in :
>
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-May/010558.html
>
>
> In "Spherical Morphing" section, They
> mentioned that " Using the
> mris_register [Fischl et al., 1999b]
> routine, each individual subjectÿÿs
> surface was registered to the
> FreeSurfer average7 template prior to
> node
> number standardization.
> Standardization and averaging were
> then performed
> on
> the surfaces as described
> above" (using SUMA FYI).
> ---- From this part, I assume that all
> the deformed surfaces are in
> spherical representation.
>
> Then in the result part, in section
> "Intersubject Averaging of Functional
> Data: Different Surface Methods", they
> mentioned they " in order to
> compare
> the ACÿÿPC method to these more
> complex algorithms, the FreeSurfer
> program
>
> mris_register [used in Fischl et al.,
> 1999b] was used to morph the
> cortical
> surface models to a predeÿÿned
> template, and these morphed surface
> models
> were then used to create a morphed
> surface average."
>
> In Fig7C ÿÿAverage surface created by
> averaging the same 28 subjects using
>
> mris_register standardization. You can
> see that they show the average
> surface in a folded surface
> representation, not a sphere.
>
> Could you give me a hint that how they
> do this since you only have a
> sphere
> representation of the aligned surface?
>
>
>
>
>
>
>
>
>
> --
> Regards,
>
> Jidan
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