Hi Donna,
I think maybe I found the answer for my question, just want to confirm with
you.
In the caret GUI, “surface"->"deformation"->"run spherical surface
deformation"->"individual"-> "deform coodinate file to atlas": If I choose "
fiducial", does it mean that the deformation can be applied to the fiducial
coordinates, then I can get the deformed subject fiducial surface?
I'm not sure whether this is right because when I check the resulting deformed
fiducial surface , it really aligned pretty well with the template fiducial
surface. But when I check the result on the sphere through the landmarks, it
doesn't look like the "perfect match " in the spherical coordinates when
compared to the difucial surface match.
And I have another question, could you clear my confusion? After registration,
you have the deformed subject sphere and template sphere which should have
similar pattern. How do you find the correspondances of the vertices if they
have different number of vertices? Do you calculate the geodesic distance of
the vertices based on the sphere to find which vertex on the deformed sphere
corresponds to the template sphere?
Thanks.
Jidan
> From: [email protected]
> Subject: caret-users Digest, Vol 75, Issue 10
> To: [email protected]
> Date: Mon, 28 Dec 2009 12:00:02 -0600
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> Today's Topics:
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> 1. way to go back to the original surface space after spherical
> registration (z??)
> 2. Re: way to go back to the original surface space after
> spherical registration (Donna Dierker)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Mon, 28 Dec 2009 16:55:49 +0800
> From: z?? <[email protected]>
> Subject: [caret-users] way to go back to the original surface space
> after spherical registration
> To: caret_list <[email protected]>
> Message-ID: <[email protected]>
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>
> Hi Donna,
>
> I want to ask a question related to the spherical registration. When we have
> the original surface, we need to make it into a sphere to register it to a
> template sphere. After this step, we will get the deformed sphere. Do you
> have any way to make this deformed sphere go back into the original surface
> space? I mean, after this, I can have one original surface, one deformed
> original surface which is from the deformed shpere, when I superimpose them
> together, we can know which part deformed a lot. Is that possible? Or do you
> just compare the deformation in the spherical space?
>
> Thanks a lot.
>
> Jidan
>
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> ------------------------------
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> Message: 2
> Date: Mon, 28 Dec 2009 08:22:45 -0600
> From: Donna Dierker <[email protected]>
> Subject: Re: [caret-users] way to go back to the original surface
> space after spherical registration
> To: "Caret, SureFit, and SuMS software users"
> <[email protected]>
> Message-ID: <[email protected]>
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>
> Jidan,
>
> That is way too hard of a question on the Monday morning following a
> long weekend. ;-)
>
> See inline replies below.
>
> Donna
>
> On 12/28/2009 02:55 AM, z?? wrote:
> > Hi Donna,
> >
> > I want to ask a question related to the spherical registration. When
> > we have the original surface, we need to make it into a sphere to
> > register it to a template sphere. After this step, we will get the
> > deformed sphere. Do you have any way to make this deformed sphere go
> > back into the original surface space?
> If you selected a bidirectional deformation (source to target AND target
> to source), then you could apply the inverse deformation to the deformed
> sphere, but in practice no one ever does this, as far as I know.
>
> The typical reason for deforming in the reverse direction (target to
> source) is viewing atlas "goodies" on the individual's surface (e.g.,
> visuotopic or orbito-frontal parcellations).
>
> > I mean, after this, I can have one original surface, one deformed
> > original surface which is from the deformed shpere, when I superimpose
> > them together, we can know which part deformed a lot.
> I think viewing the deformation field is probably a better way to do
> this. See figure 5 in David Van Essen's PALS paper
> (http://brainvis.wustl.edu/resources/-Pals.wcover.pdf), panel C.
>
> This isn't something I do every day, but I think you use File: Open Data
> File to open the deform_field file that gets written during
> registration. Then look at Toolbar: D/C: Deformation Field to see your
> visualization options.
> > Is that possible? Or do you just compare the deformation in the
> > spherical space?
> To be honest, I generally don't look at these deformations. I do sanity
> check the registration output, to make sure the deformed fiducials look
> reasonable and the depth maps are sane looking. Then I do group
> analyses, where depth or coordinate differences are computed and put
> through statistical tests.
> >
> > Thanks a lot.
> >
> > Jidan
> >
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