[caret-users] questions about deformed fiducials

Donna Dierker donna at brainvis.wustl.edu
Wed Dec 30 09:57:10 CST 2009


Hi Jidan,

I have seen David's replies that address your questions about node 
correspondences.

And I think you got past some of the questions posed below, but I'm 
addressing a few of them to be sure:

* The deformed fiducial surfaces are in the atlas target directory.

* They will be in the same mesh as the target sphere (e.g., if the PALS 
target is used, the deformed fiducial will have 73730 nodes).

* Here is what a bunch of deformed fiducial surfaces look like, all in 
the same standard mesh (73730 PALS):

http://brainmap.wustl.edu/pub/donna/TODD/ADHD/CHECK_SCENES/DEFORM_SANITY_CHECK/views.html
login pub
password download

* Here is a thread that discusses automating the generation of such 
captures for sanity checking:

http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg01897.html

More generally, the nature of your questions suggests that your goals 
intersect substantially with those of a grad student here at Wash U, 
Andy Knutsen. I am bcc'ing him, in case he has any pointers for you. For 
Andy's benefit, here are relevant threads:

http://brainvis.wustl.edu/pipermail/caret-users/2009-December/001980.html
http://brainvis.wustl.edu/pipermail/caret-users/2009-December/001981.html
http://brainvis.wustl.edu/pipermail/caret-users/2009-December/001982.html
http://brainvis.wustl.edu/pipermail/caret-users/2009-December/001984.html

Donna

On 12/28/2009 10:00 PM, z丹丹 wrote:
> 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: caret-users-request at brainvis.wustl.edu
> > Subject: caret-users Digest, Vol 75, Issue 10
> > To: caret-users at brainvis.wustl.edu
> > Date: Mon, 28 Dec 2009 12:00:02 -0600
> >
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> > Today's Topics:
> >
> > 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)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 28 Dec 2009 16:55:49 +0800
> > From: z?? <jidanz at hotmail.com>
> > Subject: [caret-users] way to go back to the original surface space
> > after spherical registration
> > To: caret_list <caret-users at brainvis.wustl.edu>
> > Message-ID: <COL102-W342BEB45FDBF4F89FD7E65DD7B0 at phx.gbl>
> > Content-Type: text/plain; charset="gb2312"
> >
> >
> > 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
> >
> > _________________________________________________________________
> > MSN????????MSN???????????
> > http://10.msn.com.cn
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> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 28 Dec 2009 08:22:45 -0600
> > From: Donna Dierker <donna at brainvis.wustl.edu>
> > Subject: Re: [caret-users] way to go back to the original surface
> > space after spherical registration
> > To: "Caret, SureFit, and SuMS software users"
> > <caret-users at brainvis.wustl.edu>
> > Message-ID: <4B38BF35.701 at brainvis.wustl.edu>
> > Content-Type: text/plain; charset=GB2312
> >
> > 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), pa n el 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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