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/[email protected]/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: [email protected] > > Subject: caret-users Digest, Vol 75, Issue 10 > > To: [email protected] > > Date: Mon, 28 Dec 2009 12:00:02 -0600 > > > > Send caret-users mailing list submissions to > > [email protected] > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > or, via email, send a message with subject or body 'help' to > > [email protected] > > > > You can reach the person managing the list at > > [email protected] > > > > When replying, please edit your Subject line so it is more specific > > th a n "Re: Contents of caret-users digest..." > > > > > > 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?? <[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]> > > 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 > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://brainvis.wustl.edu/pipermail/caret-users/attachments/20091228/ec57cf2f/attachment-0001.html > > > > > > ------------------------------ > > > > 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]> > > 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 > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
