Hi Tristan, As you know, the target keeps moving. If you haven't done so, read this paper:
http://cercor.oxfordjournals.org/content/early/2011/11/02/cercor.bhr290.long It's been a while since I read it, and I noticed one of the sumsdb links was bad, but this looks like the right thing: http://sumsdb.wustl.edu/sums/directory.do?id=8286148&dir_name=MACAQUE_ATLAS_CC11 This won't answer all your questions, but it might buy me more time, until I get caught up. ;-) Donna On Feb 17, 2012, at 12:09 AM, Tristan Chaplin wrote: > Thanks for information, but I must confess I don't understand why you create > the sphere first. I thought the procedure for atlases was to make a surface, > then resample it as a standard mesh, then do spherical morphing etc. Is the > idea instead to create the fiducial surface, do spherical morphing, then > align the sphere to one of these standard spheres? > > FYI we've already made a fiducial surface with cytoarchitecure as paint. > > On Fri, Feb 17, 2012 at 16:08, Timothy Coalson <[email protected]> wrote: > We have moved away from the 73730 mesh, we are now using a new method to > generate meshes which results in much more regular node spacing. Making a > sphere is actually relatively easy, especially with the new release of caret. > The hard part is making it into an atlas, which I defer to someone else. > The command: > > caret_command -surface-create-spheres > > Will generate a pair of matched left/right spheres (mirror node > correspondence, topologies with normals oriented out). I think that command > made it into the 5.65 release, if not you can use spec file change > resolution, and grab just the new sphere, and ditch the rest. The odd bit > about spec file change resolution, though, is if you give it an old node > count, like 73730, it will give you the old sphere (this is in case someone > is relying on its old behavior). However, ask it for 73731 nodes, and you > will get a new highly regular sphere instead (though it won't have 73730 > nodes, because the 73730 node mesh wasn't a regularly divided geodesic > sphere, but it will give you something close). If all else fails, there are > a few spheres in the caret data directory. > > Tim > > > On Thu, Feb 16, 2012 at 6:56 PM, Tristan Chaplin <[email protected]> > wrote: > Hi, > > A while back I asked about creating standard mesh of 73,730 nodes, similar to > what is used for PALS atlas. I never got a chance to follow it up then but > I'd like to give it a go now. It seemed at the time that the knowledge for > creating such meshes was limited to a select few so if anyone has any > experience with this or has the contact details of someone I would greatly > appreciate hearing from them. > > The reason for creating this mesh is for making atlas for the marmoset > monkey. We are very interested registering this atlas to the macaque monkey > and doing analyses similar to Hill et al. (2010). > > Thanks, > Tristan Chaplin > > On Mon, Feb 7, 2011 at 16:04, Tristan Chaplin <[email protected]> > wrote: > Ok thanks for the information. > > > On Fri, Feb 4, 2011 at 03:25, Donna Dierker <[email protected]> wrote: > On 02/01/2011 07:31 PM, Tristan Chaplin wrote: > > Hi, > > > > I've been reading about the creation of your atlases, and I see that > > PALS and the macaque atlases have standard size mesh of 73,730 nodes. > > I was wondering, is this the same across species to allow > > interspecies registration? i.e. is it still possible to do > > interspecies comparisons of other species with different size meshes? > Possible, but more difficult. Not to say that achieving vertex > correspondence across species is trivial. Interspecies comparisons are > really hard. I think David Van Essen is the only one in our lab that is > doing them, although Matt Glasser might also be doing some. > > > > I was also wondering how the standard mesh was was actually made. The > > PALS paper refers to the Saad 2004 paper, which I think uses SUMA. > > SUMA has a program called MapIcosahedron to create standard meshes. > > Is this still how you would recommend making a standard mesh? > Tim Coalson (a student who works summers here) also developed a utility > that creates meshes of specified resolution. > > Making a standard mesh is not something I ever do. You do it with a > specific motivation -- typically some other important data is already > available on that mesh. And the way you usually get your data on that > mesh is to register it to an atlas target already on that mesh. > > If you are talking about creating, say, a sparser mesh for mice/rats, > then you're out of my orbit. > > > > Thanks, > > Tristan > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
