Ah I think that change resolution command is what I want. It made a nice fiducial mesh for me. I must admit I hadn't payed much attention to the command line caret features, I see now there is a lot of cool things in there. If run into any problems later with the actual registration I'll post a new topic.
One quick question though - does flat morphing work better if the fiducial mesh is first "standardised"? On Wed, Feb 22, 2012 at 05:47, Timothy Coalson <tsc...@mst.edu> wrote: > The way I understand it, if you already have an atlas sphere, you can (and > probably should) register the native mesh to the spherical atlas directly, > and the result is that (among other things) you get a new surface that > aligns with your native surface, but has topology and node spacing similar > to the atlas sphere. > > However, if you do not yet have an atlas sphere, the way I understand it, > we made our atlas sphere without any dependence on the native mesh, by > taking the borders on the subject sphere and unprojecting them to not rely > on a mesh (then averaging them across subjects, but since you have only one > subject, this doesn't apply), and then projecting them onto the sphere we > wanted to use, giving us our atlas sphere with landmarks. Again though, I > haven't done this, it is just my understanding of how it was described to > me. > > If what you want is a surface with more regular spacing than what you have > in the subject native surface, you can do that and then register to the new > atlas sphere, or maybe just use the subject sphere and a new sphere to > generate a deformation map, and deform the subject native surfaces to the > new mesh (this is approximately what spec file change resolution does). > > Tim > > > On Mon, Feb 20, 2012 at 6:55 PM, Tristan Chaplin < > tristan.chap...@gmail.com> wrote: > >> Sorry I should have specified this before, for our "atlas" we have only a >> single indvidual with cytoarchitecture. We have a native mesh for this and >> the associated morphed spherical and flat meshes, as well as >> the cytoarchitecture as a paint file. >> >> I thought that to register this atlas to another individual, or for >> interespecies registration (which is want we really want to do) it >> was necessary to make standard fiducial mesh which has evenly spaced nodes, >> rather than the "native" mesh created after reconstruction from contours. >> >> I think I understand how to make a standard spherical mesh but do I need >> to make a standard fiducial mesh to allow intra and interspecies >> registration? >> >> Cheers, >> Tristan >> >> >> On Sat, Feb 18, 2012 at 05:31, Timothy Coalson <tsc...@mst.edu> wrote: >> >>> The new atlases we are making (I think they may be included in the 5.65 >>> release, but I am not sure, the fs_LR atlases are the ones I mean) use this >>> new kind of sphere. If you want to take a look at node spacing regularity, >>> there is an option in caret to generate the node areas of a surface under >>> Surface->Region Of Interest Operations... >>> >>> Select all the nodes (clicking select with the default settings should >>> do this), click next, select "Assign metric with node areas", click the >>> "Assign Metric Node Areas" button, and there you have it. Of course, the >>> node regularity on the sphere doesn't translate directly to node regularity >>> on subject surfaces, there is distortion inherent to registering on a >>> sphere, since the brain isn't a sphere, but it should help. >>> >>> The new sphere code is only used in a few commands, so I would have to >>> know more about what commands generate the surfaces in your current methods >>> to hazard a guess at whether you would need to do something different to >>> get a new sphere. >>> >>> Tim >>> >>> >>> On Fri, Feb 17, 2012 at 11:02 AM, Colin Reveley <cm...@sussex.ac.uk>wrote: >>> >>>> Tim - what you say is interesting. >>>> >>>> I have actually wondered about node spacing in fiducial surfaces >>>> registered to F99 via macaque.sphere6. >>>> >>>> It's not always 100% super straight forward to register (without lots >>>> of crossovers and issues). I'm fairly pleased with what I have. the matches >>>> are quite good. >>>> >>>> however, for my purposes, a node spacing that is a regular as possible >>>> in the context just of registering my surface to F99 has real advantages, >>>> because I use nodes as tractography seeds and I'd like their spacing to be >>>> roughly even. >>>> >>>> Might I benefit from trying your new approach? How hard would it be? >>>> f99 is still 73730, as are all the atlas files. DVE's most recent free >>>> surfer macaque to F99 tutorial still very much uses 73730. >>>> >>>> My surfaces are from FS and look pretty evenly spaced. So maybe >>>> register F99 on to my mesh, and make a deform_map for the F99 data? >>>> essentially following the menu driven landmark pinned reg. >>>> >>>> Other than fiducials (WM,GM, mean) the topos and other surfaces are >>>> made with caret operations. I'm guessing if I repeat those operations with >>>> caret5.65, it will follow the new scheme of things in terms of how node >>>> spacing is decided? >>>> >>>> Colin Reveley, sussex. >>>> >>>> On 17 February 2012 05:17, <caret-users-requ...@brainvis.wustl.edu>wrote: >>>> >>>>> Send caret-users mailing list submissions to >>>>> caret-users@brainvis.wustl.edu >>>>> >>>>> 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 >>>>> caret-users-requ...@brainvis.wustl.edu >>>>> >>>>> You can reach the person managing the list at >>>>> caret-users-ow...@brainvis.wustl.edu >>>>> >>>>> When replying, please edit your Subject line so it is more specific >>>>> than "Re: Contents of caret-users digest..." >>>>> >>>>> Today's Topics: >>>>> >>>>> 1. Re: caret-users Digest, Vol 101, Issue 2 (Colin Reveley) >>>>> 2. Interspecies comparisons - creating a new atlas for a >>>>> different primate species (Tristan Chaplin) >>>>> 3. Re: Interspecies comparisons - creating a new atlas for a >>>>> different primate species (Timothy Coalson) >>>>> >>>>> >>>>> ---------- Forwarded message ---------- >>>>> From: Colin Reveley <cm...@sussex.ac.uk> >>>>> To: <caret-users@brainvis.wustl.edu> >>>>> Cc: >>>>> Date: Thu, 16 Feb 2012 18:52:56 +0000 >>>>> Subject: Re: [caret-users] caret-users Digest, Vol 101, Issue 2 >>>>> One would expect the caret GUI to become unresponsive, and also expect >>>>> the process to be listed as "not responding" in the task manager even if >>>>> things were going well. >>>>> >>>>> but it crashes. >>>>> >>>>> might I suggest the neurodebian virtual machine? there is a 32bit >>>>> windows version. Loads of great stuff on there including caret. >>>>> >>>>> http://neuro.debian.net/vm.html#installation >>>>> >>>>> even if things are slow due to hardware limitations you may have, you >>>>> could segment in the virtual machine, and then use caret in plain windows >>>>> to work with the results. >>>>> >>>>> hope helps, >>>>> >>>>> Colin >>>>> >>>>> On 16 February 2012 18:00, <caret-users-requ...@brainvis.wustl.edu>wrote: >>>>> >>>>>> Send caret-users mailing list submissions to >>>>>> caret-users@brainvis.wustl.edu >>>>>> >>>>>> 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 >>>>>> caret-users-requ...@brainvis.wustl.edu >>>>>> >>>>>> You can reach the person managing the list at >>>>>> caret-users-ow...@brainvis.wustl.edu >>>>>> >>>>>> When replying, please edit your Subject line so it is more specific >>>>>> than "Re: Contents of caret-users digest..." >>>>>> >>>>>> Today's Topics: >>>>>> >>>>>> 1. Not Responding Error (Maestri, Matthew) >>>>>> 2. Re: Not Responding Error (Donna Dierker) >>>>>> >>>>>> >>>>>> ---------- Forwarded message ---------- >>>>>> From: "Maestri, Matthew" <mmaes...@georgiahealth.edu> >>>>>> To: "caret-users@brainvis.wustl.edu" <caret-users@brainvis.wustl.edu> >>>>>> Cc: >>>>>> Date: Wed, 15 Feb 2012 20:07:37 +0000 >>>>>> Subject: [caret-users] Not Responding Error >>>>>> >>>>>> Matthew Maestri**** >>>>>> >>>>>> mmaes...@georgiahealth.edu**** >>>>>> >>>>>> caret5**** >>>>>> >>>>>> CARET v5.65 (Jan. 27, 2012)**** >>>>>> >>>>>> Windows XP**** >>>>>> >>>>>> After I hit the ‘OK’ button for the *Segmenting an Anatomical >>>>>> Volume*process to begin, the program froze. No specific error message >>>>>> was given >>>>>> but it did say that the program was *Not Responding*. After this, >>>>>> the program closed. This happened twice. Do you know of any reason why >>>>>> this >>>>>> may have occurred? Thanks.**** >>>>>> >>>>>> Run the tutorial from the website**** >>>>>> >>>>>> Not Responding error and then it closes**** >>>>>> >>>>>> It should segment an anatomical volume**** >>>>>> >>>>>> >>>>>> ---------- Forwarded message ---------- >>>>>> From: Donna Dierker <do...@brainvis.wustl.edu> >>>>>> To: "Caret, SureFit, and SuMS software users" < >>>>>> caret-users@brainvis.wustl.edu> >>>>>> Cc: >>>>>> Date: Wed, 15 Feb 2012 15:59:48 -0600 >>>>>> Subject: Re: [caret-users] Not Responding Error >>>>>> Not really, but if you are using a non-English character set, >>>>>> switching to an English one seems to solve all sorts of seemingly >>>>>> unrelated >>>>>> problems. >>>>>> >>>>>> It has been a very long time since I have segmented on Windows, but >>>>>> from what I recall, Caret launched from a command prompt, and you could >>>>>> often see progress messages echo to the command prompt terminal. Do you >>>>>> see any messages at all there before it closes? >>>>>> >>>>>> >>>>>> On Feb 15, 2012, at 2:07 PM, Maestri, Matthew wrote: >>>>>> >>>>>> > Matthew Maestri >>>>>> > >>>>>> > mmaes...@georgiahealth.edu >>>>>> > >>>>>> > caret5 >>>>>> > >>>>>> > CARET v5.65 (Jan. 27, 2012) >>>>>> > >>>>>> > Windows XP >>>>>> > >>>>>> > After I hit the ‘OK’ button for the Segmenting an Anatomical Volume >>>>>> process to begin, the program froze. No specific error message was given >>>>>> but it did say that the program was Not Responding. After this, the >>>>>> program >>>>>> closed. This happened twice. Do you know of any reason why this may have >>>>>> occurred? Thanks. >>>>>> > >>>>>> > Run the tutorial from the website >>>>>> > >>>>>> > Not Responding error and then it closes >>>>>> > >>>>>> > It should segment an anatomical volume >>>>>> >>>>>> > >>>>>> > _______________________________________________ >>>>>> > caret-users mailing list >>>>>> > caret-users@brainvis.wustl.edu >>>>>> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> caret-users mailing list >>>>>> caret-users@brainvis.wustl.edu >>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>> >>>>>> >>>>> >>>>> >>>>> ---------- Forwarded message ---------- >>>>> From: Tristan Chaplin <tristan.chap...@gmail.com> >>>>> To: "Caret, SureFit, and SuMS software users" < >>>>> caret-users@brainvis.wustl.edu> >>>>> Cc: >>>>> Date: Fri, 17 Feb 2012 11:56:45 +1100 >>>>> Subject: [caret-users] Interspecies comparisons - creating a new atlas >>>>> for a different primate species >>>>> 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 < >>>>> tristan.chap...@gmail.com> wrote: >>>>> >>>>>> Ok thanks for the information. >>>>>> >>>>>> >>>>>> On Fri, Feb 4, 2011 at 03:25, Donna Dierker <do...@brainvis.wustl.edu >>>>>> > 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 >>>>>>> > caret-users@brainvis.wustl.edu >>>>>>> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>>> > >>>>>>> >>>>>>> _______________________________________________ >>>>>>> caret-users mailing list >>>>>>> caret-users@brainvis.wustl.edu >>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> ---------- Forwarded message ---------- >>>>> From: Timothy Coalson <tsc...@mst.edu> >>>>> To: "Caret, SureFit, and SuMS software users" < >>>>> caret-users@brainvis.wustl.edu> >>>>> Cc: >>>>> Date: Thu, 16 Feb 2012 23:08:30 -0600 >>>>> Subject: Re: [caret-users] Interspecies comparisons - creating a new >>>>> atlas for a different primate species >>>>> 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 < >>>>> tristan.chap...@gmail.com> 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 < >>>>>> tristan.chap...@gmail.com> wrote: >>>>>> >>>>>>> Ok thanks for the information. >>>>>>> >>>>>>> >>>>>>> On Fri, Feb 4, 2011 at 03:25, Donna Dierker < >>>>>>> do...@brainvis.wustl.edu> 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 >>>>>>>> > caret-users@brainvis.wustl.edu >>>>>>>> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>>>> > >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> caret-users mailing list >>>>>>>> caret-users@brainvis.wustl.edu >>>>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> caret-users mailing list >>>>>> caret-users@brainvis.wustl.edu >>>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> caret-users mailing list >>>>> caret-users@brainvis.wustl.edu >>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> caret-users@brainvis.wustl.edu >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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