I am not familiar with that command, but I think LVD stands for landmark vector difference, it is a method of doing surface based registration. I suspect that what you need is to replace the atlas spec file with a spec file containing an atlas on your desired sphere. I also suspect that the deformation map file is being used for a different purpose than deformation, for instance to get parameters and what kind of method to use to generate the registration. I am guessing the individual spec file isn't on a standard mesh yet? If it is not on a standard mesh, I don't see how it could be applying a deformation before it registers it or at least resamples it onto a standard mesh (and I would not expect it to apply a deformation other than that obtained by the registration afterwards).
I can only make a wild guess as to what the comment about "fixed for new spheres" is about, but I suspect the behavior it refers to has not been changed, partly because my wild guess is that it was based on misuse of a command, and partly because caret5 hasn't been modified much recently. Tim On Fri, Feb 17, 2012 at 3:48 PM, Colin Reveley <[email protected]> wrote: > > I'm very sorry I see it's basically trivial to register in both > directions. My registrations can be tricky though. > > if caret command has been fixed for new spheres, I'd be most grateful to > learn how I might leverage that. It also simplifies the scripts in places. > > I need a replacement for *.LVD.deform_map presumably? > > many thanks. > > On 17 February 2012 19:15, <[email protected]> wrote: > >> 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 >> than "Re: Contents of caret-users digest..." >> >> Today's Topics: >> >> 1. Re: Interspecies comparisons - creating a new atlas for a >> different primate species (Timothy Coalson) >> >> >> ---------- Forwarded message ---------- >> From: Timothy Coalson <[email protected]> >> To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> Cc: >> Date: Fri, 17 Feb 2012 12:31:56 -0600 >> Subject: Re: [caret-users] Interspecies comparisons - creating a new >> atlas for a different primate species >> 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 <[email protected]>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, <[email protected]>wrote: >>> >>>> 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 >>>> 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 <[email protected]> >>>> To: <[email protected]> >>>> 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, <[email protected]>wrote: >>>> >>>>> 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 >>>>> 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" <[email protected]> >>>>> To: "[email protected]" <[email protected]> >>>>> Cc: >>>>> Date: Wed, 15 Feb 2012 20:07:37 +0000 >>>>> Subject: [caret-users] Not Responding Error >>>>> >>>>> Matthew Maestri**** >>>>> >>>>> [email protected]**** >>>>> >>>>> 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 <[email protected]> >>>>> To: "Caret, SureFit, and SuMS software users" < >>>>> [email protected]> >>>>> 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 >>>>> > >>>>> > [email protected] >>>>> > >>>>> > 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 >>>>> > [email protected] >>>>> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> caret-users mailing list >>>>> [email protected] >>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>> >>>>> >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: Tristan Chaplin <[email protected]> >>>> To: "Caret, SureFit, and SuMS software users" < >>>> [email protected]> >>>> 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 < >>>> [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 >>>>>> >>>>> >>>>> >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: Timothy Coalson <[email protected]> >>>> To: "Caret, SureFit, and SuMS software users" < >>>> [email protected]> >>>> 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 < >>>> [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 >> >> > > _______________________________________________ > 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
