thanks tim. this line is germane. the specs have: my fiducial, sphere and topo. the other spec has f99 fid, Macaque.sphere_6.RIGHT_HEM.74k.topo, Macaque.ATLAS.sphere.6.74k.coord - plus borders
## USE CARET LVD SBR UNTIL caret_command fixed for new spheres. caret_command -surface-register-sphere-spec-only N $ATLAS_DIR/Macaque.TEMPLATE.FS-to-F99.LVD.deform_map $CASE.$HEM_FLAG.For-Reg-with-F99.$NUMBER_NODES.spec $ATLAS_DIR/Macaque.F99.R.For-Registration-with-$CASE.$HEM_FLAG.74k_f99.spec I'm guessing that might be pretty relevant. I don't know what LVD is. and I think if regular node spacing is what I want in the fiducial (that's the brain one right?) which is so, then I'd want to maybe adapt this so that F99 registers to my free surfer fiducial since the node spacing there is fairly even, corresponding loosely to voxel locations, which is what I would like. sadly I fail to understand why there is a deformation map involved at all when then thing to be deformed hasn't yet been deformed. these are generic parameters of some sort? My understanding of surface based registration is conceptual at best. regardless of the node spacing issue, my registrations could certainly improve and so if you have any comment on the comment at the top of the code I'd be very grateful indeed. has "caret_command been fixed for new spheres"? If so, how can I update this process? Colin 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 > >
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