On Feb 21, 2012, at 12:49 PM, Colin Reveley wrote: > it doesn't have to be freesurfer; you can just skip the bits where a > midthickness is made and hack it a little and use straight from caret. Most > if it is just really good registration code. > > the freesurfer tutorial and code and data is in summs somewhere, and I forget > where exactly. the data for it is in two parts, but that's not made clear.
http://sumsdb.wustl.edu/sums/directory.do?id=8285961 > > There is recent paper by VE looking at some monkey visual anatomy. http://www.ncbi.nlm.nih.gov/pubmed/22052704 > the code was for that. the paper references the tutorial text, and code but > some of the code or data is missing, you have to fiddle with it. My own > original version of the scripts are lost in the mists of time now, or at > least I don't have anything I can guarantee I haven't touched. > > you can find it. > > it takes a midthickness of a macaque and registers it to f99 73730. > > your surface would stay the same shape, but have 73730 nodes as you > requested, it would have the macaque atlas topo. > > It would work as well as the landmarks probably. > > I don't think the nodes in f99 are evenly spaced as such at the fiducial or > sphere. I don't in general see why it would be important, unless you have a > specific reason for them to have certain spacing properties.. > > freesurfer produces a white matter surface with evenly spaced nodes relative > to the WM volume you give it. By eye they correspond to the voxel locations, > but I wouldn't stand by that claim it just looks like that. It's close enough > for what I want to do. > > hope helps > > Colin > > > > > On 21 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. Re: Interspecies comparisons - creating a new atlas for a > different primate species (Donna Dierker) > > > ---------- Forwarded message ---------- > From: Donna Dierker <[email protected]> > To: "Caret, SureFit, and SuMS software users" <[email protected]> > Cc: > Date: Tue, 21 Feb 2012 10:13:34 -0600 > Subject: Re: [caret-users] Interspecies comparisons - creating a new atlas > for a different primate species > I have never done interspecies registration, so my help will be limited there. > > But in the interest of mental model refinement, my own doesn't think of > getting a hemisphere on a standard mesh, with evenly spaced nodes, as a > precondition to registration; rather, I think of it as a step in the > registration, or a consequence thereof. Something the user doesn't do, but > the registration algorithm does. > > Typically, when we put surfaces through registration, they are not on a > standard, evenly spaced mesh going into the process. (Our preborder.sh > script in the Freesurfer to PALS pipeline does downsample first, but this is > for other reasons having to do with landmark identification/trimming.) > > With monkeys, I think we still go straight from native mesh to F99, and if > your monkey surface was generated by Freesurfer, Colin can probably point you > to David's recent tutorial more quickly than I can, since he's used it. > > But if you're going from monkey to human, I don't think a tutorial exists. > > > On Feb 20, 2012, at 6:55 PM, Tristan Chaplin 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 <[email protected]> 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 <[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 > > > _______________________________________________ > 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
