thanks Matt. Chimp sounds interesting! I was really addressing the person who was making their own atlas, which I suspected of being marmoset. possibly not.
On 16 March 2012 16:37, <[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. .annot or .label conversion to caret (Sam Carpenter) > 2. marmoset atlas (Colin Reveley) > 3. Re: .annot or .label conversion to caret (Donna Dierker) > 4. Re: marmoset atlas (Matt Glasser) > 5. Mapping 2D ROIs to 3D surface (Carissa Philippi) > > > ---------- Forwarded message ---------- > From: Sam Carpenter <[email protected]> > To: "[email protected]" <[email protected]> > Cc: > Date: Thu, 15 Mar 2012 17:54:46 -0700 > Subject: [caret-users] .annot or .label conversion to caret > Hi All, > > We currently have surface regions generated in FreeSurfer and are trying > to get them over to the PALS atlas in caret. They are in .annot and > .label format currently. Once in Caret I plan to apply the > *Reg-to-PALS_fsaverage.RIGHT.RegWithPALS-B12.163842.spec.deform_map > *to map them to the PALS atlas. > > The problem: currently I am unable to load or view them in caret. Does > anybody know of a conversion method or way to load them into caret? (Caret > apparently accepts .label files, but they are not loading correctly) > > All help/suggestions is appreciated. > > Thanks All, > > -S > > > ---------- Forwarded message ---------- > From: Colin Reveley <[email protected]> > To: <[email protected]> > Cc: > Date: Fri, 16 Mar 2012 12:39:43 +0000 > Subject: [caret-users] marmoset atlas > I wonder, is there a caret atlas for any marmoset anatomy? > > There was a discussion a little while back regarding the construction of > an atlas for a new species. > > Is that in fact common marmoset? > > will it be publicly available if so? > > I am presenting my own work to a lab in late june. the lab is located near > washington DC. > > Their work involves comparing the visual systems of marmoset, macaque and > human with fMRI. > > I thought it would be nice to demonstrate interspecies registrations and > morphometry. Just monkey to human would be ok, and there are publications > there of course, but marmoset <-> macaque would be of interest to them I'd > say. > > best, > > Colin > > > ---------- Forwarded message ---------- > From: Donna Dierker <[email protected]> > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Cc: > Date: Fri, 16 Mar 2012 10:00:26 -0500 > Subject: Re: [caret-users] .annot or .label conversion to caret > I don't have the answers at my fingertips, but here are a couple of clues > that I recall from recent experience doing this: > > * Enter "caret_command -help-full > /tmp/caret_command.txt" at the command > line, and then use a text editor to read /tmp/caret_command.txt. Search > for "file-convert" and look for an example that shows conversion from label > to paint. > > * Make sure when you write your .label from Freesurfer that you use the > appropriate reference surface. I don't remember the appropriate Freesurfer > commands for this, but if you google Freesurfer aparc you might find it. I > don't understand the annot and aparc formats as well as I'd like, but there > is some command that writes this out vertex-wise relative to a reference > surface, and it's important that this be the right surface. > > To use that deform_map file, your source labels need to be on fsaverage > *right* standard mesh. This might affect the reference surface you use > when writing your labels. I haven't digested all of this: > > http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation > > We do have a script that makes it easy to get stuff on the new fs_LR > atlas, to which we're transitioning from PALS. Some parcellation schemes > have been moved to this new atlas already, so it would be helpful to know > what is already on PALS that you want to view with your data. > > > On Mar 15, 2012, at 7:54 PM, Sam Carpenter wrote: > > Hi All, > > We currently have surface regions generated in FreeSurfer and are trying > to get them over to the PALS atlas in caret. They are in .annot and > .label format currently. Once in Caret I plan to apply the > *Reg-to-PALS_fsaverage.RIGHT.RegWithPALS-B12.163842.spec.deform_map > *to map them to the PALS atlas. > > The problem: currently I am unable to load or view them in caret. Does > anybody know of a conversion method or way to load them into caret? (Caret > apparently accepts .label files, but they are not loading correctly) > > All help/suggestions is appreciated. > > Thanks All, > > -S > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > ---------- Forwarded message ---------- > From: Matt Glasser <[email protected]> > To: "'Caret, SureFit, and SuMS software users'" < > [email protected]> > Cc: > Date: Fri, 16 Mar 2012 10:05:09 -0500 > Subject: Re: [caret-users] marmoset atlas > ** ** ** ** > > Unfortunately not. We’ll have a chimpanzee atlas at some point in the > future though.**** > > ** ** > > Peace,**** > > > Matt.**** > > ** ** > ------------------------------ > > *From:* **[email protected]** [mailto:** > [email protected]**] *On Behalf Of *Colin Reveley > *Sent:* Friday, March 16, 2012 7:40 AM > *To:* [email protected] > *Subject:* [caret-users] marmoset atlas**** > > ** ** > > I wonder, is there a caret atlas for any marmoset anatomy?**** > > ** ** > > There was a discussion a little while back regarding the construction of > an atlas for a new species.**** > > ** ** > > Is that in fact common marmoset?**** > > ** ** > > will it be publicly available if so?**** > > ** ** > > I am presenting my own work to a lab in late june. the lab is located near > ****washington** **DC****.**** > > ** ** > > Their work involves comparing the visual systems of marmoset, macaque and > human with fMRI.**** > > ** ** > > I thought it would be nice to demonstrate interspecies registrations and > morphometry. Just monkey to human would be ok, and there are publications > there of course, but marmoset <-> macaque would be of interest to them I'd > say.**** > > ** ** > > best,**** > > ** ** > > Colin**** > > > ---------- Forwarded message ---------- > From: Carissa Philippi <[email protected]> > To: <[email protected]> > Cc: > Date: Fri, 16 Mar 2012 10:10:11 -0500 > Subject: [caret-users] Mapping 2D ROIs to 3D surface > Hello, > > I am a new CARET user. I would like to create a figure to display a > number of seed regions of interest (belonging to different attention > networks) that I used for a resting-state functional connectivity > analysis. I looked into the tutorials available for displaying foci as > well as for mapping volumes to surfaces. However, I'm not sure which > option is best for the purpose of creating the figure I mentioned > above. > > I currently have all of the spherical (6mm radius) seed regions of > interest in Talairach space. I would appreciate your recommendation > for the best way to create ROIs for display in CARET. Would you > recommend converting these to PALS coordinate space, to be displayed > on the PALS surface? If so, what is the best way to create ROIs? By > creating foci or mapping volumes to surfaces? > > Alternatively, is there a way to convert and display another > standardized atlas (e.g., MNI or Talairach) to be displayed in CARET? > > Thank you very much in advance for your help. > > Best, > > Carissa > > -- > Carissa L. Philippi, PhD > Postdoctoral Research Scholar > Department of Psychiatry, University of Wisconsin-Madison > 6001 Research Park Blvd > Madison, WI 53719 > Email: [email protected] > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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