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
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