the code that I sent creates the paintfiles on native space of subjects. before that you have to make new labels on fsaverage spcae by using mri_label2label like: for rh.V1.label
mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject fsaverage --trglabel rh.V1_fsaverage.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh Then you need to apply the deformation map to get the new paint file on fsaverage caret space. Best Rouhi On Fri, Mar 16, 2012 at 10:10 PM, Rouhollah Abdollahi <[email protected]>wrote: > Hi , > Donna I had done that for our project if you remember. > The easy way is to read the label files ( they are in text format). > I have added the simple code and a sample paint file to create paint file > on fsaverage. (74K) > I hope you have Matlab. if not let me know to send you bash script one. > > Best > Rouhi > > > On Fri, Mar 16, 2012 at 4:00 PM, Donna Dierker < > [email protected]> wrote: > >> 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 >> >> >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> > > > -- > With Best Regards > Rouhollah Abdollahi > > > > -- With Best Regards Rouhollah Abdollahi
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