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= PALS-B12 based ROIs on fsaverage =

A number of ROIs created by the [[http://brainvis.wustl.edu|Van Essen Lab]] using the [[http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases|PALS-B12 atlas of human cerebral cortex]] have been mapped to !FreeSurfer's fsaverage subject included with v5.0.0, taking the form of !FreeSurfer annotation files. The ROI .annot files are found in the fsaverage/label directory. You can map the annotation from fsaverage to the surface of a subject using this command:

{{{
 mri_surf2surf --srcsubject fsaverage --trgsubject subj1 --hemi lh \
   --sval-annot $SUBJECTS_DIR/fsaverage/label/lh.PALS_B12_Brodmann.annot \
   --tval       $SUBJECTS_DIR/subj1/label/lh.PALS_B12_Brodmann.annot
}}}

This will create $SUBJECTS_DIR/subj1/label/lh.PALS_B12_Brodmann.annot where subj1 should be substituted with the name of your subject. You will also have to rerun the above command for the right hemisphere to get that as well. 

The --sval-annot flag will change the map method to nnf so that the annot indices are not averaged. 



Provenance and reference information originating from Caret about the ROIs can be viewed by:
{{{
mris_info lh.PALS_B12.labels.gii
}}}

##[[{{attachment:PALS-B12-raw-text.txt}}|Here is that raw output]].

The label table for these .annot files can be extracted by:
{{{
mris_info lh.PALS_B12_Brodmann.annot
}}}

##[[{{attachment:PALS-B12-labeltable.txt}}|Here is that label table]]. Note that all ROIs are in this one table.

The ROIs are displayed below on the fsaverage inflated surface:
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== ?h.PALS_B12_Brodmann.annot ==
{{attachment:lh.palsbrodmannlat.jpg}}
{{attachment:lh.palsbrodmannmed.jpg}}
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== ?h.PALS_B12_Lobes.annot ==
{{attachment:lh.palslobeslat.jpg}}
{{attachment:lh.palslobesmed.jpg}}
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== ?h.PALS_B12_OrbitoFrontal.annot ==
{{attachment:lh.palsorbitofrontal.jpg}}
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== ?h.PALS_B12_Visuotopic.annot ==
{{attachment:lh.palsvisuotopic.jpg}}