help > display freesurfer annotation file as outline in surf ice
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Jun 14, 2018  12:06 PM | nblauch - Carnegie Mellon University
display freesurfer annotation file as outline in surf ice
hi,

beautiful rendering in surf ice. i am wondering, is there a way to display a freesurfer annotation file as an outline in surf ice? or perhaps a tool which can convert freesurfer annotation files to something compatible for viewing as outlined labels in surf ice? 

thanks,
Nick
Jun 14, 2018  02:06 PM | Chris Rorden
RE: display freesurfer annotation file as outline in surf ice
Nick

Take a look at the wiki for an example of loading the included boggle.annot. The script below should load the files included with Surfice and generate the attached image. Note that the annot files also save a text string with the name of each region.


begin
resetdefaults();
meshload('lh.pial');
overlayload('boggle.annot');
atlassaturationalpha(0.5, 0.7);
overlayload('fhlin_toolbox.w');
overlayminmax(2, 0.7, 0.8);
overlaycolorname(2, 'red');
end.


Surfice does not display these text labels, which would be nice. Displaying the core region names in an uncluttered way might be best done with a vector art tool, but Surfice is open source, so feel free to make (and share) any changes you wish.
Attachment: bogglex.jpg