Viewing a Freesurfer .annot in SUMA


I would like to have the Yeo7 and Yeo17 resting state network ROIs in a format that I can view/work with in SUMA. I’ve been having trouble converting them over from Freesurfer’s .annot format into a .niml.dset format. (If there is another format you would recommend, please let me know!) So far, the closest I’ve come is with the following command:

FSread_annot -input Yeo2011_7networks_N1000.annot -FScmap Yeo7ColorLUT.txt -FScmaprange 1 7 -hemi lh -dset lh.Yeo2011_7Networks.niml.dset

And the resulting image is attached for your viewing pleasure. (On the bright side, the colors are the right colors!) I look forward to hearing your ideas!



The FreeSurfer output is not on a standard mesh. Use this example :,160805,160838#msg-160838

I think you’re running into the issue that the Yeo atlases are only defined in fsaverage space, not in the native space of each participant. (Unlike aparc and the like). So, first, try using FreeSurfer’s mri_surf2surf to transform the Yeo atlas(es) to the mesh of each of your subjects:

(Start with setting your $SUBJECTS_DIR to a directory that includes both a copy of fsaverage and your subject’s freesurfer output folder)
Your command should look something like…
mri_surf2surf --srcsubject fsaverage --trgsubject MySubject --sval-annot $SUBJECTS_DIR/fsaverage/label/${hemi}.Yeo2011_7Networks_N1000.annot --tval Yeo_for_MySubject.annot --mapmethod nnf --hemi $hemi

If written as above, the output will be cleverly hidden in $SUBJECTS_DIR/MySubject/label. You should then be able to move forward with the FSread_annot command as you had.

Good Luck.