Hi, I’m trying to use the Yeo2011 annotations to create individual volume masks in subject space.

I first use mri_surf2surf to map the annotations from fsaverage to individual subjects:

mri_surf2surf --srcsubject fsaverage --trgsubject subject --hemi rh --sval-annot fsaverage/label/rh.Yeo2011_7Networks_N1000.annot --tval $SUBJECTS_DIR/subject/label/rh.Yeo2011_7Networks_N1000

Then I use mri_apar2aseg to map the annotation from the surface to the volume and thought he annot-table flag would use the labels provided in the custom color lut file.

mri_aparc2aseg --s subject --o test.mgz --annot Yeo2011_7Networks_N1000 --annot-table path_to/Yeo2011_7Networks_ColorLUT.txt

However the output is using different segmentation/color assignments. I can certainly find out which segmentation corresponds to which color and extract them separately (i.e. with fslmath or mri_binarize)..just wandering if I missed something or something changed since these posts?

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35247.html

Thanks Dorit