Hi Freesurfer experts,

I am attempting to turn my surface-based parcellation into a segmentation file using the following command:

mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask

However, when I load the resulting volume using my custom LUT the ROIs get labeled to the white matter and subcortical structures leaving the grey matter unlabeled.

When I examine the annotation files, they look appropriate and there isn't any overlap.

Do I need to include the subcortical structures in my custom LUT to avoid this from happening or is there a better solution?

Thank you!

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