Hi Sara

mri_aparc2aseg should do the trick. I don't think there's an easy way to do #2 though. The make_face_parcellation stuff samples relatively uniformly over the cortex so the parcels in it won't correspond to the aparc.annot labels in any real way.

cheers Bruce

On Mon, 18 Apr 2011, Jahfari, Sara wrote:

Dear Freesurfer crew,

We would like to use freesurfer to do the high resolution parcellation of gray matter reported in Hagmann et all. 2008.

This far I have used (looking also at previous postings on this matter)

mris_divide_parcellation pp0672 rh aparc.annot 150 rh.split150.annot (but this creates a parcellation of long strips per region, that is not fully suited for what we want).

mris_make_face_parcellation lh.inflated $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot

The make_face_parcellation looks very nice, but I have the following questions:

1. How can I convert the .annot file to an actual .mgz volume segmentation. ( I have tried mri_annotation2label but I am not sure how the ? segbase should be specified)
2. Is there a way to match the aparc.annot labels to the ic3.annot parcellation (in the way that is done with mris_divide_parcellation)

( I have converted the both annot files to labels to look at the vertex numbers, but preferably I would like the eventual segmentation to contain label info?s per volume such as in aparc+aseg.mgz)

Any help would be appreciated a lot.

Thanks,

Sara