Hi Dr. Greve,

Thanks for your reply.

Could you please confirm once recon-all -all is done, following steps are correct to get cortical thickness, volume and area stats using Yeo atlas:

(1). Use "-sval-annot" option to transfer annotation (Ref. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-July/039348.html )

mri_surf2surf --srcsubject fsaverage --trgsubject XYZ --hemi lh --sval-annot $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot

(2). Use "sval" option to transfer confidence map. (Ref. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-July/039348.html) mri_surf2surf --srcsubject fsaverage --trgsubject XYZ --hemi lh --sval $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz

(3). mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh

(4). aparcstats2table --subjectsfile SubIDs.txt --hemi lh --meas thickness -t LH_Thickness.txt

Thanks.

On Wed, Dec 14, 2016 at 4:34 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

You will need to create the yeo parcellation for each subject as well as run mris_anatomical_stats to create the stats file, then run aparcstats2table specifying the new stats file. Look in the recon-all.log file to see how to call mris_anatomical_stats

On 12/14/2016 03:56 PM, Martin Juneja wrote:

...

Hi,

I would like to use aparcstats2table command. By default, it uses Killiany/Desikan parcellation atlas. But I would like to use atlas by Yeo and colleagues (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011

).

...

Could you please let me know how can I use this atlas instead of default --parc and what would be the aparcstats2table command for this?

Thanks.

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