Hi Khalid, it might be easier to create your own annotation of your lobe definition, then run mris_anatomical_stats with this annotation. To do this, first break up the Desikan atlas into labels (mri_annotation2label), then merge the labels that comprise each lobe into a single label (mri_mergelabels), then create a new annotation from the lobe labels (mris_label2annot). You can do all of these from the cmd line. doug

On 10/28/2012 01:46 PM, Khalid Hamandi wrote:

Dear FSers

I am looking for help in determining the average thickness for each lobe, frontal, temporal, parietal, occipital and cingulate by merging Desikan atlas ROI values. I have had a look at the parcellation wiki http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation and see the basic principles, i think....

I believe i could extract labels from each subject using mri_annotation2label, multiply the number of vertices per ROI by the average ROI thickness from asegstats and sum the lobar ROIs (no of vertices x av thickness), then divide by the total number of vertices in that lobe. I have 82 subjects. If mris_anatomical_stats is the way to go then i'm having trouble following the command line options.

Is there an 'easy' way to do this, are there Freesurf command tools that help? or does someone already have a script they are willing to share?

I'm using Freesurf version 4.4.0. so don't have --lobesStrict if that was going to be on offer.

many thanks

Khalid

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