Thanks! Instead of aparcstats2table, I just used grep and awk to retrieve those directly from the ?h.aparc.stats, and then I calculated the mean_thickness = ((lh_mean_thickness * lh_white_surface_area ) + (rh_mean_thickness * rh_white_surface_area)) / (lh_white_surface_area + rh_white_surface_area)...

Best, Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edu

On 3/30/14 2:40 PM, "Douglas Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

I think aparcstats2table automatically includes these measures. Can you check? And, yes, mean thickness can be computed as (lh+rh)/2 doug

On 3/30/14 12:58 PM, Yang, Daniel wrote: Dear FreeSurfer Experts,

I would like to extract the mean thickness for each subject, and I can see that in the lh.aparc.stats, there are three lines. For example:

# Measure Cortex, NumVert, Number of Vertices, 107414, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 73280.4, mm^2 # Measure Cortex, MeanThickness, Mean Thickness, 2.56763, mm

I am wondering what command I can run with aparcstats2table or mris_calc to retrieve these three pieces of information for each subject?

And is the MeanThickness across the whole brain supposed to be (lh + rh)/2?

Best, Daniel

-- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu

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