Thanks for pointing that out Kayle!
On 10/07/2013 10:40 AM, Kayle Sawyer wrote:
If you want the global thickness for all your subjects in a single table, use asegstats2table, e.g.
aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile rh.aparc_stats.txt
The first column will be the rh thickness, which you can average with the lh in a spreadsheet. Or, you can use aparcstats2table again with "--meas area", and then in your spreadsheet use the equation you described to give additional weight to the hemisphere with larger area.
Because it's in a table, you can then use this as a covariate in your FSGD, but I thought I read that some people do not recommend using global thickness as a covariate.
-Kayle
Date: Fri, 04 Oct 2013 19:25:07 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Global thickness calculation To: freesurfer@nmr.mgh.harvard.edu Message-ID: 524F4E53.3020802@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
you can do something like this
cd $SUBJECTS_DIR/$subject
mri_segstats --slabel $subject lh label/lh.cortex.label --i surf/lh.thickness --id 1 --sum stats/lh.meanthickness.dat
On 10/04/2013 05:22 PM, Mollie Bayda wrote:
Hi, I am trying to calculate whole-brain mean cortical thickness in each individual subject for correction of regional mean thicknesses. I see on the wiki that this is recommended to be done by: bh.thickness = (lh.thickness X lh.area) + (rh.thickness X rh.area) / (lh.area +rh.area) In my table I see lh and rh total area but I do not see lh and rh thickness. All I see is mean thicknesses for each region. Are the total rh and lh mean thicknesses supposed to appear in the table? Thanks!
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