Maartje,

I think you can make use of aparcstats2table when you first run

mris_anatomical_stats -l ?h.cortex.label -b -f path_to_homedirectory/subject/stats/?h.cortex.stats subject ?h

for every subject and every hemisphere (preferably using a batch file where you can list up all the commands). You will get a ?h.cortex.stats file in the stats subdirectory of every subject which you can read out with aparcstats2table to generate a simple text file with the following command:

aparcstats2table --subjects subject1 subject2 subject3 subject4.... --h ?h --meas volume --parc cortex --t yourfilename.txt

Best wishes, Christian

--- University of Cologne Department of Psychiatry

Nick Schmansky schrieb:

Maartje,

You can get total gray matter volume for a hemi with this:

mris_anatomical_stats -l ?h.cortex.label nick12 ?h

replacing ?h with lh and rh. the label file causes it to exclude the non-cortical region (medial wall including corpus callosum) to give the most accurate measure. you'll have to do some script work to gather this up for your group of subjects (we ought to update aparcstats2table with a new flag to do this for you).

Per your need to find a local maximum, there is no automated way to do this in qdec (or tksurfer, as far as i know). It is feature that is on the list to add (to search a neighbor of vertices around the currently selected vertex to find the maximum). Pushing the threshold to just short of the color disappearing is the only way to find a maximum currently.

Nick

On Tue, 2008-12-09 at 18:59 +0100, Maartje Katzenbauer wrote:

...

Dear Freesurfer,

I have two questions.

My first question is about the cortical parcellation. It's possible to make an aparcstats2table for the hemispheres on the paramaters volume, thickness, area and mean curvature. I would like to know the total gray matter volume, because I want to know if I need to correct for it, like we do in volumetry studies. One needs to correct for intracranial brainvolume differences between specific groups. I can't find the total gray matter volume in the aparcstats2table for volume. And I can't figure out how I can destilate it from QDEC.

My second question is about de brainpicture in QDEC. If you have set your threshold and you define a ROI, I would like to know the 'local maximum' in the colored area. (You can set the arrow manually by changing the threshold maximum to a level that the color keeps on changing). But I would like to find a structured and more reliable way. Does anybody know if it's possible?

Thanks a lot.

Kind regards, Maartje Katzenbauer

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