It will be more involved than that. You will need to create an annotation that contains your label (maybe in addition to other labels), then uses mri_aparc2aseg with the --labelwm option, something like

mri_aparc2aseg --s subject-anat --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot yourannot

doug

dolphinede@aol.com wrote:

Hi Doug,

thanks a lot for your answer.

So i understand you right that i can get "exact" knowledge about the thickness, grey matter volume and pial surface area in my ROI, but in case of "the" ROI white matter volume, i have to look to which cortical label my ROI counts and then I use the wmparc.files for this label?

Best regards

Daniel Klein

-----Ursprüngliche Mitteilung----- Von: Douglas N Greve greve@nmr.mgh.harvard.edu An: dolphinede dolphinede@aol.com Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Verschickt: Mo, 24 Okt 2011 4:48 pm Betreff: Re: [Freesurfer] white matter volume in a ROI

For GM area and volume, you can use mris_anatomical_stats. See the recent thread on how. For the WM volume, how would you define the WM volume that corresponds to you label? We have a routine that parcellates WM based on closest proximity to a cortical label. doug

dolphinede@aol.com wrote:

...

Dear FreeSurfer experts,

i have created a ROI in qdec , where i have found a significant correlation between lgi and age.

I mapped this ROI to all subjects.

I am interested to compare in this ROI the pial-surface area, the grey matter volume and if possible the white matter volume for this specific region and i am not sure how to do this?

Best regards

Daniel Klein

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