Try this

cd $SUBJECTS_DIR/subject

mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz

mri_segstats --seg mri/wmparc.a2009s.mgz --sum stats/wmparc.a2009s.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject --surf-wm-vol --ctab $FREESURFER_HOME/WMParcStatsLUT.txt --etiv

doug

On 03/22/2012 12:57 PM, sam bedford wrote:

Dear All

We want to find frontal lobe grey and white matter volumes in a patient group to compare it with control group. In particular, we want to see the grey and white matter volumes in the dorsolateral prefrontal cortex (DLPFC). However we seem to be having problems finding this region on the processed data for white matter volume (after recon-all command). It was previously suggested in this mailing list that we can get grey matter volume for the DLPFC by combining the following volumes:

$hemi.G_frontal_middle.label $hemi.S_frontal_inferior.label $hemi.S_frontal_middle.label

We are wondering how to get white matter volumes in the same region...

If getting the DLPFC volume is difficult then can we just use the frontal grey and white matter volumes to make between group comparisons. From aseg and aparc files in the stats folder, adding all the following values below would give us frontal white and grey matter volumes. Or is there a simpler and less time consuming way to calculate grey and white matter volume in the frontal lobe?

Frontal lobes - White Matter volume

caudalmiddlefrontal

lateralorbitofrontal

medialorbitofrontal

paracentral

parsopercularis

parsorbitalis

parstriangularis

precentral

rostralmiddlefrontal

superiorfrontal

frontalpole

Frontal lobes - Grey Matter volumes

G_and_S_frontomargin

G_and_S_paracentral

G_and_S_subcentral QQQ???

G_and_S_transv_frontopol

G_front_inf-Opercular

G_front_inf-Orbital

G_front_inf-Triangul

G_front_middle

G_front_sup

G_precentral

S_front_inf

S_front_middle

S_front_sup

Thanks in advance

Sam

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