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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