We don't usually use the Destrieux atlas for this as the wmparc was oritinally intended to measure gyral white matter. However, you can still run the commands, something like
cd $SUBJECTS_DIR/subject
mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown \ --volmask --annot aparc.a2009s --o mri/wmparc.aparc.a2009s.mgz --ctxseg aparc+aseg.mgz
mri_segstats --seg mri/wmparc.aparc.a2009s.mgz --sum stats/wmparc.aparc.a2009s.stats \ --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --empty\ --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm \ --in-intensity-units MR --subject subject --surf-wm-vol \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt
doug
Lena Palaniyappan wrote:
I want to extract wm volumes using wmparc for parcellations contained in Destrieux 2009 atlas – but when I inspect my wmparc stats file, most of the volumes that I am interested in are reported as zero. What should I do to read these volumes?
Many thanks Lena _______________________________________________________ *Lena Palaniyappan *Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
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