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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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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
also be sure to add the flag --a2009s to the end of the mri_aparc2aseg command shown below (i forgot to mention this the first time aroun). this will fix the problem where you were not seeing the correct labels (you should now see the Destrieux labels when viewing in tkmedit).
per the Segmentation Fault problem you encountered with mri_segstats, it turns out it was a bug in our code. i've posted a fix for mri_segstats for the 32b and 64b linux platforms here:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/
n.
On Wed, 2010-02-17 at 11:03 -0500, Douglas N Greve wrote:
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
This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Lena Palaniyappan -
Nick Schmansky