To get the Destrieux atlas parcellations in the wmparc, first have a look at the -wmparc section of the recon-all table:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
those last two commands would be modified like this:
mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz
mri_segstats --seg mri/wmparc.a2009s.mgz --sum stats/wmparc.a2009s.stats ... (all those other args)
the important change was to mri_aparc2aseg, where i change the --ctxseg arg to aparc.a2009s+aseg.mgz, as that is the Destrieux atlas. the other change was just changing the 'wmparc' name to 'wmparc.a2009s', just to be consistent with naming.
probably we should modify recon-all so that wmparc.a2009s.stats is created by default.
you could also 'cheat' by just copying aparc.a2009s+aseg.mgz overtop aparc+aseg.mgz and then running 'recon-all -s subj -wmparc', but that can make keeping track of what's what more difficult.
n.
On Mon, 2010-02-15 at 15:19 +0000, Lena Palaniyappan wrote:
Hi all
Could anyone help me with extracting the wmparc volume stats in accordance with Destrieux atlas?
As it stands now the segmentations corresponding to whitematter beneath Destrieux 2009 parcellations are returned empty when called for
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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