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 > > > > > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
