On 12/15/2015 01:00 PM, Sabrina Yu wrote: > > Hi, > > > Just following up on my previous email (see below) as I have not yet > heard back. I also have another question regarding the lh.wm.mgh and > rh.wm.mgh generated by pctsurfcon. How do I view these as surface > overlays on T1 brain scans? > If you want to view them on a volume instead of a surface, you can use mri_surf2vol > > > Thank you very much. > > > > ------------------------------------------------------------------------ > *From:* Sabrina Yu > *Sent:* Thursday, December 10, 2015 2:47 PM > *To:* Freesurfer support list > *Subject:* Gray matter intensity > > Hello, > > > > I have been following the instructions in this email thread: > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html. > <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html> > And > have successfully gotten the wm-gm signal intensity contrast, but > now have a few questions regarding signal intensity for white matter > and gray matter intensity. > > > 1) Does the wmparc.stats contain mean white matter intensity values > for each ROI? > Yes > > 2) Is it possible to extract these same mean intensity values for gray > matter? There is no gmparc.stats file. We know that it's possible to > calculate these from the WM/GM ratio from pctsurfcon, but it'd be > great if there was a more direct way to get this data. > There is not one by default that includes the cortical parcellation. You can create your own with mri_segstats passing it the aparc+aseg.mgz as the segmentation. Look in the recon-all.log file for the command line that creates the aseg.stats or wmparc.stats. You will probably need to change the --ctab flag to --ctab-default (no argument) > > > Thank you, > > Sabrina Yu > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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