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.
- Does the wmparc.stats contain mean white matter intensity values
for each ROI?
Yes
- 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