Hello, Thank you for the very helpful replies! I have another quick question. Which commands would I use to generate images like the ones in Figure 1 (C) generated in the Salat paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?
Thank you Sabrina ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Tuesday, December 15, 2015 10:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
