Hi, Sorry for bringing this thread up again. Referring back to the figure in the Salat paper, what map do I load as an overlay to get the intensity maps? How do I generate these maps?
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: Monday, December 21, 2015 10:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity freeview or tksurfer. Load the relevant map as an overlay On 12/21/2015 12:57 PM, Sabrina Yu wrote: > 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 > > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
