which figure(s) in particular? On 01/28/2016 01:41 PM, Sabrina Yu wrote: > 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 > >
-- 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
