Hi Sabrina you need to tell us what you did the caused the crash. What was the command line? How did you try to load it?
cheers Bruce On Mon, 21 Dec 2015, Sabrina Yu wrote: > When I try to load the overlay in freeview, it crashes immediately. Any > thoughts on why this happens? > > Thanks > > ________________________________________ > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
