My idea is to convert the registered white surface into a volume, so it can be shown in a volume viewer (not a surface viewer). I need to display a DTI image and mark the edges of the white matter as a line on top if it.
This is not the exact command, I am not sitting in front of my station, but it goes something like it. I tried many combinations, the general error was related to the template files not on the correct format (it could have been they couldn't be found to be opened too, the error seemed generic). mri_surf2vol --surfval white --hemi lh --outvol test.mgz --template T1.mgz --volreg T1.mgz --sd /home/user/Desktop/sf/sub1 I am at a loss for the --volreg flag. The sd seems to indicate the directory of freesurfer (but then how is the command aware of the specficic subject I am trying to process? I tried using: --identity subject no luck. 'sub1' us my subject, located not in the default freesurfer directory. There are no examples or a lot of help using it https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol If this is not enough I can get back to you with the specific error tomorrow. On Mon, May 15, 2017 at 10:02 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > what was your mri_surf2vol cmd line? And what was the terminal output? > > On 5/15/17 9:59 PM, Gamaliz wrote: > > I looked at the ribbon.mgz, but it is a pial surface, not really > delineated white matter the way I need it. There is a command called > mri_sur2vol, I have tried to use it, but unsuccessfully, no idea if that is > the solution to my problem. > > On Mon, May 15, 2017 at 9:57 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> > wrote: > >> not sure what you mean. Have you looked at the ribbon.mgz file? >> >> On 5/15/17 5:20 PM, Gamaliz wrote: >> >> I need to create an image which overlaps the T1/mgz and the outer surface >> of the white matter. How do I convert the surface into a mgz volume? >> >> >> -- >> gAbE >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e >> du/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. > > -- > gAbE > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 > > > 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. > > -- gAbE
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