This is a bug in 5.3. I've put a new version for you here. Let me know if that works ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol
On 01/27/2015 01:26 PM, Benjamin Zimmerman wrote: > Hello, > > When I try your recommended code, I am able to get the data back into > volumetric space, but one hemisphere's cortex is significantly thinner > than the other. If I do mri_surf2vol separately on each hemisphere, I > don't have this problem. It seems to occur only if I try merging the > two files. I assume that this is because I am using the volume that I > am merging to as a template instead of inputting the template > directly. Do you have any ideas how to solve this problem? > > Thanks for your help, > > Ben > > > > > > > > On Wed, Dec 24, 2014 at 2:57 PM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > I don't think we have a tool to display the color wheel in a > volume. FreeView might be able to do it. For the color wheel in > tksurfer, you are looking at the angle file (one for eccen and one > for polar), so you would map them. You can run mri_surf2vol > something like > > mri_surf2vol --surfval lh.angle.nii.gz --identity yoursubject > --hemi lh --template path/orig.mgz --fillribbon --o vol.angle.mgz > mri_surf2vol --surfval rh.angle.nii.gz --identity yoursubject > --hemi rh --fillribbon --merge vol.angle.mgz --o vol.angle.mgz > > doug > > > On 12/18/14 1:24 PM, Benjamin Zimmerman wrote: >> I mean the individual's anatomical volumetric space. >> >> On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> >> wrote: >> >> >> What do you mean by the individual's volumetric space? The >> anatomical >> space or the functional space? >> >> >> On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: >> > Thanks for the advice. I thought I would like to use >> mri_surf2vol, but >> > I am a little confused about the parameters and how they >> relate to >> > what the retinotopy analysis outputs. >> > >> > To be explicit, I want to view the real.nii.gz and >> imag.nii.gz files >> > in an individual's volumetric space. I can load these as >> overlays to >> > the inflated surface using tksurfer <subject> <hemisphere> >> inflated. >> > Then I can configure the overlay to use a color wheel color >> scale and >> > display as complex to see the retinotopic mapping. >> > >> > I'm not sure how I would go about using mri_surf2vol to >> recreate this >> > map in volumetric space. Should I just use real.nii.gz and >> imag.nii.gz >> > as surfval? Where is the registration file outputted in a >> retinotopy >> > analysis? >> > >> > Thank you for any more help that you can provide, >> > >> > Ben >> > >> > On Mon, Dec 15, 2014 at 3:26 PM, dgw <dgwake...@gmail.com >> <mailto:dgwake...@gmail.com> >> > <mailto:dgwake...@gmail.com <mailto:dgwake...@gmail.com>>> wrote: >> > >> > Hi Ben, >> > >> > You should be able to map it back with mri_surf2vol. I >> haven't done >> > this, but the wiki page looks fairly detailed: >> > http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol >> > >> > HTH >> > D >> > >> > On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman >> > <benjamin.zimmerm...@gmail.com >> <mailto:benjamin.zimmerm...@gmail.com> >> > <mailto:benjamin.zimmerm...@gmail.com >> <mailto:benjamin.zimmerm...@gmail.com>>> wrote: >> > > Hi all, >> > > >> > > FsFast has an excellent individual retinotopy >> analysis that >> > allows me to see >> > > phase data on the inflated surface of the brain. Is >> there a way >> > to view the >> > > results of the retinotopy analysis in the subject's >> original >> > volumetric >> > > space rather than on the subject's surface space? >> > > >> > > Thank you for any help, >> > > >> > > Ben >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto: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 >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://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 >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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
