yes, I have it On Tue, 19 Mar 2013, Longchuan Li wrote:
Hi, Bruce The command line I used is: mris_fill -r 1 -c rh.white rh.white.nii.gz I attached the rh.white in my previous mail. Could you see it in the attachment? Thank you! Longchuan _________________________________________________________________________________________________________________________ From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> To: Longchuan Li <leonad...@yahoo.com> Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu> Sent: Tuesday, March 19, 2013 8:10 PM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates can you send your mris_fill command line? And maybe the lh.white surface you are trying to fill? Bruce On Tue, 19 Mar 2013, Longchuan Li wrote: > Hi, Bruce > > This is the lh.white that gives me the empty volume when I use mris_fill to > sample it to the volume space. Could you help diagnose what is causing it? > Thank you very much in advance! > > Lognchuan > > > ____________________________________________________________________________ > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > To: Longchuan Li <leonad...@yahoo.com> > Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu> > Sent: Sunday, March 17, 2013 11:47 AM > Subject: Re: [Freesurfer] make a volume template from the surface-based > template for non-human primates > > Hi Longchuan > > I'm not sure what space the volume average is constructed in - Doug would > know. Probably talairach, in which case it won't match the surfaces well. > Can you send along your mris_fill command line? It shouldn't produce an > empty volume. There's no reason to look at the inflated surfaces in the > volume though - they have no volumetric meaning. > > cheers > Bruce > > > On Fri, 15 Mar 2013, Longchuan Li wrote: > > > Hi, Bruce > > > > Sorry for the late reply as I was trying to figure it out by myself. > > I mean the average of the subjects in the volume space that were used for > > generating the surface template. Actually I kind of found a volume average > > in the mri folder named as T1.mgz that seems to correspond to the surface > > template for the non-human primates. Perhaps because my ?h.white and > ?.pial > > surface files do not have the identical origins as that of the volume > > template, when I used the function "mri_surf2vol" to project the mgh > surface > > file to the volume average, I always got the outputs telling me there is 0 > > hits. I tried to diagnose it by projecting the ?h.white and ?h.pial to the > > volume using "mri_fill" and I got an empty volume. I then tried to project > > ?h.inflated to the volume space using the "mri_fill" and this time, I got > a > > mask in the output volume space. Therefore, i suspect that there is a > > mismatch of the origins between the ?h.white and the volume template in > the > > mri folder. > > > > Could you please show me what are the best strategies to correctly project > > the mgh file to the volume template in the 'mri' folder? > > > > Many thanks > > > > Longchuan > > > >___________________________________________________________________________ > _ > > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > > To: Longchuan Li <leonad...@yahoo.com> > > Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu> > > Sent: Friday, March 15, 2013 4:56 PM > > Subject: Re: [Freesurfer] make a volume template from the surface-based > > template for non-human primates > > > > Hi Longchuan > > > > what kind of volume template do you mean? > > Bruce > > On Fri, 15 Mar 2013, Longchuan Li > > wrote: > > > > > Hi, FreeSurfer experts > > > > > > I have a question regarding making a volume template based on the > surface > > > template for non-human primates. I have made a surface template using a > > > group of monkeys and now, we want to see the result, which is a mgh > > surface > > > file, on the coronal slices of the template. So I am planning to > generate > > a > > > volume template corresponding to the surface template and then project > the > > > mgh file to the volume for viewing. Could someone tell me what is the > best > > > way to generate such a volume template? > > > > > > Many thanks in advance! > > > > > > Longchuan > > > > > > > > > > > > > > > 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 > > > 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 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.
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