We use the MNI305through the (affine) talairach.xfm transform. doug On 03/17/2013 11:47 AM, Bruce Fischl wrote: > 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
-- 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: 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
