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 <fischl@nmr.mgh.harvard.edu>
> To: Longchuan Li <leonado78@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
> >
> >
> >
>
>
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