> To: freesurfer@nmr.mgh.harvard.edu
> From: greve@nmr.mgh.harvard.edu
> Date: Fri, 15 Jan 2016 12:00:02 -0500
> Subject: Re: [Freesurfer] mri_surf2vol {Disarmed}
>
> it is hard to tell from that view. Can you click on a point that appears
> to be outside the brain so we can see what it looks like around that
> point in all three views?
>
> On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
> > Hi All,
> >
> > In fs5.3, I tried to generate a volume mask from the pial surface
> > using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg
> > $subjsess/bold/001/register.dof6.dat --template
> > $subjsess/bold/001/template.nii --surf pial --o
> > $subjsess/bold/001/lh.pialmask.vol.nii. The command run successfully.
> > I doubled check the registration between the EPI and high resolution
> > T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898.
> > however, when I overlaid the mask on the T1.mgz, it is clear that
> > some voxels outside brain are in the mask, and some voxels in the gray
> > matter are not in the mask (see attached figure). Did I use the
> > function incorrectly?
> >
> > Thanks very much for your help.
> >
> > Xiaomin
> >
> >
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
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>
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