The pial surface is the boundary between the gray matter and the tissue on the outside of the brain. It is not gray matter itself. If you want a mask of cortical gray matter, then use mri_label2vol --seg ribbon.mgz ..., then binarize the output of that to give you cortical GM.
On 01/15/2016 12:32 PM, Xiaomin Yue wrote:
Maybe, I misunderstand it. Is the pial surface same as gray matter? If not, how could I create a gray matter mask?
Thanks,
Xiaomin
On Fri, Jan 15, 2016 at 9:31 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think you could easily hit all those voxels with a 1.5mm voxel size. Not sure what you are asking about in terms of gray matter.
On 01/15/2016 12:27 PM, Xiaomin Yue wrote:
The voxel size is 1.5mm. Some of voxels in the gray matter are not included in the mask as well. Why?
Xiaomin
On Fri, Jan 15, 2016 at 9:21 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That point is fairly close to the pial surface. What is your voxel size? It will include any voxel even if only a corner of it has some surface in it.
On 01/15/2016 12:16 PM, Xiaomin Yue wrote:
here it is. thanks,
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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