Hello, Bruce,

Thanks a lot for your reply, I reload the pictures with surface overlayed.

So,

fig. 1 is the segmentation results and surface overlayed to the original volume
fig.2 is the wm.mgz
fig.3 is the surface overlayed to wm.mgz
fig.4 is the segmentation results overlayed to the wm.mgz
fig.5 is the surface overlayed to the wm mask I created using SPM5
fig.6 is the segmentation results overlayed to the wm mask I created using SPM5

In fig.4, we can see part of the wm mask were classified as gm after the FreeSurfer analysis was done.
It is quite different from what I see when I load the wm.mgz and the segmentation results of the bert subject from FreeSurfer tutorial. In bert subject, the wm.mgz quite match with the final segmentation results.

So I am wondering if I used my own wm.mask to replace freesurfer built wm mask, could I get a better result?

Thanks!
Guang

> Date: Mon, 29 Mar 2010 20:48:20 -0400
> From: fischl@nmr.mgh.harvard.edu
> To: freesurfer_zg@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] FW: how to modify the wm.mgz
>
> Hi Guang,
>
> it's hard to tell without looking at the surfaces. I don't think a wm
> mask will help. You could try using the expert options to change the
> intensity bounds that are automatically detected by mri_segment and
> mris_make_surfaces.
>
> cheers
> Bruce
> On Mon, 29 Mar 2010, Guang Zeng wrote:
>
> >
> >
> >
> >
> >
> >
> >
> > Hi there,
> >
> > Recently, I use FreeSurfer analyze a clinic data, the result show a very thin cortex layer, (see figure. 1).
> > I load the wm,mgz (see figure.2), and then overlay the segmentation results, (see figure. 3).
> > As you can see, part of wm.mgz around the wm mask boundary are classified as gm, I guess this
> > is because of partial volume.
> >
> > My question is if I use a better wm mask to replace freesurefer's brainmask (see figure. 4), could I get a better result?
> >
> >
> > Thanks!
> > Guang
> >
> >
> >
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