Hello, Bruce,

I'd like to send you this subject data, could you please let me know where I 
can drop it?

Thanks!
Guang

> Date: Wed, 31 Mar 2010 08:44:42 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] FW: how to modify the wm.mgz
> 
> Hi Guang,
> 
> yes, it looks like the segmentation didn't do a great job on your data. 
> if you send us the orig.mgz we'll take a look (or the individual runs 
> 00?.mgz in the orig dir if you have more than one). You could copy the SPM 
> results to wm.mgz and proceed from there I think, or you can use the expert 
> options to correct the intensity thresholds
> 
> cheers,
> Bruce
> 
> 
> On Tue, 30 Mar 2010, Guang Zeng wrote:
> 
> >
> > 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: fis...@nmr.mgh.harvard.edu
> >> To: freesurfer...@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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