probably not, although it's hard to say. If you upload the whole subject dir I'll take a look. How does the aseg look?
On Thu, 14 Feb 2013, Rongxiang Tang wrote:

> Hi Bruce,
>
> I checked the skullstrip stage using this command:
>
> tkmedit subjectid brainmask.mgz -aux T1.mgz -surfs....
> and both of the brainmask and T1 images look fine.... the wm.mgz is problema
> tic, with some area missing..... I was wondering if I need to manually adding control points to solve the pro
> blem.
> Thanks,
> Catherine
>
> ____________________________________________________________________________
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> To: Rongxiang Tang <rongxiangtang@yahoo.com>
> Sent: Thursday, February 14, 2013 2:03 PM
> Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
>
> Hi Catherine
>
> that looks like something went wrong in the surface recon, not in the
> talairaching. Maybe a skullstrip problem? You need to investigate. Also,
> please cc the list so that others can answer!
>
> thanks
> Bruce
> On Thu, 14 Feb 2013, Rongxiang Tang wrote:
>
> > Hi Bruce,
> >
> > I attached two images...one is the target view and the other is the
> moveable
> > view.
> >
> > Thanks,
> > Catherine
> >
> >
> >___________________________________________________________________________
> _
> > From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> > To: Rongxiang Tang <rongxiangtang@yahoo.com>
> > Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> > Sent: Thursday, February 14, 2013 1:33 PM
> > Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
> >
> > Hi Catherine
> >
> > can you send us an image of what you are looking at?
> >
> > thanks
> > Bruce
> > On Thu, 14 Feb 2013,
> > Rongxiang Tang wrote:
> >
> > > Dear All,
> > >
> > > When I was checking the talairach transformation output, I noticed that
> > some of the white matter was not included inside
> > > the green line. Instead of drawing the green line to include all of the
> > white matter of the whole brain, it somehow only
> > > includes the bottom half of the white matter of the brain.
> > >
> > > Is there a way to fix that? 
> > >
> > > Thanks,
> > > Catherine
> > >
> > >
> >
> >
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