overlay the white and pial surfaces and see if the skull is included inside
the pial

On Sun, 18 Nov
2018, Rosalia Dacosta Aguayo wrote:

>
>         External Email - Use Caution        
>
> Hi  Bruce,
> Thank you a lot for your reply. How could I inspect if affects the surfaces?
>
> Yours sincerely,
> Rosalia
>
>
> El dom., 18 nov. 2018 16:58, Bruce Fischl <fischl@nmr.mgh.harvard.edu> escribió:
>       that should work ok. It only matter if it affects the surfaces though (or
>       the aseg)
>       cheers
>       Bruce
>
>       On Sun, 18 Nov 2018, Rosalia Dacosta Aguayo wrote:
>
>       >
>       >         External Email - Use Caution        
>       >
>       > Hi Bruce,
>       > Sorry for my intromission. 
>       > I am replacing the brainmask because dura mater or skull were left behind with
>       independence of the
>       > WM and GM segmemtation. Does this is useless?
>       >
>       > Regards,
>       > Rosalia 
>       >
>       > El dom., 18 nov. 2018 16:16, Bruce Fischl <fischl@nmr.mgh.harvard.edu> escribió:
>       >       Hi yujunjie
>       >
>       >       you need to look at the *.nofix surfaces and see where the defect is.
>       >       Skull and neck being left is around isn't a problem unless they are
>       >       included in the surfaces.
>       >
>       >       cheers
>       >       Bruce
>       >       On Sun, 18 Nov 2018, 1013364183 wrote:
>       >
>       >       >
>       >       >         External Email - Use Caution        
>       >       >
>       >       > Dear Bruce Fischl,
>       >       >   Thank you very much for your reply. I checked the effect of going down the
>       skull and
>       >       found that a
>       >       > large part of the skull has not been removed. The appendix contains images of
>       skull
>       >       removal. I want
>       >       > to know how we should handle it.
>       >       >
>       >       > yours yujunjie
>       >       > ------------------ Original ------------------
>       >       > From:  "Bruce Fischl"<fischl@nmr.mgh.harvard.edu>;
>       >       > Date:  Sun, Nov 18, 2018 00:10 AM
>       >       > To:  "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;
>       >       > Subject:  Re: [Freesurfer] Modify defect failed
>       >       >
>       >       > Hi yujunjie
>       >       >
>       >       > the last entry in the log file is:
>       >       >
>       >       > CORRECTING DEFECT 5 (vertices=53772, convex hull=1434, v0=15308)
>       >       > XL defect detected...
>       >       >
>       >       >
>       >       > this is a giant defect - about 1/4 of your total surface. It means that
>       >       > something major went wrong - skull attached, or hemis connected or
>       >       > something. You should look at the rh.orig.nofix and the
>       >       > rh.inflated.nofix surfaces to see what it is.
>       >       >
>       >       > cheers
>       >       > Bruce
>       >       >
>       >       >
>       >       > On Sat, 17
>       >       > Nov 2018, 1013364183 wrote:
>       >       >
>       >       > >
>       >       > >  External Email - Use Caution
>       >       > >
>       >       > > Dear FS,
>       >       > >  I ran the recon-all command and it failed to fix it for many days when I
>       fixed the
>       >       defect. I have
>       >       > > modified the threshold of the split algorithm. I want to know if there are
>       other
>       >       ways to fix the
>       >       > Its
>       >       > > log file is in the attachment.
>       >       > >
>       >       > > Thank you in advance
>       >       > >
>       >       > > yours yujunjie
>       >       > >
>       >       > >
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