Re: [Freesurfer] Modify defect failed

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:

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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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