Re: [Freesurfer] Modify defect failed

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
  > >
  > >
  > _______________________________________________
  > Freesurfer mailing list
  > Freesurfer@nmr.mgh.harvard.edu
  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer