Re: [Freesurfer] Modify defect failed

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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:

...

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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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