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 <fis...@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 <fis...@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"<fis...@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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> > Freesurfer@nmr.mgh.harvard.edu
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> >
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