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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