with freeview
On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:

>
>         External Email - Use Caution        
>
> Hi Bruce,
>
> I cannot examine those files with gedit. Could you tell me how to open them?
> Thank you,
> Rosalia
>
> On Mon, Oct 22, 2018 at 9:35 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>       Hi Lisa
>
>       no, likely you have to identify and correct the source of the giant defect,
>       typically be either fixing the skull stripping, or editing the wm.mgz or
>       adding control points
>
>       cheers
>       Bruce
>
>
>       On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote:
>
>       >        External Email - Use Caution
>       >
>       > Hi all,
>       >
>       > I have a stroke brain with a large lesion that runs into this same problem. Is there a
>       way to push the process along? No white matter segmentations are created to try and edit
>       the surface.
>       >
>       > Best,
>       > -Lisa Krishnamurthy
>       >
>       > -----Original Message-----
>       > From: freesurfer-bounces@nmr.mgh.harvard.edu
>       [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
>       > Sent: Monday, October 22, 2018 3:30 PM
>       > To: Freesurfer support list
>       > Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
>       >
>       > Hi Rosaila
>       >
>       > usually when you have a defect that large (>30,000) vertices, which is about 1/4 of
>       the total surface more or less, something is dramatically wrong and it is not worth
>       waiting for it to finish (it might take days or weeks). Examine the ?h.orig.nofix and
>       ?h.inflated.nofix surfaces and see if there is some big problem like skull or cerebellum
>       attached to the surface.
>       >
>       > cheers
>       > Bruce
>       >
>       >
>       > On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
>       >
>       >>
>       >>         External Email - Use Caution
>       >>
>       >> Dear FreeSurfer team,
>       >>
>       >> I Have run -autorecon1 in my sample and the report.log was "finished without errors"
>       >> Now, running recon-all -all I have seen that a participant is stuck in
>       >> CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more
>       >> than an hour. I wonder if this is normal or if I should be worried
>       >> because recon-all takes 4.5 hours approximately for every participant but for this
>       one, it seems that is not moving from this step.
>       >>
>       >> Anyone could help me with this?
>       >>
>       >> Best regards,
>       >> Rosaila
>       >>
>       >>
>       >>
>       >>
>       >
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>       >
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