yes, they are surfaces. You need to specify -f on the command line before
listing the surfaces you want to load
On Mon, 22 Oct 2018, Rosalia Dacosta
Aguayo wrote:
External Email - Use Caution
I tried. I cannot open them. They are not .mgz files, they are binary files.I
will try though, and
see what is happening.
Thank you,
Rosalia
El lun., 22 oct. 2018 21:49, Bruce Fischl <fis...@nmr.mgh.harvard.edu> escribió:
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
<fis...@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-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@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
> >>
> >>
> >>
> >>
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >_______________________________________________
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>
>
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