Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

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 fischl@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 <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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