Re: [Freesurfer] Recon-all with mris_fix_topology error

usually that means that the partition you are working on ran out of space. Can you check?

cheers Bruce On Wed, 29 Jun 2011, Jordi Casals wrote:

Hi Bruce,

What I included on te previous e-mail was the content of the recon-all.error. I thought that this would be sufficient. I think that this is the error that you're asking me about. CORRECTING DEFECT 60 (vertices=8674, convex hull=4036) normal vector of length zero at vertex 111480 with 0 faces vertex 111480 has 0 face Numerical result out of range

Thank you :)

On Tue, Jun 28, 2011 at 6:12 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Jordi,

  what is the error? You didn't include it
  Bruce

On Tue, 28 Jun 2011, Jordi Casals wrote:

  Hello FreeSurfer community,
  I am Jordi Casals, from Barcelona.

  After few days trying to process a set of modificactions done to a subject (pial, white matter and control points), I still have this error, about
  mris_fix_topology. I don't know where is
  the problem, because I have done a lot of subjects in the same way as these one and the other two that give me this error.

  SUBJECT SRN_005
  DATE Wed Jun 22 00:58:31 CEST 2011
  USER neuro
  HOST td560.pic.es
  PROCESSOR x86_64
  OS Linux
  Linux td560.pic.es 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:53:46 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux
  $Id: recon-all,v 1.133.2.43 2009/04/22 22:34:03 nicks Exp $
  /SOFTWR/freesurfer/bin/recon-all
  PWD $PATH/SRN_005/scripts
  CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga SRN_005 rh

  It would be be really great if someone can help me or give me some guides to understand a little bit more the problem and to reach a proper execution.

  Thank you again,

  Jordi.

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