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.
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.
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.eduwrote:
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.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 BruceOn 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.The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Jordi Casals