Hi Gabriel
something is wrong with some surface in the lh. Maybe your disk was full?
Can you go through each of them and visualize them in tksurfer? One
should fail (lh.orig, lh.white, lh.smoothwm, lh.inflated. lh.sphere,
lh.sphere.reg)
sorry I can't be more specific. I've never seen this particular error
before
Bruce
On Tue, 11
Jun 2013, Gabriel Gonzalez Escamilla wrote:
I'm re-sending an old problem, because I received no answer.
Cheers,
Gabriel
----- Mensaje original -----
De: Gabriel Gonzalez Escamilla <ggon...@upo.es>
Fecha: Lunes, 10 de Junio de 2013, 4:56 pm
Asunto: Re: [Freesurfer] autorecon3 error
A: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
CC: freesurfer@nmr.mgh.harvard.edu
> Dear Doug
>
> Sorry for late answer.
>
> I did open as:
> tksurfer qsm1_17 lh inflated, and then File >>load surface >>
lh.sphere.reg
> and
> tksurfer qsm1_17 lh sphere.reg
>
> Neither of them look bad, it looks very spherical, an has nothing strange
to my eyes...
> Any other ideas???
>
> Best Regards
> Gabriel
>
>
>
> ----- Mensaje original -----
> De: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> Fecha: Jueves, 6 de Junio de 2013, 6:16 pm
> Asunto: Re: [Freesurfer] autorecon3 error
> A: Gabriel Gonzalez Escamilla <ggon...@upo.es>
> CC: freesurfer@nmr.mgh.harvard.edu
>
> > Hi Gabriel
> >
> > seems like something is wrong with that surface file. Can you
> > load the lh.sphere.reg in tksurfer and see if it looks ok?
> > Bruce
> >
> >
> > On Thu, 6 Jun 2013, Gabriel Gonzalez Escamilla wrote:
> >
> > >Dear Freesurfers
> > >
> > >I am running an autorecon3 to the same subject that Rafa sent
> > you (the name
> > >looks different but is exactly the same subject), with the
> > command to fix
> > >the ribbon.mgz the autorecon-2 has finished, so I continued with
> > >-autorecon3, but now is encountering the following error, this
> > time seems to
> > >be something with the seg.mgz.
> > >
> > >
> > >
> > >#-----------------------------------------
> > >#@# Cortical Parc lh Thu Jun 6 17:01:26 CEST 2013
> > >/root/trabajo/freesurfer/subjects/qsm1_17/scripts
> > >
> > > mris_ca_label -l ../label/lh.cortex.label -aseg
> > ../mri/aseg.mgz -seed 1234
> > >qsm1_17 lh
> >../surf/lh.sphere.reg/root/trabajo/freesurfer/average/lh.curvature.buckner4
0.filled.desikan_kill>iany.2010-03-25.gcs ../label/lh.aparc.annot
> > >
> > >setting seed for random number generator to 1234
> > >using ../mri/aseg.mgz aseg volume to correct midline
> > >$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
> > > $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
> > >f[113526]->v[1] = 539832625 - out of range!
> > >
> > >reading atlas
> >from/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_
kill>iany.2010-03-25.gcs...
> > >reading color table from GCSA file....
> > >average std = 1.0 using min determinant for regularization = 0.011
> > >0 singular and 384 ill-conditioned covariance matrices regularized
> > >Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9
> > 06:23:23 GMT
> > >2006 x86_64 x86_64 x86_64 GNU/Linux
> > >
> > >recon-all -s qsm1_17 exited with ERRORS at Thu Jun 6 17:01:33
> > CEST 2013
> > >
> > >For more details, see the log file
> > >/root/trabajo/freesurfer/subjects/qsm1_17/scripts/recon-all.log
> > >To report a problem, see
> > >http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > >
> > >
> > >Any ideas how to fix this?
> > >
> > >Bests,
> > >Gabriel>> _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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
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>
> <font size="3">--------------------------<br />PhD. student Gabriel
González-Escamilla<br />Laboratory of Functional Neuroscience<br
/>Department of Physiology, Anatomy, and Cell Biology<br />University Pablo
de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br
/><br />Email: ggon...@upo.es<br />http://www.upo.es/neuroaging/es/</font>
<font size="3">--------------------------<br />PhD. student Gabriel
González-Escamilla<br />Laboratory of Functional Neuroscience<br
/>Department of Physiology, Anatomy, and Cell Biology<br />University Pablo
de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br
/><br />Email: ggon...@upo.es<br />http://www.upo.es/neuroaging/es/</font>
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