Re: [Freesurfer] autorecon3 error

[Bruce Fischl]

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 
Fecha: Lunes, 10 de Junio de 2013, 4:56 pm
Asunto: Re: [Freesurfer] autorecon3 error
A: Bruce Fischl 
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 
> Fecha: Jueves, 6 de Junio de 2013, 6:16 pm
> Asunto: Re: [Freesurfer] autorecon3 error
> A: Gabriel Gonzalez Escamilla 
> 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
> > 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.
>
> --PhD. student Gabriel
González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo
de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/


-

Re: [Freesurfer] autorecon3 error

[Gabriel Gonzalez Escamilla]

I'm re-sending an old problem, because I received no answer.

Cheers,
Gabriel

- Mensaje original -
De: Gabriel Gonzalez Escamilla 
Fecha: Lunes, 10 de Junio de 2013, 4:56 pm
Asunto: Re: [Freesurfer] autorecon3 error
A: Bruce Fischl 
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 
> Fecha: Jueves, 6 de Junio de 2013, 6:16 pm
> Asunto: Re: [Freesurfer] autorecon3 error
> A: Gabriel Gonzalez Escamilla 
> 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.buckner40.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
> > 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.
> 
> --PhD. student Gabriel 
> González-EscamillaLaboratory of Functional NeuroscienceDepartment 
> of Physiology, Anatomy, and Cell BiologyUniversity Pablo de Olavide />Ctra. de Utrera, Km.141013 - Seville- Spain -Email: 
> ggon...@upo.eshttp://www.upo.es/neuroaging/es/
 

--PhD. student Gabriel 
González-EscamillaLaboratory of Functional NeuroscienceDepartment 
of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: 
ggon...@upo.eshttp://www.upo.es/neuroaging/es/


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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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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] autorecon3 error

[Gabriel Gonzalez Escamilla]

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 
Fecha: Jueves, 6 de Junio de 2013, 6:16 pm
Asunto: Re: [Freesurfer] autorecon3 error
A: Gabriel Gonzalez Escamilla 
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.buckner40.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
> 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.

--PhD. student Gabriel 
González-EscamillaLaboratory of Functional NeuroscienceDepartment 
of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: 
ggon...@upo.eshttp://www.upo.es/neuroaging/es/


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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.

Re: [Freesurfer] autorecon3 error

[Bruce Fischl]

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.buckner40.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
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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] autorecon3 error

[Gabriel Gonzalez Escamilla]

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.buckner40.filled.desikan_killiany.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_killiany.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

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Re: [Freesurfer] autorecon3 error

[Claudia Dacquino]

Ok.
Thanks a lot!
Cheers
Claudia

Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:

> yes, you should be running
>
> recon-all -autorecon2-cp 
>
> cheers
> Bruce
>
> On Mon, 3 Jun 2013, Claudia Dacquino wrote:
>
>  Is this the problem? Is there an incorrect command?
>> Thanks.Cheers
>> Claudia
>>
>> Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:
>>   Hi Claudia
>>
>>   there is no autorecon3-cp, just autorecon2-cp
>>
>>   cheers
>>   Bruce
>>   On Mon, 3 Jun 2013, Claudia Dacquino wrote:
>>
>> Hi Freesurfers,
>> I did autorecon3-cp and exited with errors.
>> Ould anyone help me to understand what's the roblem?
>> You can find the recon-all.log attached.
>> Thanks in advance.
>> Claudia
>>
>>
>>
>>
>>
>>   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.
>>
>>
>>
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Re: [Freesurfer] autorecon3 error

[Bruce Fischl]

yes, you should be running

recon-all -autorecon2-cp 

cheers
Bruce

On Mon, 3 Jun 2013, Claudia Dacquino wrote:


Is this the problem? Is there an incorrect command?
Thanks.Cheers
Claudia

Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:
  Hi Claudia

  there is no autorecon3-cp, just autorecon2-cp

  cheers
  Bruce
  On Mon, 3 Jun 2013, Claudia Dacquino wrote:

Hi Freesurfers,
I did autorecon3-cp and exited with errors.
Ould anyone help me to understand what's the roblem?
You can find the recon-all.log attached.
Thanks in advance.
Claudia





  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.


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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] autorecon3 error

[Claudia Dacquino]

Is this the problem? Is there an incorrect command?
Thanks.
Cheers
Claudia

Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:

> Hi Claudia
>
> there is no autorecon3-cp, just autorecon2-cp
>
> cheers
> Bruce
> On Mon, 3 Jun 2013, Claudia Dacquino wrote:
>
>  Hi Freesurfers,
>> I did autorecon3-cp and exited with errors.
>> Ould anyone help me to understand what's the roblem?
>> You can find the recon-all.log attached.
>> Thanks in advance.
>> Claudia
>>
>>
>>
>>
>
> 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.
>
>
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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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but does not contain patient information, please contact the sender and properly
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