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
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
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 fischl@nmr.mgh.harvard.edu Fecha: Jueves, 6 de Junio de 2013, 6:16 pm Asunto: Re: [Freesurfer] autorecon3 error A: Gabriel Gonzalez Escamilla ggonesc@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.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.
<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: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font>
I'm re-sending an old problem, because I received no answer.
Cheers, Gabriel
----- Mensaje original ----- De: Gabriel Gonzalez Escamilla ggonesc@upo.es Fecha: Lunes, 10 de Junio de 2013, 4:56 pm Asunto: Re: [Freesurfer] autorecon3 error A: Bruce Fischl fischl@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 fischl@nmr.mgh.harvard.edu Fecha: Jueves, 6 de Junio de 2013, 6:16 pm Asunto: Re: [Freesurfer] autorecon3 error A: Gabriel Gonzalez Escamilla ggonesc@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.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.
<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: ggonesc@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: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font>
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 ggonesc@upo.es Fecha: Lunes, 10 de Junio de 2013, 4:56 pm Asunto: Re: [Freesurfer] autorecon3 error A: Bruce Fischl fischl@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 fischl@nmr.mgh.harvard.edu Fecha: Jueves, 6 de Junio de 2013, 6:16 pm Asunto: Re: [Freesurfer] autorecon3 error A: Gabriel Gonzalez Escamilla ggonesc@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 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.
<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: ggonesc@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: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font>
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Gabriel Gonzalez Escamilla