Re: [Freesurfer] Recon-all GNU parallel Error. : Segmentation fault
Not sure, can you run
mri_convert /media/vasudev/Daten/VBCT/PAT30.nii.gz
/media/vasudev/Daten/VBCT_results/PAT30/mri/orig/001.mgz
and send all the screen output?
On 09/02/2016 12:17 PM, Dev vasu wrote:
>
>
>
> Dear Sir / madam,
>
> I have tried running recon-all with GNU parallel and i am incurring
> following error kindly review the recon-all.log ( see below ).
>
> Could you please let me know why such problem persists for me. Is it
> the issue with memory space ?
>
>
> Thanks
> Vasudev
>
>
> Calling the GNU parallel in terminal
>
> " ls PAT*.nii.gz | sed 's/.nii.gz//' | parallel --jobs 5 recon-all -s
> {} -i {}.nii.gz -all -qcache "
>
>
>
>
>
> recon-all-log
>
>
> Fr 2. Sep 17:59:48 CEST 2016
> /media/vasudev/Daten/VBCT_results/PAT30
> /usr/local/bin/freesurfer/bin/recon-all
> -s PAT30 -i PAT30.nii.gz -all -qcache
> subjid PAT30
> setenv SUBJECTS_DIR /media/vasudev/Daten/VBCT_results
> FREESURFER_HOME /usr/local/bin/freesurfer
> Actual FREESURFER_HOME /usr/local/bin/freesurfer
> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
> Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed
> Jun 29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
> cputime unlimited
> filesize unlimited
> datasize unlimited
> stacksize8192 kbytes
> coredumpsize 0 kbytes
> memoryuseunlimited
> vmemoryuse unlimited
> descriptors 1024
> memorylocked 64 kbytes
> maxproc 15208
> maxlocks unlimited
> maxsignal15208
> maxmessage 819200
> maxnice 0
> maxrtprio0
> maxrttimeunlimited
>
> total used free shared buffers cached
> Mem: 39154323730516 184916 17476 21512 505448
> -/+ buffers/cache:3203556 711876
> Swap:0 0 0
>
>
> program versions used
> $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
> $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
> FLIRT version 5.5
> $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
> Program nu_correct, built from:
> Package MNI N3, version 1.10, compiled by nicks@minerva
> (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
> ###
> GCADIR /usr/local/bin/freesurfer/average
> GCA RB_all_2008-03-26.gca
> GCASkull RB_all_withskull_2008-03-26.gca
> AvgCurvTif average.curvature.filled.buckner40.tif
> GCSDIR /usr/local/bin/freesurfer/average
> GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
> ###
> /media/vasudev/Daten/VBCT_results/PAT30
>
> mri_convert /media/vasudev/Daten/VBCT/PAT30.nii.gz
> /media/vasudev/Daten/VBCT_results/PAT30/mri/orig/001.mgz
>
> Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed
> Jun 29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s PAT30 exited with ERRORS at Fr 2. Sep 17:59:56 CEST 2016
>
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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[Freesurfer] Recon-all GNU parallel Error. : Segmentation fault
Dear Sir / madam,
I have tried running recon-all with GNU parallel and i am incurring
following error kindly review the recon-all.log ( see below ).
Could you please let me know why such problem persists for me. Is it the
issue with memory space ?
Thanks
Vasudev
Calling the GNU parallel in terminal
" ls PAT*.nii.gz | sed 's/.nii.gz//' | parallel --jobs 5 recon-all -s {} -i
{}.nii.gz -all -qcache "
recon-all-log
Fr 2. Sep 17:59:48 CEST 2016
/media/vasudev/Daten/VBCT_results/PAT30
/usr/local/bin/freesurfer/bin/recon-all
-s PAT30 -i PAT30.nii.gz -all -qcache
subjid PAT30
setenv SUBJECTS_DIR /media/vasudev/Daten/VBCT_results
FREESURFER_HOME /usr/local/bin/freesurfer
Actual FREESURFER_HOME /usr/local/bin/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun
29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 15208
maxlocks unlimited
maxsignal15208
maxmessage 819200
maxnice 0
maxrtprio0
maxrttimeunlimited
total used free sharedbuffers cached
Mem: 39154323730516 184916 17476 21512 505448
-/+ buffers/cache:3203556 711876
Swap:0 0 0
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
###
GCADIR /usr/local/bin/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/bin/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
###
/media/vasudev/Daten/VBCT_results/PAT30
mri_convert /media/vasudev/Daten/VBCT/PAT30.nii.gz
/media/vasudev/Daten/VBCT_results/PAT30/mri/orig/001.mgz
Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun
29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s PAT30 exited with ERRORS at Fr 2. Sep 17:59:56 CEST 2016
To report a problem, see http://surfer.nmr.mgh.harvard.
edu/fswiki/BugReporting
___
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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.
[Freesurfer] Recon-all GNU parallel Error. : Segmentation fault
Dear Sir / madam,
I have tried running recon-all with GNU parallel and i am incurring
following error kindly review the recon-all.log ( see below ).
Could you please let me know why such problem persists for me. Is it the
issue with memory space ?
Thanks
Vasudev
Calling the GNU parallel in terminal
" ls PAT*.nii.gz | sed 's/.nii.gz//' | parallel --jobs 5 recon-all -s {} -i
{}.nii.gz -all -qcache "
recon-all-log
Fr 2. Sep 17:59:48 CEST 2016
/media/vasudev/Daten/VBCT_results/PAT30
/usr/local/bin/freesurfer/bin/recon-all
-s PAT30 -i PAT30.nii.gz -all -qcache
subjid PAT30
setenv SUBJECTS_DIR /media/vasudev/Daten/VBCT_results
FREESURFER_HOME /usr/local/bin/freesurfer
Actual FREESURFER_HOME /usr/local/bin/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun
29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 15208
maxlocks unlimited
maxsignal15208
maxmessage 819200
maxnice 0
maxrtprio0
maxrttimeunlimited
total used free sharedbuffers cached
Mem: 39154323730516 184916 17476 21512 505448
-/+ buffers/cache:3203556 711876
Swap:0 0 0
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
###
GCADIR /usr/local/bin/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/bin/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
###
/media/vasudev/Daten/VBCT_results/PAT30
mri_convert /media/vasudev/Daten/VBCT/PAT30.nii.gz
/media/vasudev/Daten/VBCT_results/PAT30/mri/orig/001.mgz
Linux vasudev-OptiPlex-780 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun
29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s PAT30 exited with ERRORS at Fr 2. Sep 17:59:56 CEST 2016
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
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.
