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
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 15208
maxlocks unlimited
maxsignal 15208
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 3915432 3730516 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.
