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 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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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