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>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
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.
