Hi Alan,
Thanks for getting back to me. The full command and output at the terminal is below.
There is no output in /logs/comlogs/ but there is output in /runlogs/ which seems strange.
I’m attaching the batch file in case there is something I am doing wrong there!
batch_psyscan_test.txt (2.0 KB)
Many thanks,
George
[k1328096@login1 ~/qunex]0% ./qunexContainer hcp4
? --container=“${QUNEX_CONTAINER}”
? --sessions=“/home/k1328096/qunex/PSYSCAN_test_qunex/sessions/PSYC16023_Baseline/session_hcp.txt”
? --sessionids=“PSYC16023_Baseline”
? --batchfile=“/home/k1328096/qunex/PSYSCAN_test_qunex/processing/batch_psyscan_test.txt”
? --overwrite=“no”
? --path=“/home/k1328096/qunex/PSYSCAN_test_qunex/”
[k1328096@login1 ~/qunex]0% → unsetting all environment variables: PATH MATLABPATH PYTHONPATH QUNEXVer TOOLS QUNEXREPO QUNEXPATH TemplateFolder FSL_FIXDIR FREESURFERDIR FREESURFER_HOME FREESURFER_SCHEDULER FreeSurferSchedulerDIR WORKBENCHDIR DCMNIIDIR DICMNIIDIR MATLABDIR MATLABBINDIR OCTAVEDIR OCTAVEPKGDIR OCTAVEBINDIR RDIR HCPWBDIR AFNIDIR PYLIBDIR FSLDIR FSLGPUDIR PALMDIR QUNEXMCOMMAND HCPPIPEDIR CARET7DIR GRADUNWARPDIR HCPPIPEDIR_Templates HCPPIPEDIR_Bin HCPPIPEDIR_Config HCPPIPEDIR_PreFS HCPPIPEDIR_FS HCPPIPEDIR_PostFS HCPPIPEDIR_fMRISurf HCPPIPEDIR_fMRIVol HCPPIPEDIR_tfMRI HCPPIPEDIR_dMRI HCPPIPEDIR_dMRITract HCPPIPEDIR_Global HCPPIPEDIR_tfMRIAnalysis MSMBin HCPPIPEDIR_dMRITracFull HCPPIPEDIR_dMRILegacy AutoPtxFolder FSLGPUBinary EDDYCUDADIR USEOCTAVE QUNEXENV CONDADIR MSMBINDIR MSMCONFIGDIR R_LIBS FSL_FIX_CIFTIRW
Loading Quantitative Neuroimaging Environment & ToolboX (Qu|Nex) Version: v0.61.17
Logged in as User: k1328096
Node info: login1.nan.kcl.ac.uk
OS: RedHat Linux #1 SMP Tue Dec 15 08:51:23 CST 2020
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DEVELOPED & MAINTAINED BY:
Anticevic Lab
MBLab led by Grega Repovs
COPYRIGHT & LICENSE NOTICE:
Use of this software is subject to the terms and conditions defined by the
Yale University Copyright Policies:
http://ocr.yale.edu/faculty/policies/yale-university-copyright-policy
and the terms and conditions defined in the file ‘LICENSE.md’ which is
a part of the Qu|Nex Suite source code package:
https://bitbucket.org/hidradev/qunextools/src/master/LICENSE.md
—> Setting up Octave
—> Qu|Nex environment set successfully!
… Running Qu|Nex v0.61.17 …
Using /home/k1328096/qunex/PSYSCAN_test_qunex/sessions/PSYC16023_Baseline/session_hcp.txt for input.
— Full Qu|Nex call for command: hcp4
gmri hcp4 --sessions=/home/k1328096/qunex/PSYSCAN_test_qunex/sessions/PSYC16023_Baseline/session_hcp.txt --sessionids=PSYC16023_Baseline --batchfile=/home/k1328096/qunex/PSYSCAN_test_qunex/processing/batch_psyscan_test.txt --overwrite=no --path=/home/k1328096/qunex/PSYSCAN_test_qunex/
Quantitative Neuroimaging Environment & Toolbox (Qu|Nex) Suite Version 0.61.17
=================================================================
gmri hcp4
–sessionids=“PSYC16023_Baseline”
–path=“/home/k1328096/qunex/PSYSCAN_test_qunex/”
–batchfile=“/home/k1328096/qunex/PSYSCAN_test_qunex/processing/batch_psyscan_test.txt”
–overwrite=“no”
–sessions=“/home/k1328096/qunex/PSYSCAN_test_qunex/sessions/PSYC16023_Baseline/session_hcp.txt” \
Starting multiprocessing sessions in /home/k1328096/qunex/PSYSCAN_test_qunex/sessions/PSYC16023_Baseline/session_hcp.txt with a pool of 1 concurrent processes
---- Running local
Starting processing of sessions PSYC16023_Baseline at Thursday, 18. February 2021 19:19:40
Session id: PSYC16023_Baseline
[started on Thursday, 18. February 2021 19:19:40]
Running HCP fMRI Volume registration [HCPStyleData] …
—> PreFS results present.
—> FS results present.
—> PostFS results present.
Running 1 BOLD images in parallel
HCP fMRIVolume completed on Thursday, 18. February 2021 19:19:40
===> Final report for command hcp4
… PSYC16023_Baseline —> HCP fMRI Volume: bolds
===> Successful completion of all tasks