Hi Jure,
Thanks again for your help.
- The file content seems to be okay:
source /opt/qunex/env/qunex_environment.sh
bash /opt/qunex/bin/qunex.sh hcp_icafix --sessionsfolder="sessions" --parsessions="2" --batchfile="processing/batch.txt" --sessions="04,05,06,07,08,09,10,11"
Actually, based on your suggestion, I re-installed the qunex_container
script and new error came up.
This is the folder structure that I try to run ICA+FIX on:
RESEARCH
βββ bids
βββ test_study (this is the qunex study folder)
βββ RAW
The aforementioned error happens when I run the code when I am at RESEARCH
folder.
And now qunex returns a new error:
--> QuNex will run the command over 8 sessions. It will utilize:
Maximum sessions run in parallel for a job: 2.
Maximum elements run in parallel for a session: 1.
Up to 2 processes will be utilized for a job.
Job #1 will run sessions: 04,05,06,07,08,09,10,11
--> unsetting the following environment variables: PATH MATLABPATH PYTHONPATH QUNEXVer TOOLS QUNEXREPO QUNEXPATH QUNEXLIBRARY QUNEXLIBRARYETC TemplateFolder FSL_FIXDIR FREESURFERDIR FREESURFER_HOME FREESURFER_SCHEDULER FreeSurferSchedulerDIR WORKBENCHDIR DCMNIIDIR DICMNIIDIR MATLABDIR MATLABBINDIR OCTAVEDIR OCTAVEPKGDIR OCTAVEBINDIR RDIR HCPWBDIR AFNIDIR ANTSDIR 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 HCPCIFTIRWDIR MSMBin HCPPIPEDIR_dMRITractFull HCPPIPEDIR_dMRILegacy AutoPtxFolder FSL_GPU_SCRIPTS FSLGPUBinary EDDYCUDADIR USEOCTAVE QUNEXENV CONDADIR MSMBINDIR MSMCONFIGDIR R_LIBS FSL_FIX_CIFTIRW FSFAST_HOME SUBJECTS_DIR MINC_BIN_DIR MNI_DIR MINC_LIB_DIR MNI_DATAPATH FSF_OUTPUT_FORMAT
Generated by QuNex
------------------------------------------------------------------------
Version: 0.94.11
User: root
System: 804ce9fdc2a0
OS: RedHat Linux #142~18.04.1-Ubuntu SMP Thu Sep 1 16:25:16 UTC 2022
------------------------------------------------------------------------
ββββββ\ β ββ\ ββ\
ββ __ββ\ β βββ\ ββ |
ββ / ββ |ββ\ ββ\ β ββββ\ ββ | ββββββ\ ββ\ ββ\
ββ | ββ |ββ | ββ | β ββ ββ\ββ |ββ __ββ\\ββ\ ββ |
ββ | ββ |ββ | ββ | β ββ \ββββ |ββββββββ |\ββββ /
ββ ββ\ββ |ββ | ββ | β ββ |\βββ |ββ ____|ββ ββ\
\ββββββ / \ββββββ | β ββ | \ββ |\βββββββ\ββ /\ββ\
\___βββ\ \______/ β \__| \__| \_______\__/ \__|
\___| β
DEVELOPED & MAINTAINED BY:
Anticevic Lab, Yale University
Mind & Brain Lab, University of Ljubljana
Murray Lab, Yale University
COPYRIGHT & LICENSE NOTICE:
Use of this software is subject to the terms and conditions defined in
'LICENSES' which is a part of the QuNex Suite source code package:
--- Full QuNex call for command: hcp_icafix
gmri hcp_icafix --sessionsfolder="sessions" --parsessions="2" --batchfile="test_study/processing/batch.txt" --sessions="04,05,06,07,08,09,10,11"
---------------------------------------------------------
--------------------==== QuNex failed! ====--------------------
ERROR: Execution of qunex command hcp_icafix failed!
ERROR: The specified session file is not found! [test_study/processing/batch.txt]!
The call received was:
(please note that when run through scheduler, all possible parameters,
even non relevant ones are passed)
qunex hcp_icafix \
--sessionsfolder=sessions \
--parsessions=2 \
--batchfile=test_study/processing/batch.txt \
--sessions=04,05,06,07,08,09,10,11
Traceback (most recent call last):
File "/opt/qunex/python/qx_utilities/gmri", line 522, in <module>
main()
File "/opt/qunex/python/qx_utilities/gmri", line 491, in main
runCommand(comm, opts)
File "/opt/qunex/python/qx_utilities/gmri", line 182, in runCommand
gp.run(command, args)
File "/opt/qunex/python/qx_utilities/general/process.py", line 711, in run
sessions, gpref = gc.get_sessions_list(options['sessions'], filter=options['filter'], sessionids=options['sessionids'], verbose=False)
File "/opt/qunex/python/qx_utilities/general/core.py", line 260, in get_sessions_list
raise ValueError("ERROR: The specified session file is not found! [%s]!" % listString)
ValueError: ERROR: The specified session file is not found! [test_study/processing/batch.txt]!
If I change path of the batchfile
to processing/batch.txt
(staying in the same directory RESEARCH
), the error is as follow:
Traceback (most recent call last):
File "/home/mshin/qunex/qunex_container", line 1088, in <module>
main()
File "/home/mshin/qunex/qunex_container", line 868, in main
g_sessionids = get_sessionids(batchfile, sessions, batchfilter)
File "/home/mshin/qunex/qunex_container", line 433, in get_sessionids
raise ValueError("ERROR: The specified file is not found! [%s]!" % batchfile)
ValueError: ERROR: The specified file is not found! [processing/batch.txt]!
-
Thanks. I will keep this in mind. I guess run_turnkey
managed this inside the container so setting the path of batch file was different.
-
Glad to hear that! I look forward to it!