Description:
Hi, I’m trying to create conc files using the create_conc command but got an error. Please see below. Thank you.
Estephan
Call:
subjID_list="10001,10002,10004,10005,10006,10007,10009,10011,10012,10013,10014,10015,10016,10018,10019,10021,10022,10023,10024,10030,10031,10033,10034,10035,10037,10038,10039,10041,10042,11004,11006,11009,11015,20001,20004,20005,20006,20008,20010,20011,20012,20013,20015,20016,20017,20018,20019,20021,20022"; \
study_sharedfolder=/home/moanae/shared/project_K99_ChrTMDHCP_qunex02; \
qunex_container create_conc \
--batchfile=${study_sharedfolder}/processing/batch_K99Aim2.txt --sessionsfolder=${study_sharedfolder}/sessions --sessions=${subjID_list} \
--concname="dentalvpress" --bolds="3,4" --boldname="BOLD" --bold_tail="_Atlas_MSMAll_hp0_clean.dtseries.nii" \
-bind=${study_sharedfolder}:${study_sharedfolder} --container=${HOME}/qunex/qunex_suite-0.97.3.sif
Logs:
cn2107:~ moana004$ subjID_list="10001,10002,10004,10005,10006,10007,10009,10011,10012,10013,10014,10015,10016,10018,10019,10021,10022,10023,10024,10030,10031,10033,10034,10035,10037,10038,10039,10041,10042,11004,11006,11009,11015,20001,20004,20005,20006,20008,20010,20011,20012,20013,20015,20016,20017,20018,20019,20021,20022"; \
> study_sharedfolder=/home/moanae/shared/project_K99_ChrTMDHCP_qunex02; \
> qunex_container create_conc \
> --batchfile=${study_sharedfolder}/processing/batch_K99Aim2.txt --sessionsfolder=${study_sharedfolder}/sessions --sessions=${subjID_list} \
> --concname="dentalvpress" --bolds="3,4" --boldname="BOLD" --bold_tail="_Atlas_MSMAll_hp0_clean.dtseries.nii" \
> -bind=${study_sharedfolder}:${study_sharedfolder} --container=${HOME}/qunex/qunex_suite-0.97.3.sif
--> QuNex will run the command over 49 sessions. It will utilize:
Maximum sessions run in parallel for a job: 1.
Maximum elements run in parallel for a session: 1.
Up to 1 processes will be utilized for a job.
Job #1 will run sessions: 10001,10002,10004,10005,10006,10007,10009,10011,10012,10013,10014,10015,10016,10018,10019,10021,10022,10023,10024,10030,10031,10033,10034,10035,10037,10038,10039,10041,10042,11004,11006,11009,11015,20001,20004,20005,20006,20008,20010,20011,20012,20013,20015,20016,20017,20018,20019,20021,20022
cn2107:~ moana004$ --> unsetting the following environment variables: PATH MATLABPATH PYTHONPATH QUNEXVer TOOLS QUNEXREPO QUNEXPATH QUNEXEXTENSIONS QUNEXLIBRARY QUNEXLIBRARYETC 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 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: 0.97.3
User: moana004
System: cn2107
OS: RedHat Linux #1 SMP Tue Mar 7 15:41:52 UTC 2023
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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:
https://gitlab.qunex.yale.edu/qunex/qunex/-/tree/master/LICENSES
---> Setting up Octave
........................ Running QuNex v0.97.3 ........................
--- Full QuNex call for command: create_conc
gmri create_conc --sessionsfolder="/home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions" --concname="dentalvpress" --bolds="3,4" --boldname="BOLD" --bold_tail="_Atlas_MSMAll_hp0_clean.dtseries.nii" --batchfile="/home/moanae/shared/project_K99_ChrTMDHCP_qunex02/processing/batch_K99Aim2.txt" --sessions="10001,10002,10004,10005,10006,10007,10009,10011,10012,10013,10014,10015,10016,10018,10019,10021,10022,10023,10024,10030,10031,10033,10034,10035,10037,10038,10039,10041,10042,11004,11006,11009,11015,20001,20004,20005,20006,20008,20010,20011,20012,20013,20015,20016,20017,20018,20019,20021,20022"
---------------------------------------------------------
started running create_conc at 2023-05-10 15:39:44, track progress in /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/processing/logs/comlogs/create_conc_/home/moanae/shared/project_K99_ChrTMDHCP_qunex02/processing/tmp_batch_K99Aim2.txt_2023-05-10_15.39.44.536926.log
call: gmri create_conc sessionsfolder="/home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions" concname="dentalvpress" bolds="3,4" boldname="BOLD" bold_tail="_Atlas_MSMAll_hp0_clean.dtseries.nii" sessions="/home/moanae/shared/project_K99_ChrTMDHCP_qunex02/processing/batch_K99Aim2.txt" sessionids="10001,10002,10004,10005,10006,10007,10009,10011,10012,10013,10014,10015,10016,10018,10019,10021,10022,10023,10024,10030,10031,10033,10034,10035,10037,10038,10039,10041,10042,11004,11006,11009,11015,20001,20004,20005,20006,20008,20010,20011,20012,20013,20015,20016,20017,20018,20019,20021,20022"
-----------------------------------------
ERROR
Traceback (most recent call last):
File "/opt/qunex/python/qx_utilities/general/core.py", line 570, in runWithLog
result = function(**args)
TypeError: create_conc() got an unexpected keyword argument 'sessionids'
-----------------------------------------
Finished at 2023-05-10 15:39:44