I tried the command you suggested, it still could not find BOLD_5 and BOLD_6.
cn2107:~ moana004$ qunex_container hcp_msmall --batchfile="${study_sharedfolder}/processing/batch_FM_Gracely.txt" --sessionsfolder="${study_sharedfolder}/sessions" --parsessions="1" --hcp_icafix_bolds=CONCAT_STIM:BOLD_3,BOLD_1,BOLD_2,BOLD_4 --hcp_msmall_bolds=BOLD_5,BOLD_6 --test --bind="${study_sharedfolder}:/${study_sharedfolder}" --container="${HOME}/qunex/qunex_suite-0.94.7.sif"
--> QuNex will run the command over 1 sessions. It will utilize:
Maximum sessions run in parallel for a job: 1.
Maximum elements run in parallel for a session: 1.
Up to 1 processes will be utilized for a job.
Job #1 will run sessions: FM0007
cn2107:~ moana004$ --> 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: 0.94.7
User: moana004
System: cn2107
OS: RedHat Linux #1 SMP Tue Jun 28 15:37:28 UTC 2022
------------------------------------------------------------------------
ââââââ\ â ââ\ ââ\
ââ __ââ\ â âââ\ ââ |
ââ / ââ |ââ\ ââ\ â ââââ\ ââ | ââââââ\ ââ\ ââ\
ââ | ââ |ââ | ââ | â ââ ââ\ââ |ââ __ââ\\ââ\ ââ |
ââ | ââ |ââ | ââ | â ââ \ââââ |ââââââââ |\ââââ /
ââ ââ\ââ |ââ | ââ | â ââ |\âââ |ââ ____|ââ ââ\
\ââââââ / \ââââââ | â ââ | \ââ |\âââââââ\ââ /\ââ\
\___âââ\ \______/ â \__| \__| \_______\__/ \__|
\___| â
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 v0.94.7 ........................
--- Full QuNex call for command: hcp_msmall
gmri hcp_msmall --sessionsfolder="/home/moanae/shared/project_FM_Gracely_TEST_FM0007/sessions" --parsessions="1" --hcp_icafix_bolds="CONCAT_STIM:BOLD_3,BOLD_1,BOLD_2,BOLD_4" --hcp_msmall_bolds="BOLD_5,BOLD_6" --test --batchfile="/home/moanae/shared/project_FM_Gracely_TEST_FM0007/processing/batch_FM_Gracely.txt" --sessions="FM0007"
---------------------------------------------------------
WARNING: Parameter qx_cifti_tail was not specified. Its value was imputed from parameter hcp_cifti_tail and set to '"_Atlas"'!
WARNING: Parameter qx_nifti_tail was not specified. Its value was imputed from parameter hcp_nifti_tail and set to ''!
WARNING: Parameter cifti_tail was not specified. Its value was imputed from parameter qx_cifti_tail and set to '"_Atlas"'!
WARNING: Parameter nifti_tail was not specified. Its value was imputed from parameter qx_nifti_tail and set to ''!
# Generated by QuNex 0.94.7 on 2022-08-19_10.17.02.650630
#
=================================================================
gmri hcp_msmall \
--sessionsfolder="/home/moanae/shared/project_FM_Gracely_TEST_FM0007/sessions" \
--parsessions="1" \
--hcp_icafix_bolds="CONCAT_STIM:BOLD_3,BOLD_1,BOLD_2,BOLD_4" \
--hcp_msmall_bolds="BOLD_5,BOLD_6" \
--test="True" \
--sessions="/home/moanae/shared/project_FM_Gracely_TEST_FM0007/processing/batch_FM_Gracely.txt" \
--sessionids="FM0007" \
=================================================================
Running test on /home/moanae/shared/project_FM_Gracely_TEST_FM0007/processing/batch_FM_Gracely.txt ...
---- Running local
Starting testing of sessions FM0007 at Friday, 19. August 2022 10:17:02
------------------------------------------------------------
Session id: FM0007
[started on Friday, 19. August 2022 10:17:02]
Test running HCP MSMAll pipeline [LegacyStyleData] ...
Comparing bolds with those specifed via parameters
... skipping BOLD_5: it is not specified in hcp_icafix_bolds
... skipping BOLD_6: it is not specified in hcp_icafix_bolds
Multi-run HCP ICAFix on 1 groups
---> ERROR: bold BOLD_5 defined in hcp_msmall_bolds but not found in the used hcp_icafix_bolds!
---> ERROR: bold BOLD_6 defined in hcp_msmall_bolds but not found in the used hcp_icafix_bolds!
ERROR in completing hcp_msmall:
... invalid input parameters!
HCP MSMAll test completed on Friday, 19. August 2022 10:17:02
------------------------------------------------------------
===> Final report for command hcp_msmall
... FM0007 ---> HCP MSMAll failed
===> Success status not reported for some or all tasks
Then I tried specifying the rest runs in both parameters, than I got a Python error.
cn2107:~ moana004$ qunex_container hcp_msmall --batchfile="${study_sharedfolder}/processing/batch_FM_Gracely.txt" --sessionsfolder="${study_sharedfolder}/sessions" --parsessions="1" --hcp_icafix_bolds=CONCAT_REST:BOLD_5,BOLD_6 --hcp_msmall_bolds=BOLD_5,BOLD_6 --test --bind="${study_sharedfolder}:/${study_sharedfolder}" --container="${HOME}/qunex/qunex_suite-0.94.7.sif"
--> QuNex will run the command over 1 sessions. It will utilize:
Maximum sessions run in parallel for a job: 1.
Maximum elements run in parallel for a session: 1.
Up to 1 processes will be utilized for a job.
Job #1 will run sessions: FM0007
cn2107:~ moana004$ --> 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: 0.94.7
User: moana004
System: cn2107
OS: RedHat Linux #1 SMP Tue Jun 28 15:37:28 UTC 2022
------------------------------------------------------------------------
ââââââ\ â ââ\ ââ\
ââ __ââ\ â âââ\ ââ |
ââ / ââ |ââ\ ââ\ â ââââ\ ââ | ââââââ\ ââ\ ââ\
ââ | ââ |ââ | ââ | â ââ ââ\ââ |ââ __ââ\\ââ\ ââ |
ââ | ââ |ââ | ââ | â ââ \ââââ |ââââââââ |\ââââ /
ââ ââ\ââ |ââ | ââ | â ââ |\âââ |ââ ____|ââ ââ\
\ââââââ / \ââââââ | â ââ | \ââ |\âââââââ\ââ /\ââ\
\___âââ\ \______/ â \__| \__| \_______\__/ \__|
\___| â
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 v0.94.7 ........................
--- Full QuNex call for command: hcp_msmall
gmri hcp_msmall --sessionsfolder="/home/moanae/shared/project_FM_Gracely_TEST_FM0007/sessions" --parsessions="1" --hcp_icafix_bolds="CONCAT_REST:BOLD_5,BOLD_6" --hcp_msmall_bolds="BOLD_5,BOLD_6" --test --batchfile="/home/moanae/shared/project_FM_Gracely_TEST_FM0007/processing/batch_FM_Gracely.txt" --sessions="FM0007"
---------------------------------------------------------
WARNING: Parameter qx_cifti_tail was not specified. Its value was imputed from parameter hcp_cifti_tail and set to '"_Atlas"'!
WARNING: Parameter qx_nifti_tail was not specified. Its value was imputed from parameter hcp_nifti_tail and set to ''!
WARNING: Parameter cifti_tail was not specified. Its value was imputed from parameter qx_cifti_tail and set to '"_Atlas"'!
WARNING: Parameter nifti_tail was not specified. Its value was imputed from parameter qx_nifti_tail and set to ''!
# Generated by QuNex 0.94.7 on 2022-08-19_10.17.58.863302
#
=================================================================
gmri hcp_msmall \
--sessionsfolder="/home/moanae/shared/project_FM_Gracely_TEST_FM0007/sessions" \
--parsessions="1" \
--hcp_icafix_bolds="CONCAT_REST:BOLD_5,BOLD_6" \
--hcp_msmall_bolds="BOLD_5,BOLD_6" \
--test="True" \
--sessions="/home/moanae/shared/project_FM_Gracely_TEST_FM0007/processing/batch_FM_Gracely.txt" \
--sessionids="FM0007" \
=================================================================
Running test on /home/moanae/shared/project_FM_Gracely_TEST_FM0007/processing/batch_FM_Gracely.txt ...
---- Running local
Starting testing of sessions FM0007 at Friday, 19. August 2022 10:17:58
------------------------------------------------------------
Session id: FM0007
[started on Friday, 19. August 2022 10:17:58]
Test running HCP MSMAll pipeline [LegacyStyleData] ...
Comparing bolds with those specifed via parameters
... skipping BOLD_1: it is not specified in hcp_icafix_bolds
... skipping BOLD_2: it is not specified in hcp_icafix_bolds
... skipping BOLD_3: it is not specified in hcp_icafix_bolds
... skipping BOLD_4: it is not specified in hcp_icafix_bolds
Multi-run HCP ICAFix on 1 groups
------------------------------------------------------------
---> Test processing MSMAll MSMAll_restBOLD-only
... bold image BOLD_5 present
... bold image BOLD_6 present
... ICA CONCAT_REST present
------------------------------------------------------------
Running HCP Pipelines command via QuNex:
/opt/HCP/HCPpipelines/MSMAll/MSMAllPipeline.sh
--path="/home/moanae/shared/project_FM_Gracely_TEST_FM0007/sessions/FM0007/hcp"
--subject="FM0007"
--fmri-names-list=""
--multirun-fix-names="BOLD_5@BOLD_6"
--multirun-fix-concat-name="CONCAT_REST"
--multirun-fix-names-to-use="BOLD_5@BOLD_6"
--output-fmri-name="MSMAll_restBOLD-only"
--high-pass="0"
--fmri-proc-string="_Atlas_hp0_clean"
--msm-all-templates="/opt/HCP/HCPpipelines/global/templates/MSMAll"
--output-registration-name="MSMAll_InitialReg"
--high-res-mesh="164"
--low-res-mesh="32"
--input-registration-name="MSMSulc"
--matlab-run-mode="0"
------------------------------------------------------------
--- Failed during processing of group CONCAT_REST with error:
Traceback (most recent call last):
File "/opt/qunex/python/qx_utilities/hcp/process_hcp.py", line 5760, in executeHCPMultiMSMAll
passed, _, r, failed = pc.checkRun(None, None, 'HCP MSMAll ' + groupname, r, overwrite=True)
File "/opt/qunex/python/qx_utilities/processing/core.py", line 634, in checkRun
log = open(logFile, 'r')
TypeError: expected str, bytes or os.PathLike object, not NoneType
HCP MSMAll test completed on Friday, 19. August 2022 10:17:58
------------------------------------------------------------
===> Final report for command hcp_msmall
... FM0007 ---> HCP MSMAll: bolds CONCAT_REST failed
===> Not all tasks completed fully!