Hi all,
I am trying to run HCP MSMALL Pipeline. Everything works well until running “hcp_msmall” command. Could you help me find out the problems?
I have two subjects as example data, which are HCP001 and HCP002. Here is my commands:
qunex_container hcp_icafix \
--sessionsfolder="${WORK_DIR}/${STUDY_NAME}/sessions" \
--batchfile="${WORK_DIR}/${STUDY_NAME}/processing/batch.txt" \
--parsessions="${PARSES}" \
--sessions="${SUBJ}" \
--hcp_icafix_bolds="GROUP_1:BOLD_1,BOLD_2" \
--bind="${WORK_DIR}:${WORK_DIR}" \
--container="${QUNEX_CONTAINER}"
qunex_container hcp_post_fix \
--sessionsfolder="${WORK_DIR}/${STUDY_NAME}/sessions" \
--batchfile="${WORK_DIR}/${STUDY_NAME}/processing/batch.txt" \
--parsessions="${PARSES}" \
--hcp_matlab_mode="compiled" \
--hcp_icafix_bolds="GROUP_1:BOLD_1,BOLD_2" \
--bind="${WORK_DIR}:${WORK_DIR}" \
--container="${QUNEX_CONTAINER}"
qunex_container hcp_reapply_fix \
--sessionsfolder="${WORK_DIR}/${STUDY_NAME}/sessions" \
--batchfile="${WORK_DIR}/${STUDY_NAME}/processing/batch.txt" \
--parsessions="${PARSES}" \
--sessions="${SUBJ}" \
--hcp_icafix_bolds="GROUP_1:BOLD_1,BOLD_2" \
--bind="${WORK_DIR}:${WORK_DIR}" \
--container="${QUNEX_CONTAINER}"
qunex_container hcp_msmall \
--sessionsfolder="${WORK_DIR}/${STUDY_NAME}/sessions" \
--batchfile="${WORK_DIR}/${STUDY_NAME}/processing/batch.txt" \
--bind="${WORK_DIR}:${WORK_DIR}" \
--hcp_matlab_mode="compiled" \
--hcp_icafix_bolds="GROUP_1:BOLD_1,BOLD_2" \
--container="${QUNEX_CONTAINER}";
And the error is:
---> QuNex will run the command over 2 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: HCP001,HCP002
---> 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 FSLBINDIR PALMDIR QUNEXMCOMMAND HCPPIPEDIR CARET7DIR GRADUNWARPDIR HCPPIPEDIR_Templates HCPPIPEDIR_Bin HCPPIPEDIR_Config HCPPIPEDIR_PreFS HCPPIPEDIR_FS HCPPIPEDIR_FS_CUSTOM HCPPIPEDIR_PostFS HCPPIPEDIR_fMRISurf HCPPIPEDIR_fMRIVol HCPPIPEDIR_tfMRI HCPPIPEDIR_dMRI HCPPIPEDIR_dMRITract HCPPIPEDIR_Global HCPPIPEDIR_tfMRIAnalysis HCPCIFTIRWDIR MSMBin HCPPIPEDIR_dMRITractFull HCPPIPEDIR_dMRILegacy AutoPtxFolder EDDYCUDA 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 ANTSDIR CUDIMOT
========================================================================
Generated by QuNex
------------------------------------------------------------------------
Version: 1.0.4 [QIO]
User: root
System: f888cd86a1cc
OS: Debian Linux #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 19:18:46 UTC 2
------------------------------------------------------------------------
██████\ ║ ██\ ██\
██ __██\ ║ ███\ ██ |
██ / ██ |██\ ██\ ║ ████\ ██ | ██████\ ██\ ██\
██ | ██ |██ | ██ | ║ ██ ██\██ |██ __██\\██\ ██ |
██ | ██ |██ | ██ | ║ ██ \████ |████████ |\████ /
██ ██\██ |██ | ██ | ║ ██ |\███ |██ ____|██ ██\
\██████ / \██████ | ║ ██ | \██ |\███████\██ /\██\
\___███\ \______/ ║ \__| \__| \_______\__/ \__|
\___| ║
DEVELOPED & MAINTAINED BY:
Mind & Brain Lab, University of Ljubljana
Cho Lab, Yale University
COPYRIGHT & LICENSE NOTICE:
Use of this software is subject to the terms and conditions defined in
QuNex LICENSES which can be found in the LICENSES folder of the QuNex
repository or at https://qunex.yale.edu/qunex-registration
========================================================================
---> Setting up Octave
.......................... Running QuNex v1.0.4 [QIO] ..........................
--- Full QuNex call for command: hcp_msmall
qunex hcp_msmall --sessionsfolder="/home/yumingz/qunex/TRY/sessions" --hcp_matlab_mode="compiled" --hcp_icafix_bolds="GROUP_1:BOLD_1,BOLD_2" --batchfile="/home/yumingz/qunex/TRY/processing/batch.txt" --sessions="HCP001,HCP002"
---------------------------------------------------------
# Generated by QuNex 1.0.4 [QIO] on 2025-03-16_07.08.06.792386#
=================================================================
qunex hcp_msmall \
--sessionsfolder="/home/yumingz/qunex/TRY/sessions" \
--hcp_matlab_mode="compiled" \
--hcp_icafix_bolds="GROUP_1:BOLD_1,BOLD_2" \
--sessions="/home/yumingz/qunex/TRY/processing/batch.txt" \
--sessionids="HCP001,HCP002" \
=================================================================
Starting multiprocessing sessions in /home/yumingz/qunex/TRY/processing/batch.txt with a pool of 1 concurrent processes
Starting processing of sessions HCP001 at Sunday, 16. March 2025 07:08:06
------------------------------------------------------------
Session id: HCP001
[started on Sunday, 16. March 2025 07:08:06]
Running HCP MSMAll pipeline [HCPStyleData] ...
Comparing bolds with those specifed via parameters
... all bolds specified via hcp_icafix_bolds are present
Multi-run HCP ICAFix on 1 groups
------------------------------------------------------------
---> Processing MSMAll rfMRI_REST
... bold image BOLD_1 present
... bold image BOLD_2 present
... ICA GROUP_1 present
--- Failed during processing of group GROUP_1 with error:
Traceback (most recent call last):
File "/opt/qunex/python/qx_utilities/hcp/process_hcp.py", line 9237, in executeHCPMultiMSMAll
fixnamestouse = "@".join(group["msmall_bolds"])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: sequence item 0: expected str instance, tuple found
HCP MSMAll completed on Sunday, 16. March 2025 07:08:06
------------------------------------------------------------
Starting processing of sessions HCP002 at Sunday, 16. March 2025 07:08:06
------------------------------------------------------------
Session id: HCP002
[started on Sunday, 16. March 2025 07:08:06]
Running HCP MSMAll pipeline [HCPStyleData] ...
Comparing bolds with those specifed via parameters
... all bolds specified via hcp_icafix_bolds are present
Multi-run HCP ICAFix on 1 groups
------------------------------------------------------------
---> Processing MSMAll rfMRI_REST
... bold image BOLD_1 present
... bold image BOLD_2 present
... ICA GROUP_1 present
--- Failed during processing of group GROUP_1 with error:
Traceback (most recent call last):
File "/opt/qunex/python/qx_utilities/hcp/process_hcp.py", line 9237, in executeHCPMultiMSMAll
fixnamestouse = "@".join(group["msmall_bolds"])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: sequence item 0: expected str instance, tuple found
HCP MSMAll completed on Sunday, 16. March 2025 07:08:06
------------------------------------------------------------
---> Final report for command hcp_msmall
... HCP001 ---> HCP MSMAll: bolds GROUP_1 failed
... HCP002 ---> HCP MSMAll: bolds GROUP_1 failed
---> Not all tasks completed fully!
My qunex_container is:QUNEX_CONTAINER=“gitlab.qunex.yale.edu:5002/qunex/qunexcontainer:1.0.4”
Best,
Acacius