[RESOLVED] Error running hcp_freesurfer according to the Getting Started guide

yzhong · February 23, 2025, 7:15am

Hi,
I’m just getting started with QuNex and trying to run the sample data according to the guide, but I’m getting an error when running hcp_freesurfer:

---> PreFS results present.

------------------------------------------------------------
Running HCP Pipelines command via QuNex:

/opt/HCP/HCPpipelines/FreeSurfer/FreeSurferPipeline.sh 
    --session-dir="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w" 
    --session="HCPA001" 
    --processing-mode="HCPStyleData" 
    --t1="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore.nii.gz" 
    --t1brain="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz" 
    --t2="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz" 
    --gpu="True"
------------------------------------------------------------


Running HCP FS

ERROR: Running HCP FS failed with error 2
... 
command executed:
/opt/HCP/HCPpipelines/FreeSurfer/FreeSurferPipeline.sh --session-dir="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w" --session="HCPA001" --processing-mode="HCPStyleData" --t1="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore.nii.gz" --t1brain="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz" --t2="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz" --gpu="True"

---> logfile: /home/aca/qunex/quickstart/processing/logs/comlogs/error_hcp_freesurfer_HCPA001_2025-02-23_06.08.03.595057.log

HCP FS completed on Sunday, 23. February 2025 06:08:03
------------------------------------------------------------


---> Final report for command hcp_freesurfer
... HCPA001 ---> Error
---> Not all tasks completed fully!

This seems to be caused by the fact that my laptop doesn’t have a gpu, if so how do I make the change? To make it easier to troubleshoot the problem, my com
error_hcp_freesurfer_HCPA001_2025-02-23_04.44.42.708691.log (6.7 KB)
log is attached below.

Thanks for your patience.

Acacius

demsarjure · February 23, 2025, 9:08am

Hi Acacius,

Welcome to the QuNex forum!

hcp_freesurfer does not need a GPU. Not sure where gpu="True" part comes from, can you paste everything that you executed so I can investigate?

Also, you are using a slightly dated container, the latest is 1.0.4, a new version 1.1.0 will be released in a couple of days. It is always best to use the latest version as some of the bugs you encounter might be already fixed.

Best, Jure

yzhong · February 26, 2025, 2:04pm

Dear Jure,

Thanks for your patience and sugguestion. Your advice is very effective. I have updated my qunex container from 1.0.0 to 1.0.4. This bug was fixed in version 1.0.4, but I encountered a new problem in the next processing step.This was what I run:

# hcp_fmri_volume
# note the parelements parameter which makes QuNex process all 4 BOLDs in parallel
qunex_container hcp_fmri_volume\
    --sessionsfolder="${STUDY_FOLDER}/sessions" \
    --batchfile="${STUDY_FOLDER}/processing/batch.txt" \
    --parelements=4 \
    --container="${QUNEX_CONTAINER}"

And this was what I got:

---> 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: 4.
    Up to 4 processes will be utilized for a job.

    Job #1 will run sessions: HCPA001
aca@aca-virtual-machine:~/qunex$ ---> 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: af0b3c5664a2
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_fmri_volume

qunex hcp_fmri_volume --sessionsfolder="/home/aca/qunex/quickstart/sessions" --parelements="4" --batchfile="/home/aca/qunex/quickstart/processing/batch.txt" --sessions="HCPA001"

---------------------------------------------------------


# Generated by QuNex 1.0.4 [QIO] on 2025-02-26_04.59.04.609236#
=================================================================
qunex hcp_fmri_volume \
  --sessionsfolder="/home/aca/qunex/quickstart/sessions" \
  --parelements="4" \
  --sessions="/home/aca/qunex/quickstart/processing/batch.txt" \
  --sessionids="HCPA001" \
=================================================================

Starting multiprocessing sessions in /home/aca/qunex/quickstart/processing/batch.txt with a pool of 1 concurrent processes


Starting processing of sessions HCPA001 at Wednesday, 26. February 2025 04:59:04
=======================================================================================================================================
=======================================================================================================================================
Running external command: /opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh --path="/home/aca/qunex/quickstart/sessions/HCPA001/hcp" --subject="HCPA001" --fmriname="1" --fmritcs="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_1_AP/HCPA001_BOLD_1_AP.nii.gz" --fmriscout="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_1_AP_SBRef/HCPA001_BOLD_1_AP_SBRef.nii.gz" --SEPhaseNeg="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" --SEPhasePos="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" --fmapmag="NONE" --fmapphase="NONE" --fmapcombined="NONE" --echospacing="0.000580009" --echodiff="NONE" --unwarpdir="y-" --fmrires="2" --dcmethod="TOPUP" --biascorrection="NONE" --gdcoeffs="NONE" --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" --mctype="MCFLIRT" --processing-mode="HCPStyleData" --doslicetime="FALSE"

You can follow command's progress in:
/home/aca/qunex/quickstart/processing/logs/comlogs/tmp_hcp_fmri_volume_1_HCPA001_2025-02-26_04.59.04.629429.log
------------------------------------------------------------
Running external command: /opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh --path="/home/aca/qunex/quickstart/sessions/HCPA001/hcp" --subject="HCPA001" --fmriname="2" --fmritcs="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_2_PA/HCPA001_BOLD_2_PA.nii.gz" --fmriscout="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_2_PA_SBRef/HCPA001_BOLD_2_PA_SBRef.nii.gz" --SEPhaseNeg="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" --SEPhasePos="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" --fmapmag="NONE" --fmapphase="NONE" --fmapcombined="NONE" --echospacing="0.000580009" --echodiff="NONE" --unwarpdir="y" --fmrires="2" --dcmethod="TOPUP" --biascorrection="NONE" --gdcoeffs="NONE" --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" --mctype="MCFLIRT" --processing-mode="HCPStyleData" --doslicetime="FALSE"

You can follow command's progress in:
/home/aca/qunex/quickstart/processing/logs/comlogs/tmp_hcp_fmri_volume_2_HCPA001_2025-02-26_04.59.04.658025.log
------------------------------------------------------------

------------------------------------------------------------
Session id: HCPA001 
[started on Wednesday, 26. February 2025 04:59:04]
Running HCP fMRI Volume pipeline [HCPStyleData] ... 
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Looking for spin echo fieldmap set images [PA/AP].
     ... identified folder SpinEchoFieldMap1
     ... phase negative AP spin echo fieldmap image present
     ... phase positive PA spin echo fieldmap image present
     ... identified folder SpinEchoFieldMap2
     ... phase negative AP spin echo fieldmap image present
     ... phase positive PA spin echo fieldmap image present
     ... TOPUP configuration file present

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
     ... phase encoding direction: AP
     ... unwarp direction: y-
     ... using image specific EchoSpacing: 0.000580009 s
     ... using spin echo fieldmap set 1
         -> SE Positive image : HCPA001_BOLD_PA_SB_SE.nii.gz
         -> SE Negative image : HCPA001_BOLD_AP_SB_SE.nii.gz
     ... bold image present
     ... reference image present
     ... using the HCPpipelines default BOLD mask

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 2
     ... phase encoding direction: PA
     ... unwarp direction: y
     ... using image specific EchoSpacing: 0.000580009 s
     ... using spin echo fieldmap set 1
         -> SE Positive image : HCPA001_BOLD_PA_SB_SE.nii.gz
         -> SE Negative image : HCPA001_BOLD_AP_SB_SE.nii.gz
     ... bold image present
     ... reference image present
     ... using the HCPpipelines default BOLD mask

Running 2 BOLD images in parallel


 --- Failed during processing of bold 1 with error:


------------------------------------------------------------
Running HCP Pipelines command via QuNex:

/opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh 
    --path="/home/aca/qunex/quickstart/sessions/HCPA001/hcp" 
    --subject="HCPA001" 
    --fmriname="1" 
    --fmritcs="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_1_AP/HCPA001_BOLD_1_AP.nii.gz" 
    --fmriscout="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_1_AP_SBRef/HCPA001_BOLD_1_AP_SBRef.nii.gz" 
    --SEPhaseNeg="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" 
    --SEPhasePos="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" 
    --fmapmag="NONE" 
    --fmapphase="NONE" 
    --fmapcombined="NONE" 
    --echospacing="0.000580009" 
    --echodiff="NONE" 
    --unwarpdir="y-" 
    --fmrires="2" 
    --dcmethod="TOPUP" 
    --biascorrection="NONE" 
    --gdcoeffs="NONE" 
    --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" 
    --mctype="MCFLIRT" 
    --processing-mode="HCPStyleData" 
    --doslicetime="FALSE"
------------------------------------------------------------


Running HCP fMRIVolume

ERROR: Running HCP fMRIVolume failed with error 137
... 
command executed:
/opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh --path="/home/aca/qunex/quickstart/sessions/HCPA001/hcp" --subject="HCPA001" --fmriname="1" --fmritcs="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_1_AP/HCPA001_BOLD_1_AP.nii.gz" --fmriscout="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_1_AP_SBRef/HCPA001_BOLD_1_AP_SBRef.nii.gz" --SEPhaseNeg="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" --SEPhasePos="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" --fmapmag="NONE" --fmapphase="NONE" --fmapcombined="NONE" --echospacing="0.000580009" --echodiff="NONE" --unwarpdir="y-" --fmrires="2" --dcmethod="TOPUP" --biascorrection="NONE" --gdcoeffs="NONE" --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" --mctype="MCFLIRT" --processing-mode="HCPStyleData" --doslicetime="FALSE"

---> logfile: /home/aca/qunex/quickstart/processing/logs/comlogs/error_hcp_fmri_volume_1_HCPA001_2025-02-26_04.59.04.629429.log


 --- Failed during processing of bold 2 with error:


------------------------------------------------------------
Running HCP Pipelines command via QuNex:

/opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh 
    --path="/home/aca/qunex/quickstart/sessions/HCPA001/hcp" 
    --subject="HCPA001" 
    --fmriname="2" 
    --fmritcs="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_2_PA/HCPA001_BOLD_2_PA.nii.gz" 
    --fmriscout="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_2_PA_SBRef/HCPA001_BOLD_2_PA_SBRef.nii.gz" 
    --SEPhaseNeg="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" 
    --SEPhasePos="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" 
    --fmapmag="NONE" 
    --fmapphase="NONE" 
    --fmapcombined="NONE" 
    --echospacing="0.000580009" 
    --echodiff="NONE" 
    --unwarpdir="y" 
    --fmrires="2" 
    --dcmethod="TOPUP" 
    --biascorrection="NONE" 
    --gdcoeffs="NONE" 
    --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" 
    --mctype="MCFLIRT" 
    --processing-mode="HCPStyleData" 
    --doslicetime="FALSE"
------------------------------------------------------------


Running HCP fMRIVolume

ERROR: Running HCP fMRIVolume failed with error 137
... 
command executed:
/opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh --path="/home/aca/qunex/quickstart/sessions/HCPA001/hcp" --subject="HCPA001" --fmriname="2" --fmritcs="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_2_PA/HCPA001_BOLD_2_PA.nii.gz" --fmriscout="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_2_PA_SBRef/HCPA001_BOLD_2_PA_SBRef.nii.gz" --SEPhaseNeg="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" --SEPhasePos="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" --fmapmag="NONE" --fmapphase="NONE" --fmapcombined="NONE" --echospacing="0.000580009" --echodiff="NONE" --unwarpdir="y" --fmrires="2" --dcmethod="TOPUP" --biascorrection="NONE" --gdcoeffs="NONE" --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" --mctype="MCFLIRT" --processing-mode="HCPStyleData" --doslicetime="FALSE"

---> logfile: /home/aca/qunex/quickstart/processing/logs/comlogs/error_hcp_fmri_volume_2_HCPA001_2025-02-26_04.59.04.658025.log

HCP fMRIVolume completed on Wednesday, 26. February 2025 11:30:26
------------------------------------------------------------


---> Final report for command hcp_fmri_volume
... HCPA001 ---> HCP fMRI Volume: bolds 1, 2 failed
---> Not all tasks completed fully!
qunex_container hcp_fmri_volume    --sessionsfolder="${STUDY_FOLDER}/sessions"     --batchfile="${STUDY_FOLDER}/processing/batch.txt"     --parelements=4     --container="${QUNEX_CONTAINER}"

---> 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: 4.
    Up to 4 processes will be utilized for a job.

    Job #1 will run sessions: HCPA001
aca@aca-virtual-machine:~/qunex$ ---> 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: b8db08d05f21
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_fmri_volume

qunex hcp_fmri_volume --sessionsfolder="/home/aca/qunex/quickstart/sessions" --parelements="4" --batchfile="/home/aca/qunex/quickstart/processing/batch.txt" --sessions="HCPA001"

---------------------------------------------------------


# Generated by QuNex 1.0.4 [QIO] on 2025-02-26_11.51.51.217909#
=================================================================
qunex hcp_fmri_volume \
  --sessionsfolder="/home/aca/qunex/quickstart/sessions" \
  --parelements="4" \
  --sessions="/home/aca/qunex/quickstart/processing/batch.txt" \
  --sessionids="HCPA001" \
=================================================================

Starting multiprocessing sessions in /home/aca/qunex/quickstart/processing/batch.txt with a pool of 1 concurrent processes


Starting processing of sessions HCPA001 at Wednesday, 26. February 2025 11:51:51
=======================================================================================================================================
=======================================================================================================================================
Running external command: /opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh --path="/home/aca/qunex/quickstart/sessions/HCPA001/hcp" --subject="HCPA001" --fmriname="1" --fmritcs="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_1_AP/HCPA001_BOLD_1_AP.nii.gz" --fmriscout="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_1_AP_SBRef/HCPA001_BOLD_1_AP_SBRef.nii.gz" --SEPhaseNeg="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" --SEPhasePos="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" --fmapmag="NONE" --fmapphase="NONE" --fmapcombined="NONE" --echospacing="0.000580009" --echodiff="NONE" --unwarpdir="y-" --fmrires="2" --dcmethod="TOPUP" --biascorrection="NONE" --gdcoeffs="NONE" --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" --mctype="MCFLIRT" --processing-mode="HCPStyleData" --doslicetime="FALSE"

You can follow command's progress in:
/home/aca/qunex/quickstart/processing/logs/comlogs/tmp_hcp_fmri_volume_1_HCPA001_2025-02-26_11.51.51.345115.log
------------------------------------------------------------
Running external command: /opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh --path="/home/aca/qunex/quickstart/sessions/HCPA001/hcp" --subject="HCPA001" --fmriname="2" --fmritcs="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_2_PA/HCPA001_BOLD_2_PA.nii.gz" --fmriscout="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_2_PA_SBRef/HCPA001_BOLD_2_PA_SBRef.nii.gz" --SEPhaseNeg="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" --SEPhasePos="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" --fmapmag="NONE" --fmapphase="NONE" --fmapcombined="NONE" --echospacing="0.000580009" --echodiff="NONE" --unwarpdir="y" --fmrires="2" --dcmethod="TOPUP" --biascorrection="NONE" --gdcoeffs="NONE" --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" --mctype="MCFLIRT" --processing-mode="HCPStyleData" --doslicetime="FALSE"

You can follow command's progress in:
/home/aca/qunex/quickstart/processing/logs/comlogs/tmp_hcp_fmri_volume_2_HCPA001_2025-02-26_11.51.51.440443.log
------------------------------------------------------------

------------------------------------------------------------
Session id: HCPA001 
[started on Wednesday, 26. February 2025 11:51:51]
Running HCP fMRI Volume pipeline [HCPStyleData] ... 
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Looking for spin echo fieldmap set images [PA/AP].
     ... identified folder SpinEchoFieldMap1
     ... phase negative AP spin echo fieldmap image present
     ... phase positive PA spin echo fieldmap image present
     ... identified folder SpinEchoFieldMap2
     ... phase negative AP spin echo fieldmap image present
     ... phase positive PA spin echo fieldmap image present
     ... TOPUP configuration file present

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
     ... phase encoding direction: AP
     ... unwarp direction: y-
     ... using image specific EchoSpacing: 0.000580009 s
     ... using spin echo fieldmap set 1
         -> SE Positive image : HCPA001_BOLD_PA_SB_SE.nii.gz
         -> SE Negative image : HCPA001_BOLD_AP_SB_SE.nii.gz
     ... bold image present
     ... reference image present
     ... using the HCPpipelines default BOLD mask

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 2
     ... phase encoding direction: PA
     ... unwarp direction: y
     ... using image specific EchoSpacing: 0.000580009 s
     ... using spin echo fieldmap set 1
         -> SE Positive image : HCPA001_BOLD_PA_SB_SE.nii.gz
         -> SE Negative image : HCPA001_BOLD_AP_SB_SE.nii.gz
     ... bold image present
     ... reference image present
     ... using the HCPpipelines default BOLD mask

Running 2 BOLD images in parallel


 --- Failed during processing of bold 1 with error:


------------------------------------------------------------
Running HCP Pipelines command via QuNex:

/opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh 
    --path="/home/aca/qunex/quickstart/sessions/HCPA001/hcp" 
    --subject="HCPA001" 
    --fmriname="1" 
    --fmritcs="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_1_AP/HCPA001_BOLD_1_AP.nii.gz" 
    --fmriscout="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_1_AP_SBRef/HCPA001_BOLD_1_AP_SBRef.nii.gz" 
    --SEPhaseNeg="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" 
    --SEPhasePos="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" 
    --fmapmag="NONE" 
    --fmapphase="NONE" 
    --fmapcombined="NONE" 
    --echospacing="0.000580009" 
    --echodiff="NONE" 
    --unwarpdir="y-" 
    --fmrires="2" 
    --dcmethod="TOPUP" 
    --biascorrection="NONE" 
    --gdcoeffs="NONE" 
    --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" 
    --mctype="MCFLIRT" 
    --processing-mode="HCPStyleData" 
    --doslicetime="FALSE"
------------------------------------------------------------

     ... removing preexisting working bold folder [/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/1]
     ... removing preexisting T1w results bold folder [/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/Results/1]

Running HCP fMRIVolume

ERROR: Running HCP fMRIVolume failed with error 137
... 
command executed:
/opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh --path="/home/aca/qunex/quickstart/sessions/HCPA001/hcp" --subject="HCPA001" --fmriname="1" --fmritcs="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_1_AP/HCPA001_BOLD_1_AP.nii.gz" --fmriscout="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_1_AP_SBRef/HCPA001_BOLD_1_AP_SBRef.nii.gz" --SEPhaseNeg="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" --SEPhasePos="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" --fmapmag="NONE" --fmapphase="NONE" --fmapcombined="NONE" --echospacing="0.000580009" --echodiff="NONE" --unwarpdir="y-" --fmrires="2" --dcmethod="TOPUP" --biascorrection="NONE" --gdcoeffs="NONE" --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" --mctype="MCFLIRT" --processing-mode="HCPStyleData" --doslicetime="FALSE"

---> logfile: /home/aca/qunex/quickstart/processing/logs/comlogs/error_hcp_fmri_volume_1_HCPA001_2025-02-26_11.51.51.345115.log


 --- Failed during processing of bold 2 with error:


------------------------------------------------------------
Running HCP Pipelines command via QuNex:

/opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh 
    --path="/home/aca/qunex/quickstart/sessions/HCPA001/hcp" 
    --subject="HCPA001" 
    --fmriname="2" 
    --fmritcs="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_2_PA/HCPA001_BOLD_2_PA.nii.gz" 
    --fmriscout="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_2_PA_SBRef/HCPA001_BOLD_2_PA_SBRef.nii.gz" 
    --SEPhaseNeg="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" 
    --SEPhasePos="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" 
    --fmapmag="NONE" 
    --fmapphase="NONE" 
    --fmapcombined="NONE" 
    --echospacing="0.000580009" 
    --echodiff="NONE" 
    --unwarpdir="y" 
    --fmrires="2" 
    --dcmethod="TOPUP" 
    --biascorrection="NONE" 
    --gdcoeffs="NONE" 
    --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" 
    --mctype="MCFLIRT" 
    --processing-mode="HCPStyleData" 
    --doslicetime="FALSE"
------------------------------------------------------------

     ... removing preexisting working bold folder [/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/2]
     ... removing preexisting MNINonLinar results bold folder [/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/MNINonLinear/Results/2]
     ... removing preexisting T1w results bold folder [/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/Results/2]
     ... removing preexisting xfms file [/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/xfms/22str.nii.gz]
     ... removing preexisting xfms file [/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/MNINonLinear/xfms/standard22.nii.gz]

Running HCP fMRIVolume

ERROR: Running HCP fMRIVolume failed with error 137
... 
command executed:
/opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh --path="/home/aca/qunex/quickstart/sessions/HCPA001/hcp" --subject="HCPA001" --fmriname="2" --fmritcs="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_2_PA/HCPA001_BOLD_2_PA.nii.gz" --fmriscout="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/BOLD_2_PA_SBRef/HCPA001_BOLD_2_PA_SBRef.nii.gz" --SEPhaseNeg="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" --SEPhasePos="/home/aca/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" --fmapmag="NONE" --fmapphase="NONE" --fmapcombined="NONE" --echospacing="0.000580009" --echodiff="NONE" --unwarpdir="y" --fmrires="2" --dcmethod="TOPUP" --biascorrection="NONE" --gdcoeffs="NONE" --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" --mctype="MCFLIRT" --processing-mode="HCPStyleData" --doslicetime="FALSE"

---> logfile: /home/aca/qunex/quickstart/processing/logs/comlogs/error_hcp_fmri_volume_2_HCPA001_2025-02-26_11.51.51.440443.log

HCP fMRIVolume completed on Wednesday, 26. February 2025 13:34:35
------------------------------------------------------------


---> Final report for command hcp_fmri_volume
... HCPA001 ---> HCP fMRI Volume: bolds 1, 2 failed
---> Not all tasks completed fully!

My comlog were attached below:
error_hcp_fmri_volume_1_HCPA001_2025-02-26_11.51.51.345115.log (13.4 KB)
error_hcp_fmri_volume_2_HCPA001_2025-02-26_11.51.51.440443.log (120.0 KB)

Thank you again!

Acacius

demsarjure · February 26, 2025, 3:18pm

Hi Acacius,

It seems like everything was going smoothly but then your system ran out of resources. You can see that the process got killed by the system (line 71 for BOLD 1 and line 1356 for BOLD 2, signal 137 is a process kill as well). Also, it seems like your dataset has 2 BOLDs, so setting parelements above 2 does not make much sense. Try removing parelements, which will set it to 1 and force sequential processing which needs the lowest amount of resources. What system are you using for this?

Also, the latest version is now 1.1.0, always best to use the last one :).

Best, Jure

yzhong · February 27, 2025, 2:57am

Hi, Jure,

My system is Ubantu 22.04 with 8G RAM

Acacius

demsarjure · February 27, 2025, 11:30am

8GB is quite small for neuroimaging processing. Try running without parelements so the two BOLDs are not processed in parallel, maybe it will plow through.

Best, Jure

yzhong · February 27, 2025, 1:10pm

Thanks! I will have a try

Best, Acacius

demsarjure · March 4, 2025, 9:30am

Hi,

Did you manage to get this up and running?

Best, Jure

yzhong · March 5, 2025, 6:12am

Hi, Jure

After removing the parallel commands, the pipeline worked properly. Sorry for not replying promptly, and thank you very much for your advice！

Best,
Acacius