Hi, Jure
I have reworked the data in the .zip and the mapping.txt as you suggested, and the revised mapping.txt is as follows:
# parallel mapping file
# ----------------
41 => T1w
51 => T2w
121 => bold:rest
161 => DWI:dir98_AP
221 => FM-Magnitude
231 => FM-Phase
After that I executed create_session_info, setup_hcp, create_batch) with --overwrite=yes (the setup_hcp directive doesn’t seem to have an overwrite parameter) as you requested. Because I encountered the following error while executing the setup_hcp` command:
qunex_container setup_hcp --sessionsfolder="${STUDY_FOLDER}/sessions"
--batchfile="${STUDY_FOLDER}/processing/batch.txt" --overwrite=yes --container="${QUNEX_CONTAINER}"
---> QuNex will run the command over 4 sessions. It will utilize:
Maximum sessions run in parallel for a job: 1.
Maximum elements run in parallel for a session: 1.
Up to 1 processes will be utilized for a job.
Job #1 will run sessions: 31-JA-JNLA-0001,31-JA-JNLA-0002,31-JA-JNLA-0003,31-JA-JNLA-0004
(base) jiayf@EyeOpener:~/qunex$ ---> 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: 1.1.0 [QIO]
User: root
System: da69f526ff52
OS: Debian Linux #1 SMP Tue Nov 5 00:21:55 UTC 2024
------------------------------------------------------------------------
██████\ ║ ██\ ██\
██ __██\ ║ ███\ ██ |
██ / ██ |██\ ██\ ║ ████\ ██ | ██████\ ██\ ██\
██ | ██ |██ | ██ | ║ ██ ██\██ |██ __██\\██\ ██ |
██ | ██ |██ | ██ | ║ ██ \████ |████████ |\████ /
██ ██\██ |██ | ██ | ║ ██ |\███ |██ ____|██ ██\
\██████ / \██████ | ║ ██ | \██ |\███████\██ /\██\
\___███\ \______/ ║ \__| \__| \_______\__/ \__|
\___| ║
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 v1.1.0 [QIO] ..........................
--- Full QuNex call for command: setup_hcp
qunex setup_hcp --sessionsfolder="/home/jiayf/qunex/parallel/sessions" --overwrite="yes" --batchfile="/home/jiayf/qunex/parallel/processing/batch.txt" --sessions="31-JA-JNLA-0001,31-JA-JNLA-0002,31-JA-JNLA-0003,31-JA-JNLA-0004"
---------------------------------------------------------
ERROR: Extra argument overwrite is not valid! Please check your command!
ERROR in running setup_hcp at gmri:
Invalid arguments
Provided unknown arguments: [overwrite]!
The call received was:
(please note that when run through scheduler, all possible parameters,
even non relevant ones are passed)
qunex setup_hcp \
--sessionsfolder=/home/jiayf/qunex/parallel/sessions \
--overwrite=yes \
--batchfile=/home/jiayf/qunex/parallel/processing/batch.txt \
--sessions=31-JA-JNLA-0001,31-JA-JNLA-0002,31-JA-JNLA-0003,31-JA-JNLA-0004
Please run `qunex setup_hcp --help` to get help for the failed command.
After that I encountered the following when executing the hcp_fmri_volume command:
(base) jiayf@EyeOpener:~/qunex$ qunex_container hcp_fmri_volume --sessionsfolder="${STUDY_FOLDER}/sessions" --batchfile="${STUDY_FOLDER}/processing/batch.txt" --hcp_bold_dcmethod="SiemensFieldMap" --parelements
=1 --container="${QUNEX_CONTAINER}"
---> QuNex will run the command over 4 sessions. It will utilize:
Maximum sessions run in parallel for a job: 1.
Maximum elements run in parallel for a session: 1.
Up to 1 processes will be utilized for a job.
Job #1 will run sessions: 31-JA-JNLA-0001,31-JA-JNLA-0002,31-JA-JNLA-0003,31-JA-JNLA-0004
(base) jiayf@EyeOpener:~/qunex$ ---> 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: 1.1.0 [QIO]
User: root
System: df90ddb8d837
OS: Debian Linux #1 SMP Tue Nov 5 00:21:55 UTC 2024
------------------------------------------------------------------------
██████\ ║ ██\ ██\
██ __██\ ║ ███\ ██ |
██ / ██ |██\ ██\ ║ ████\ ██ | ██████\ ██\ ██\
██ | ██ |██ | ██ | ║ ██ ██\██ |██ __██\\██\ ██ |
██ | ██ |██ | ██ | ║ ██ \████ |████████ |\████ /
██ ██\██ |██ | ██ | ║ ██ |\███ |██ ____|██ ██\
\██████ / \██████ | ║ ██ | \██ |\███████\██ /\██\
\___███\ \______/ ║ \__| \__| \_______\__/ \__|
\___| ║
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 v1.1.0 [QIO] ..........................
--- Full QuNex call for command: hcp_fmri_volume
qunex hcp_fmri_volume --sessionsfolder="/home/jiayf/qunex/parallel/sessions" --hcp_bold_dcmethod="SiemensFieldMap" --parelements="1" --batchfile="/home/jiayf/qunex/parallel/processing/batch.txt" --sessions="31-JA-JNLA-0001,31-JA-JNLA-0002,31-JA-JNLA-0003,31-JA-JNLA-0004"
---------------------------------------------------------
# Generated by QuNex 1.1.0 [QIO] on 2025-03-17_07.09.56.514061#
=================================================================
qunex hcp_fmri_volume \
--sessionsfolder="/home/jiayf/qunex/parallel/sessions" \
--hcp_bold_dcmethod="SiemensFieldMap" \
--parelements="1" \
--sessions="/home/jiayf/qunex/parallel/processing/batch.txt" \
--sessionids="31-JA-JNLA-0001,31-JA-JNLA-0002,31-JA-JNLA-0003,31-JA-JNLA-0004" \
=================================================================
Starting multiprocessing sessions in /home/jiayf/qunex/parallel/processing/batch.txt with a pool of 4 concurrent processes
Adding processing of session 31-JA-JNLA-0001 to the pool at Monday, 17. March 2025 07:09:56
Adding processing of session 31-JA-JNLA-0002 to the pool at Monday, 17. March 2025 07:09:56
Adding processing of session 31-JA-JNLA-0003 to the pool at Monday, 17. March 2025 07:09:56
Adding processing of session 31-JA-JNLA-0004 to the pool at Monday, 17. March 2025 07:09:56
=======================================================================================================================================
------------------------------------------------------------
Session id: 31-JA-JNLA-0001
[started on Monday, 17. March 2025 07:09:56]
Running HCP fMRI Volume pipeline [HCPStyleData] ...
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
... phase encoding direction: PA
... unwarp direction: j
... using image specific EchoSpacing: 0.000530002 s
---> ERROR: No fieldmap number specified for the BOLD image!
... bold image present
... reference image not used
... using the HCPpipelines default BOLD mask
Running 1 BOLD images in parallel
------------------------------------------------------------
Running HCP Pipelines command via QuNex:
/opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh
--path="/home/jiayf/qunex/parallel/sessions/31-JA-JNLA-0001/hcp"
--session="31-JA-JNLA-0001"
--fmriname="1"
--fmritcs="/home/jiayf/qunex/parallel/sessions/31-JA-JNLA-0001/hcp/31-JA-JNLA-0001/unprocessed/BOLD_1_PA/31-JA-JNLA-0001_BOLD_1_PA.nii.gz"
--fmriscout="NONE"
--fmapmag="NONE"
--fmapphase="NONE"
--fmapcombined="NONE"
--echospacing="0.000530002"
--echodiff="NONE"
--unwarpdir="j"
--fmrires="2"
--dcmethod="SiemensFieldMap"
--biascorrection="NONE"
--gdcoeffs="NONE"
--mctype="MCFLIRT"
--processing-mode="HCPStyleData"
--doslicetime="FALSE"
------------------------------------------------------------
---> ERROR: something missing, skipping this BOLD!
HCP fMRIVolume completed on Monday, 17. March 2025 07:09:56
------------------------------------------------------------
=======================================================================================================================================
=======================================================================================================================================
=======================================================================================================================================
------------------------------------------------------------
Session id: 31-JA-JNLA-0003
[started on Monday, 17. March 2025 07:09:56]
Running HCP fMRI Volume pipeline [HCPStyleData] ...
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
... phase encoding direction: PA
... unwarp direction: j
... using image specific EchoSpacing: 0.000530002 s
---> ERROR: No fieldmap number specified for the BOLD image!
... bold image present
... reference image not used
... using the HCPpipelines default BOLD mask
Running 1 BOLD images in parallel
------------------------------------------------------------
Running HCP Pipelines command via QuNex:
/opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh
--path="/home/jiayf/qunex/parallel/sessions/31-JA-JNLA-0003/hcp"
--session="31-JA-JNLA-0003"
--fmriname="1"
--fmritcs="/home/jiayf/qunex/parallel/sessions/31-JA-JNLA-0003/hcp/31-JA-JNLA-0003/unprocessed/BOLD_1_PA/31-JA-JNLA-0003_BOLD_1_PA.nii.gz"
--fmriscout="NONE"
--fmapmag="NONE"
--fmapphase="NONE"
--fmapcombined="NONE"
--echospacing="0.000530002"
--echodiff="NONE"
--unwarpdir="j"
--fmrires="2"
--dcmethod="SiemensFieldMap"
--biascorrection="NONE"
--gdcoeffs="NONE"
--mctype="MCFLIRT"
--processing-mode="HCPStyleData"
--doslicetime="FALSE"
------------------------------------------------------------
---> ERROR: something missing, skipping this BOLD!
HCP fMRIVolume completed on Monday, 17. March 2025 07:09:56
------------------------------------------------------------
------------------------------------------------------------
Session id: 31-JA-JNLA-0002
[started on Monday, 17. March 2025 07:09:56]
Running HCP fMRI Volume pipeline [HCPStyleData] ...
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
... phase encoding direction: PA
... unwarp direction: j
... using image specific EchoSpacing: 0.000530002 s
---> ERROR: No fieldmap number specified for the BOLD image!
... bold image present
... reference image not used
... using the HCPpipelines default BOLD mask
Running 1 BOLD images in parallel
------------------------------------------------------------
Running HCP Pipelines command via QuNex:
/opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh
--path="/home/jiayf/qunex/parallel/sessions/31-JA-JNLA-0002/hcp"
--session="31-JA-JNLA-0002"
--fmriname="1"
--fmritcs="/home/jiayf/qunex/parallel/sessions/31-JA-JNLA-0002/hcp/31-JA-JNLA-0002/unprocessed/BOLD_1_PA/31-JA-JNLA-0002_BOLD_1_PA.nii.gz"
--fmriscout="NONE"
--fmapmag="NONE"
--fmapphase="NONE"
--fmapcombined="NONE"
--echospacing="0.000530002"
--echodiff="NONE"
--unwarpdir="j"
--fmrires="2"
--dcmethod="SiemensFieldMap"
--biascorrection="NONE"
--gdcoeffs="NONE"
--mctype="MCFLIRT"
--processing-mode="HCPStyleData"
--doslicetime="FALSE"
------------------------------------------------------------
---> ERROR: something missing, skipping this BOLD!
HCP fMRIVolume completed on Monday, 17. March 2025 07:09:56
------------------------------------------------------------
------------------------------------------------------------
Session id: 31-JA-JNLA-0004
[started on Monday, 17. March 2025 07:09:56]
Running HCP fMRI Volume pipeline [HCPStyleData] ...
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
... phase encoding direction: PA
... unwarp direction: j
... using image specific EchoSpacing: 0.000530002 s
---> ERROR: No fieldmap number specified for the BOLD image!
... bold image present
... reference image not used
... using the HCPpipelines default BOLD mask
Running 1 BOLD images in parallel
------------------------------------------------------------
Running HCP Pipelines command via QuNex:
/opt/HCP/HCPpipelines/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh
--path="/home/jiayf/qunex/parallel/sessions/31-JA-JNLA-0004/hcp"
--session="31-JA-JNLA-0004"
--fmriname="1"
--fmritcs="/home/jiayf/qunex/parallel/sessions/31-JA-JNLA-0004/hcp/31-JA-JNLA-0004/unprocessed/BOLD_1_PA/31-JA-JNLA-0004_BOLD_1_PA.nii.gz"
--fmriscout="NONE"
--fmapmag="NONE"
--fmapphase="NONE"
--fmapcombined="NONE"
--echospacing="0.000530002"
--echodiff="NONE"
--unwarpdir="j"
--fmrires="2"
--dcmethod="SiemensFieldMap"
--biascorrection="NONE"
--gdcoeffs="NONE"
--mctype="MCFLIRT"
--processing-mode="HCPStyleData"
--doslicetime="FALSE"
------------------------------------------------------------
---> ERROR: something missing, skipping this BOLD!
HCP fMRIVolume completed on Monday, 17. March 2025 07:09:56
------------------------------------------------------------
---> Final report for command hcp_fmri_volume
... 31-JA-JNLA-0001 ---> HCP fMRI Volume: bolds 1 not ready
... 31-JA-JNLA-0003 ---> HCP fMRI Volume: bolds 1 not ready
... 31-JA-JNLA-0002 ---> HCP fMRI Volume: bolds 1 not ready
... 31-JA-JNLA-0004 ---> HCP fMRI Volume: bolds 1 not ready
---> Not all tasks completed fully!
So I changed your suggested Mag_Images => FM-Magnitude to 221 => FM-Magnitude and after this change ERROR: No fieldmap number specified for the BOLD image! disappeared but other errors appeared!
(base) jiayf@EyeOpener:~/qunex$ qunex_container hcp_fmri_volume --sessionsfolder="${STUDY_FOLDER}/sessions" --batchfile="${STUDY_FOLDER}/processing/batch.txt" --hcp_bold_dcmethod="SiemensFieldMap" --parelements=1 --container="${QUNEX_CONTAINER}"
---> QuNex will run the command over 4 sessions. It will utilize:
Maximum sessions run in parallel for a job: 1.
Maximum elements run in parallel for a session: 1.
Up to 1 processes will be utilized for a job.
Job #1 will run sessions: 31-JA-JNLA-0001,31-JA-JNLA-0002,31-JA-JNLA-0003,31-JA-JNLA-0004
(base) jiayf@EyeOpener:~/qunex$ ---> 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: 1.1.0 [QIO]
User: root
System: cc3e1ddbd0da
OS: Debian Linux #1 SMP Tue Nov 5 00:21:55 UTC 2024
------------------------------------------------------------------------
██████\ ║ ██\ ██\
██ __██\ ║ ███\ ██ |
██ / ██ |██\ ██\ ║ ████\ ██ | ██████\ ██\ ██\
██ | ██ |██ | ██ | ║ ██ ██\██ |██ __██\\██\ ██ |
██ | ██ |██ | ██ | ║ ██ \████ |████████ |\████ /
██ ██\██ |██ | ██ | ║ ██ |\███ |██ ____|██ ██\
\██████ / \██████ | ║ ██ | \██ |\███████\██ /\██\
\___███\ \______/ ║ \__| \__| \_______\__/ \__|
\___| ║
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 v1.1.0 [QIO] ..........................
--- Full QuNex call for command: hcp_fmri_volume
qunex hcp_fmri_volume --sessionsfolder="/home/jiayf/qunex/parallel/sessions" --hcp_bold_dcmethod="SiemensFieldMap" --parelements="1" --batchfile="/home/jiayf/qunex/parallel/processing/batch.txt" --sessions="31-JA-JNLA-0001,31-JA-JNLA-0002,31-JA-JNLA-0003,31-JA-JNLA-0004"
---------------------------------------------------------
# Generated by QuNex 1.1.0 [QIO] on 2025-03-17_07.11.59.372562#
=================================================================
qunex hcp_fmri_volume \
--sessionsfolder="/home/jiayf/qunex/parallel/sessions" \
--hcp_bold_dcmethod="SiemensFieldMap" \
--parelements="1" \
--sessions="/home/jiayf/qunex/parallel/processing/batch.txt" \
--sessionids="31-JA-JNLA-0001,31-JA-JNLA-0002,31-JA-JNLA-0003,31-JA-JNLA-0004" \
=================================================================
Starting multiprocessing sessions in /home/jiayf/qunex/parallel/processing/batch.txt with a pool of 4 concurrent processes
Adding processing of session 31-JA-JNLA-0001 to the pool at Monday, 17. March 2025 07:11:59
Adding processing of session 31-JA-JNLA-0002 to the pool at Monday, 17. March 2025 07:11:59
Adding processing of session 31-JA-JNLA-0003 to the pool at Monday, 17. March 2025 07:11:59
Adding processing of session 31-JA-JNLA-0004 to the pool at Monday, 17. March 2025 07:11:59
=======================================================================================================================================
=======================================================================================================================================
------------------------------------------------------------
Session id: 31-JA-JNLA-0001
[started on Monday, 17. March 2025 07:11:59]
Running HCP fMRI Volume pipeline [HCPStyleData] ...
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
... phase encoding direction: PA
... unwarp direction: j
... using image specific EchoSpacing: 0.000530002 s
... Siemens fieldmap magnitude image 1 present
... Siemens fieldmap phase image 1 present
... ERROR: hcp_bold_echodiff not defined correctly: "NONE"!
... bold image present
... reference image not used
... using the HCPpipelines default BOLD mask
Running 1 BOLD images in parallel
---> ERROR: something missing, skipping this BOLD!
HCP fMRIVolume completed on Monday, 17. March 2025 07:11:59
------------------------------------------------------------
=======================================================================================================================================
------------------------------------------------------------
Session id: 31-JA-JNLA-0002
[started on Monday, 17. March 2025 07:11:59]
Running HCP fMRI Volume pipeline [HCPStyleData] ...
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
... phase encoding direction: PA
... unwarp direction: j
... using image specific EchoSpacing: 0.000530002 s
... Siemens fieldmap magnitude image 1 present
... Siemens fieldmap phase image 1 present
... ERROR: hcp_bold_echodiff not defined correctly: "NONE"!
... bold image present
... reference image not used
... using the HCPpipelines default BOLD mask
Running 1 BOLD images in parallel
---> ERROR: something missing, skipping this BOLD!
HCP fMRIVolume completed on Monday, 17. March 2025 07:11:59
------------------------------------------------------------
=======================================================================================================================================
------------------------------------------------------------
Session id: 31-JA-JNLA-0003
[started on Monday, 17. March 2025 07:11:59]
Running HCP fMRI Volume pipeline [HCPStyleData] ...
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
... phase encoding direction: PA
... unwarp direction: j
... using image specific EchoSpacing: 0.000530002 s
... Siemens fieldmap magnitude image 1 present
... Siemens fieldmap phase image 1 present
... ERROR: hcp_bold_echodiff not defined correctly: "NONE"!
... bold image present
... reference image not used
... using the HCPpipelines default BOLD mask
Running 1 BOLD images in parallel
---> ERROR: something missing, skipping this BOLD!
HCP fMRIVolume completed on Monday, 17. March 2025 07:11:59
------------------------------------------------------------
------------------------------------------------------------
Session id: 31-JA-JNLA-0004
[started on Monday, 17. March 2025 07:11:59]
Running HCP fMRI Volume pipeline [HCPStyleData] ...
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
... phase encoding direction: PA
... unwarp direction: j
... using image specific EchoSpacing: 0.000530002 s
... Siemens fieldmap magnitude image 1 present
... Siemens fieldmap phase image 1 present
... ERROR: hcp_bold_echodiff not defined correctly: "NONE"!
... bold image present
... reference image not used
... using the HCPpipelines default BOLD mask
Running 1 BOLD images in parallel
---> ERROR: something missing, skipping this BOLD!
HCP fMRIVolume completed on Monday, 17. March 2025 07:11:59
------------------------------------------------------------
---> Final report for command hcp_fmri_volume
... 31-JA-JNLA-0001 ---> HCP fMRI Volume: bolds 1 not ready
... 31-JA-JNLA-0002 ---> HCP fMRI Volume: bolds 1 not ready
... 31-JA-JNLA-0003 ---> HCP fMRI Volume: bolds 1 not ready
... 31-JA-JNLA-0004 ---> HCP fMRI Volume: bolds 1 not ready
---> Not all tasks completed fully!
This time it was reporting the error ERROR: hcp_bold_echodiff not defined correctly: “NONE”!, so I consulted MAG_IMAGES_0022.json and PHA_IMAGES_0023_ph.json. There are two parameters in PHA_IMAGES_0023_ph.json: “EchoTime1”: 0.02, “EchoTime2”: 0.015, and there is one parameter in MAG_IMAGES_0022.json: “EchoTime”: 0.02, so I calculated and made hcp_ bold_echodiff to be 20-15=5 (ms). Now hcp_fmri_volume seems to work, expect it to turn out correctly.
These are the problems I encountered during the tuning process and the corresponding solutions, so I hope I didn’t make any mistakes in my parameter modifications. In the meantime, I have followed your advice and re-included the dMRI data, even though it only has 64 directions (which does not meet the direction requirement of the HCPpipeline), and I have also named it DWI:dir98_AP, I don’t know if the result of this process is feasible.
Mr. Jure, please give me strength and give me some good advice! 
Best,
YJia
, if your acquisition protocol deviates from HCP’s then preprocessed data quality will be most likely a bit lower. Most data I worked with and I would also say most data from our users does not exactly follow HCP acquisition, meaning that we often work with data similar as yours. Based on the attached files, your acquisition protocol looks OK and I think there is nothing to worry about.
