Description:
Hello, I tried to run QC for T2w images and it failed. QC for T1w images ran without issues. Please see below the log files. Any thoughts on what’s causing this error? Thank you.
Call:
study_sharedfolder=/home/moanae/shared/project_K99_ChrTMDHCP_qunex01; \
qunex_container run_qc \
--modality=T2w \
--batchfile=${study_sharedfolder}/processing/batch_K99Aim2.txt --sessionsfolder=${study_sharedfolder}/sessions \
--bind=${study_sharedfolder}:${study_sharedfolder} --container=${HOME}/qunex/qunex_suite-0.94.9.sif
Logs:
Log for QC T2w
# Generated by QuNex 0.94.9 on 2022-09-17_14.17.54.801382
#
Overwrite value not explicitly specified. Using default: no
---> Scene files found in:
/opt/qunex/qx_library/data/scenes/qc/template_t2w_qc.wb.scene
Time stamp for logging not found. Setting now: 2022-09-17_14.17.57.649593
---> hcp_suffix flag not explicitly provided. Using defaults:
-- qunex.sh: Specified Command-Line Options - Start --
Study Folder: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01
Session Folder: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions
Sessions: 10001
QC Modality: T2w
QC Output Path: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T2w
Custom QC requested: no
HCP suffix:
Omit default QC: no
QC Scene Template Folder: /opt/qunex/qx_library/data/scenes/qc
QC User-defined Scene:
Overwrite prior run: no
Time stamp for logging: 2022-09-17_14.17.57.649593
Zip Scene File: yes
-- qunex.sh: Specified Command-Line Options - End --
e[32m ------------------------- Start of work -------------------------------- e[0m
e[32m ---> Overwrite is set to 'no'. Running checks for previously ran QC. e[0m
e[32m --- Generating T2w QC scene here: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T2w e[0m
e[32m --- Checking and generating output folders... e[0m
e[32m RunQCLogFolder: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T2w/qclog e[0m
e[32m Output path: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T2w e[0m
cat: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/: Is a directory
e[31m ---> ERROR: T2w QC requested but T2w mapping in /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/ not detected. Check your data and re-run if needed. e[0m
Log for QC T1w for same participant
# Generated by QuNex 0.94.9 on 2022-09-17_14.08.39.180771
#
Overwrite value not explicitly specified. Using default: no
---> Scene files found in:
/opt/qunex/qx_library/data/scenes/qc/template_t1w_qc.wb.scene
Time stamp for logging not found. Setting now: 2022-09-17_14.08.42.528636
---> hcp_suffix flag not explicitly provided. Using defaults:
-- qunex.sh: Specified Command-Line Options - Start --
Study Folder: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01
Session Folder: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions
Sessions: 10001
QC Modality: T1w
QC Output Path: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T1w
Custom QC requested: no
HCP suffix:
Omit default QC: no
QC Scene Template Folder: /opt/qunex/qx_library/data/scenes/qc
QC User-defined Scene:
Overwrite prior run: no
Time stamp for logging: 2022-09-17_14.08.42.528636
Zip Scene File: yes
-- qunex.sh: Specified Command-Line Options - End --
e[32m ------------------------- Start of work -------------------------------- e[0m
e[32m ---> Overwrite is set to 'no'. Running checks for previously ran QC. e[0m
e[32m --- Generating T1w QC scene here: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T1w e[0m
e[32m --- Checking and generating output folders... e[0m
e[32m RunQCLogFolder: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T1w/qclog e[0m
e[32m Output path: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T1w e[0m
e[32m ---> T1w inputs found: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/hcp/10001/MNINonLinear/T1w_restore.nii.gz e[0m
e[32m ---> Running PNG extraction using the following command... e[0m
wb_command -show-scene /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T1w/10001.T1w.QC.wb.scene 1 /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T1w/10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636.png 1194 539 > /dev/null 2>&1
e[32m ---> Scene zip set to: yes. Relevant scene files will be zipped using the following base folder: e[0m
e[32m /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/hcp/10001 e[0m
e[32m ---> The zip file will be saved to: e[0m
e[32m /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T1w/10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636.zip e[0m
e[32m ---> T1w scene type requested. Outputs will be set relative to: e[0m
e[32m /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/hcp/10001 e[0m
13.67 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/10001.T1w.QC.wb.scene
3.63 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.L.inflated.164k_fs_LR.surf.gii
3.64 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.L.midthickness.164k_fs_LR.surf.gii
3.64 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.L.pial.164k_fs_LR.surf.gii
3.63 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.L.very_inflated.164k_fs_LR.surf.gii
3.64 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.L.white.164k_fs_LR.surf.gii
3.51 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.R.inflated.164k_fs_LR.surf.gii
3.51 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.R.midthickness.164k_fs_LR.surf.gii
3.51 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.R.pial.164k_fs_LR.surf.gii
3.51 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.R.very_inflated.164k_fs_LR.surf.gii
3.51 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.R.white.164k_fs_LR.surf.gii
3.10 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.aparc.164k_fs_LR.dlabel.nii
3.11 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.aparc.a2009s.164k_fs_LR.dlabel.nii
3.09 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.curvature.164k_fs_LR.dscalar.nii
3.39 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.sulc.164k_fs_LR.dscalar.nii
3.09 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/10001.thickness.164k_fs_LR.dscalar.nii
48.50 MB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/T1w_restore.nii.gz
644.98 KB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/aparc+aseg.nii.gz
696.88 KB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/aparc.a2009s+aseg.nii.gz
725.23 KB 10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636/MNINonLinear/wmparc.nii.gz
/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/hcp/10001/10001.T1w.QC.wb.scene
e[32m --- Running QC completion checks... e[0m
e[32m ---> Scene file found and generated: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T1w/10001.T1w.QC.wb.scene e[0m
e[32m ---> PNG file found and generated: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T1w/10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636.png e[0m
e[32m ---> Scene zip file found and generated: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T1w/10001.T1w.QC.wb.scene.2022-09-17_14.08.42.528636.zip e[0m
e[32m ------------------------- Successful completion of work -------------------------------- e[0m
Contents of folder /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/hcp/10001/MNINonLinear
cn0082:~ moana004$ ls /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/hcp/10001/MNINonLinear
10001.164k_fs_LR.wb.spec
10001.aparc.164k_fs_LR.dlabel.nii
10001.aparc.a2009s.164k_fs_LR.dlabel.nii
10001.ArealDistortion_FS.164k_fs_LR.dscalar.nii
10001.ArealDistortion_MSMSulc.164k_fs_LR.dscalar.nii
10001.corrThickness.164k_fs_LR.dscalar.nii
10001.curvature.164k_fs_LR.dscalar.nii
10001.EdgeDistortion_FS.164k_fs_LR.dscalar.nii
10001.EdgeDistortion_MSMSulc.164k_fs_LR.dscalar.nii
10001.L.aparc.164k_fs_LR.label.gii
10001.L.aparc.a2009s.164k_fs_LR.label.gii
10001.L.ArealDistortion_FS.164k_fs_LR.shape.gii
10001.L.ArealDistortion_MSMSulc.164k_fs_LR.shape.gii
10001.L.atlasroi.164k_fs_LR.shape.gii
10001.L.corrThickness.164k_fs_LR.shape.gii
10001.L.curvature.164k_fs_LR.shape.gii
10001.L.EdgeDistortion_FS.164k_fs_LR.shape.gii
10001.L.EdgeDistortion_MSMSulc.164k_fs_LR.shape.gii
10001.L.flat.164k_fs_LR.surf.gii
10001.L.inflated.164k_fs_LR.surf.gii
10001.L.midthickness.164k_fs_LR.surf.gii
10001.L.MyelinMap.164k_fs_LR.func.gii
10001.L.MyelinMap_BC.164k_fs_LR.func.gii
10001.L.pial.164k_fs_LR.surf.gii
10001.L.RefMyelinMap.164k_fs_LR.func.gii
10001.L.refsulc.164k_fs_LR.shape.gii
10001.L.SmoothedMyelinMap.164k_fs_LR.func.gii
10001.L.SmoothedMyelinMap_BC.164k_fs_LR.func.gii
10001.L.sphere.164k_fs_LR.surf.gii
10001.L.StrainJ_FS.164k_fs_LR.shape.gii
10001.L.StrainJ_MSMSulc.164k_fs_LR.shape.gii
10001.L.StrainR_FS.164k_fs_LR.shape.gii
10001.L.StrainR_MSMSulc.164k_fs_LR.shape.gii
10001.L.sulc.164k_fs_LR.shape.gii
10001.L.thickness.164k_fs_LR.shape.gii
10001.L.very_inflated.164k_fs_LR.surf.gii
10001.L.white.164k_fs_LR.surf.gii
10001.MyelinMap.164k_fs_LR.dscalar.nii
10001.MyelinMap_BC.164k_fs_LR.dscalar.nii
10001.R.aparc.164k_fs_LR.label.gii
10001.R.aparc.a2009s.164k_fs_LR.label.gii
10001.R.ArealDistortion_FS.164k_fs_LR.shape.gii
10001.R.ArealDistortion_MSMSulc.164k_fs_LR.shape.gii
10001.R.atlasroi.164k_fs_LR.shape.gii
10001.R.corrThickness.164k_fs_LR.shape.gii
10001.R.curvature.164k_fs_LR.shape.gii
10001.R.EdgeDistortion_FS.164k_fs_LR.shape.gii
10001.R.EdgeDistortion_MSMSulc.164k_fs_LR.shape.gii
10001.R.flat.164k_fs_LR.surf.gii
10001.R.inflated.164k_fs_LR.surf.gii
10001.R.midthickness.164k_fs_LR.surf.gii
10001.R.MyelinMap.164k_fs_LR.func.gii
10001.R.MyelinMap_BC.164k_fs_LR.func.gii
10001.R.pial.164k_fs_LR.surf.gii
10001.R.RefMyelinMap.164k_fs_LR.func.gii
10001.R.refsulc.164k_fs_LR.shape.gii
10001.R.SmoothedMyelinMap.164k_fs_LR.func.gii
10001.R.SmoothedMyelinMap_BC.164k_fs_LR.func.gii
10001.R.sphere.164k_fs_LR.surf.gii
10001.R.StrainJ_FS.164k_fs_LR.shape.gii
10001.R.StrainJ_MSMSulc.164k_fs_LR.shape.gii
10001.R.StrainR_FS.164k_fs_LR.shape.gii
10001.R.StrainR_MSMSulc.164k_fs_LR.shape.gii
10001.R.sulc.164k_fs_LR.shape.gii
10001.R.thickness.164k_fs_LR.shape.gii
10001.R.very_inflated.164k_fs_LR.surf.gii
10001.R.white.164k_fs_LR.surf.gii
10001.SmoothedMyelinMap.164k_fs_LR.dscalar.nii
10001.SmoothedMyelinMap_BC.164k_fs_LR.dscalar.nii
10001.StrainJ_FS.164k_fs_LR.dscalar.nii
10001.StrainJ_MSMSulc.164k_fs_LR.dscalar.nii
10001.StrainR_FS.164k_fs_LR.dscalar.nii
10001.StrainR_MSMSulc.164k_fs_LR.dscalar.nii
10001.sulc.164k_fs_LR.dscalar.nii
10001.thickness.164k_fs_LR.dscalar.nii
aparc.a2009s+aseg.nii.gz
aparc+aseg.nii.gz
BiasField.nii.gz
brainmask_fs.2.dil2x.nii.gz
brainmask_fs.2.nii.gz
brainmask_fs.nii.gz
fsaverage
fsaverage_LR32k
Native
Results
ribbon.nii.gz
ROIs
StructuralQC
T1w.nii.gz
T1w_restore.2.nii.gz
T1w_restore_brain.nii.gz
T1w_restore.nii.gz
T2w.nii.gz
T2w_restore.2.nii.gz
T2w_restore_brain.nii.gz
T2w_restore.nii.gz
wmparc.nii.gz
xfms
** For an example of how to report an issue, please refer to this post.
Can you try running:
study_sharedfolder=/home/moanae/shared/project_K99_ChrTMDHCP_qunex01; \
qunex_container run_qc \
--modality="T2w" \
--sessions="10001" \
--sessionsfolder="${study_sharedfolder}/sessions" \
--overwrite="yes"
--bind="${study_sharedfolder}:${study_sharedfolder}" \
--container="${HOME}/qunex/qunex_suite-0.94.9.sif"
I just ran a similar command with success on our end. I also added overwrite="yes" since there might be some previous partial results lingering in there.
I tried the command but it gave the same error.
ahl02:~ moana004$ study_sharedfolder=/home/moanae/shared/project_K99_ChrTMDHCP_qunex01; \
> qunex_container run_qc \
> --modality="T2w" --sessions="10001" --sessionsfolder="${study_sharedfolder}/sessions" --overwrite="yes" \
> --bind="${study_sharedfolder}:${study_sharedfolder}" --container="${HOME}/qunex/qunex_suite-0.94.9.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: 10001
ahl02:~ 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: 0.94.9
User: moana004
System: ahl02
OS: RedHat Linux #1 SMP Wed Aug 10 16:21:17 UTC 2022
------------------------------------------------------------------------
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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 v0.94.9 ........................
---> Template folder path value not explicitly specified.
---> Using QuNex defaults: /opt/qunex/qx_library/data/scenes/qc
---> Specified folder contains no scenes: /opt/qunex/qx_library/data/scenes/qc
---> Reverting to defaults: /opt/qunex/qx_library/data/scenes/qc
Output folder path value not explicitly specified. Using default: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T2w
Generation of scene zip file not explicitly provided. Using default: yes
Running run_qc with the following parameters:
--------------------------------------------------------------
Study Folder: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01
Sessions Folder: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions
Sessions: 10001
QC Modality: T2w
QC Output Path: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T2w
Study Log Folder:
Custom QC requested: no
HCP folder suffix:
Omit default QC: no
QC Scene Template Folder: /opt/qunex/qx_library/data/scenes/qc
QC User-defined Scene:
Overwrite prior run: yes
Zip Scene File: yes
--- Full QuNex call for command: run_qc
. /opt/qunex/bash/qx_utilities/run_qc.sh --sessionsfolder='/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions' --sessions='10001' --outpath='/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T2w' --overwrite='yes' --scenetemplatefolder='/opt/qunex/qx_library/data/scenes/qc' --modality='T2w' --datapath='' --datafile='' --customqc=no --omitdefaults=no --dwipath='' --dwidata='' --dwilegacy='' --dtifitqc='' --bedpostxqc='' --eddyqcstats='' --bolddata='' --boldprefix='' --boldsuffix='' --skipframes='' --snronly='' --timestamp='' --scenezip='yes' --boldfc='' --boldfcinput='' --boldfcpath='' --suffix='' --hcp_suffix='' --batchfile=''
--------------------------------------------------------------
--------------------------------------------------------------
Running run_qc locally on ahl02
Command log: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/processing/logs/runlogs/Log-run_qc_2022-09-19_20.12.30.960794.log
Command output: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/processing/logs/comlogs/tmp_run_qc_10001_2022-09-19_20.12.30.960794.log
--------------------------------------------------------------
---> Scene files found in:
/opt/qunex/qx_library/data/scenes/qc/template_t2w_qc.wb.scene
Time stamp for logging not found. Setting now: 2022-09-19_20.12.33.672092
---> hcp_suffix flag not explicitly provided. Using defaults:
-- qunex.sh: Specified Command-Line Options - Start --
Study Folder: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01
Session Folder: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions
Sessions: 10001
QC Modality: T2w
QC Output Path: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T2w
Custom QC requested: no
HCP suffix:
Omit default QC: no
QC Scene Template Folder: /opt/qunex/qx_library/data/scenes/qc
QC User-defined Scene:
Overwrite prior run: yes
Time stamp for logging: 2022-09-19_20.12.33.672092
Zip Scene File: yes
-- qunex.sh: Specified Command-Line Options - End --
------------------------- Start of work --------------------------------
--- Note: Overwrite requested. Removing existing T2w QC scene: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T2w/10001.T2w.QC.wb.scene
--- Generating T2w QC scene here: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T2w
--- Checking and generating output folders...
RunQCLogFolder: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T2w/qclog
Output path: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/QC/T2w
cat: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/: Is a directory
---> ERROR: T2w QC requested but T2w mapping in /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/ not detected. Check your data and re-run if needed.
===> ERROR during run_qc. Check final QuNex error log output:
/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/processing/logs/comlogs/error_run_qc_10001_2022-09-19_20.12.30.960794.log
QuNex FAILED!
I assume that your session has T2w data and you successfully ran the structural preprocessing pipeline (PreFS, FS, PostFS)?
That’s correct. I was able to run QC for the T1w images without trouble, but had this issue for the T2w images.
What is the code looking for when it outputs this error line?
cat: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/: Is a directory
I noticed that for the T1w it seems to look for (and found) the T1w_restore.nii.gz file in MNINonLinear:
e[32m ---> T1w inputs found: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/hcp/10001/MNINonLinear/T1w_restore.nii.gz e[0m
Is this also true for the T2w image, is it looking for T2w_restore.nii.gz in MNINonLinear or some other file in MNINonLinear or other folder?
Can you please list the contents of /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/. There should be session_hcp.txt file in there. This is what the above cat command tries to read.
If the file is there, please also provide its contents. There needs to be an image labelled as T2w in it.
I see, this may be the issue. I named the “session_hcp.txt” differently.
ahl02:~ moana004$ ls /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/
dicom inbox session_hcp_seq-name_process.txt session.txt
hcp nii session_hcp_seq-name.txt
Content of the “session_hcp_seq-name_process.txt”, which is the file I did manual interventions to have the correct field maps assigned to each corresponding image:
ahl02:~ moana004$ cat /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/session_hcp_seq-name_process.txt
# Generated by QuNex 0.94.9 on 2022-09-11_18.11.50.504751
#
session: 10001
subject: 10001
dicom: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/dicom
raw_data: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/nii
data: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/4dfp
hcp: /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10001/hcp
hcpready: true
11 : :Localizer [1/3] i00001: TR(0.04): PEDirection(i): DwellTime(7.5e-06)
12 : :Localizer [2/3] i00002: TR(0.04): PEDirection(i): DwellTime(7.5e-06)
13 : :Localizer [3/3] i00003: TR(0.04): PEDirection(j-): DwellTime(7.5e-06)
21 : :AAHScout: TR(0.00315): DwellTime(5.8e-06)
31 : :AAHScout_MPR_sag [1/4] i00001: TR(0.00315): DwellTime(5.8e-06)
32 : :AAHScout_MPR_sag [2/4] i00002: TR(0.00315): DwellTime(5.8e-06)
33 : :AAHScout_MPR_sag [3/4] i00003: TR(0.00315): DwellTime(5.8e-06)
34 : :AAHScout_MPR_sag [4/4] i00004: TR(0.00315): DwellTime(5.8e-06)
41 : :AAHScout_MPR_cor [1/3] i00001: TR(0.00315): DwellTime(5.8e-06)
42 : :AAHScout_MPR_cor [2/3] i00002: TR(0.00315): DwellTime(5.8e-06)
43 : :AAHScout_MPR_cor [3/3] i00003: TR(0.00315): DwellTime(5.8e-06)
51 : :AAHScout_MPR_tra [1/3] i00001: TR(0.00315): DwellTime(5.8e-06)
52 : :AAHScout_MPR_tra [2/3] i00002: TR(0.00315): DwellTime(5.8e-06)
53 : :AAHScout_MPR_tra [3/3] i00003: TR(0.00315): DwellTime(5.8e-06)
61 : :Localizer_aligned [1/3] i00001: TR(0.104): PEDirection(i): DwellTime(7.5e-06)
62 : :Localizer_aligned [2/3] i00008: TR(0.104): PEDirection(i): DwellTime(7.5e-06)
63 : :Localizer_aligned [3/3] i00009: TR(0.104): PEDirection(j-): DwellTime(7.5e-06)
71 : :BIAS_BC: TR(0.25): DwellTime(7.3e-06)
81 : :BIAS_32CH: TR(0.25): DwellTime(7.3e-06)
91 :SE-FM-AP :SpinEchoFieldMap_AP: TR(9.71): PEDirection(j-): EchoSpacing(0.000580009): DwellTime(2.1e-06): se(1)
101 :SE-FM-PA :SpinEchoFieldMap_PA: TR(9.71): PEDirection(j): EchoSpacing(0.000580009): DwellTime(2.1e-06): se(1)
111 :boldref1:rest :rfMRI_REST_AP_SBRef: TR(0.937): PEDirection(j-): EchoSpacing(0.000580009): DwellTime(2.1e-06): se(1)
121 :bold1:rest :rfMRI_REST_AP: TR(0.937): PEDirection(j-): EchoSpacing(0.000580009): DwellTime(2.1e-06): se(1)
131 :boldref2:rest :rfMRI_REST_PA_SBRef: TR(0.937): PEDirection(j): EchoSpacing(0.000580009): DwellTime(2.1e-06): se(1)
141 :bold2:rest :rfMRI_REST_PA: TR(0.937): PEDirection(j): EchoSpacing(0.000580009): DwellTime(2.1e-06): se(1)
161 :T1w :T1w_MPR: TR(2.4): DwellTime(7.1e-06)
181 :T2w :T2w_SPC: TR(3.2): DwellTime(2.1e-06)
191 : :dMRI_dir98_AP_SBRef: TR(4.06): PEDirection(j-): EchoSpacing(0.000689998): DwellTime(2.1e-06)
201 :DWI:dir98_AP :dMRI_dir98_AP: TR(4.06): PEDirection(j-): EchoSpacing(0.000689998): DwellTime(2.1e-06)
211 : :dMRI_dir98_PA_SBRef: TR(4.06): PEDirection(j): EchoSpacing(0.000689998): DwellTime(2.1e-06)
221 :DWI:dir98_PA :dMRI_dir98_PA: TR(4.06): PEDirection(j): EchoSpacing(0.000689998): DwellTime(2.1e-06)
231 : :dMRI_dir99_AP_SBRef: TR(4.06): PEDirection(j-): EchoSpacing(0.000689998): DwellTime(2.1e-06)
241 :DWI:dir99_AP :dMRI_dir99_AP: TR(4.06): PEDirection(j-): EchoSpacing(0.000689998): DwellTime(2.1e-06)
251 : :dMRI_dir99_PA_SBRef: TR(4.06): PEDirection(j): EchoSpacing(0.000689998): DwellTime(2.1e-06)
261 :DWI:dir99_PA :dMRI_dir99_PA: TR(4.06): PEDirection(j): EchoSpacing(0.000689998): DwellTime(2.1e-06)
271 : :Localizer [1/3] i00001: TR(0.04): PEDirection(i): DwellTime(7.5e-06)
272 : :Localizer [2/3] i00002: TR(0.04): PEDirection(i): DwellTime(7.5e-06)
273 : :Localizer [3/3] i00003: TR(0.04): PEDirection(j-): DwellTime(7.5e-06)
281 : :AAHScout: TR(0.00315): DwellTime(5.8e-06)
291 : :AAHScout_MPR_sag [1/4] i00001: TR(0.00315): DwellTime(5.8e-06)
292 : :AAHScout_MPR_sag [2/4] i00002: TR(0.00315): DwellTime(5.8e-06)
293 : :AAHScout_MPR_sag [3/4] i00003: TR(0.00315): DwellTime(5.8e-06)
294 : :AAHScout_MPR_sag [4/4] i00004: TR(0.00315): DwellTime(5.8e-06)
301 : :AAHScout_MPR_cor [1/3] i00001: TR(0.00315): DwellTime(5.8e-06)
302 : :AAHScout_MPR_cor [2/3] i00002: TR(0.00315): DwellTime(5.8e-06)
303 : :AAHScout_MPR_cor [3/3] i00003: TR(0.00315): DwellTime(5.8e-06)
311 : :AAHScout_MPR_tra [1/3] i00001: TR(0.00315): DwellTime(5.8e-06)
312 : :AAHScout_MPR_tra [2/3] i00002: TR(0.00315): DwellTime(5.8e-06)
313 : :AAHScout_MPR_tra [3/3] i00003: TR(0.00315): DwellTime(5.8e-06)
321 : :Localizer_aligned [1/3] i00001: TR(0.104): PEDirection(i): DwellTime(7.5e-06)
322 : :Localizer_aligned [2/3] i00008: TR(0.104): PEDirection(i): DwellTime(7.5e-06)
323 : :Localizer_aligned [3/3] i00009: TR(0.104): PEDirection(j-): DwellTime(7.5e-06)
341 :T1w :T1w_MPR: TR(2.4): DwellTime(7.1e-06)
351 :SE-FM-AP :SpinEchoFieldMap_AP: TR(9.71): PEDirection(j-): EchoSpacing(0.000580009): DwellTime(2.1e-06): se(2)
361 :SE-FM-PA :SpinEchoFieldMap_PA: TR(9.71): PEDirection(j): EchoSpacing(0.000580009): DwellTime(2.1e-06): se(2)
371 :boldref1:stim :rfMRI_REST_AP_SBRef: TR(0.937): PEDirection(j-): EchoSpacing(0.000580009): DwellTime(2.1e-06): se(2)
381 :bold3:stim :rfMRI_REST_AP: TR(0.937): PEDirection(j-): EchoSpacing(0.000580009): DwellTime(2.1e-06): se(2)
391 :boldref2:stim :rfMRI_REST_PA_SBRef: TR(0.937): PEDirection(j): EchoSpacing(0.000580009): DwellTime(2.1e-06): se(2)
401 :bold4:stim :rfMRI_REST_PA: TR(0.937): PEDirection(j): EchoSpacing(0.000580009): DwellTime(2.1e-06): se(2)
It sounds like the naming of the “session_hcp.txt” might be the issue here, correct? But then why would it work without problems for the T1w image? Please let me know what is the best way to address this issue. Thank you.
Sorry Estephan, I somehow missed your post, which is why I am replying quite late.
With the latest version (0.94.14), you will be able to specify --sourcefile=session_hcp_seq-name_process.txt. The version will be out tomorrow most likely.
An alternative is to create a copy of session_hcp_seq-name_process.txt and name it session_hcp.txt.
QuNex looks inside this file to check whether you actually have a T2w image, for T1w this check does not exists. The reason that we do not need this extra check for T1w is that in some weird cases some outputs that resemble T2w are generated by some external pipelines. So we have an extra safety net here.
Sorry again for the late reply and let me know if your issues have been addressed.
No worries Jure, I appreciate your help. I followed your instructions and with the new qunex container version 0.94.14 all went as expected for run_qc for T2w images. Cheers.