Description:
Hello! So Clara and I have run into a problem with the niftiQC step when preprocessing the D1 data. It seems that when we run the command, it saves the file in the general slicesdir folder rather than in a subject-specific folder. The problem arises when we try to run the command for more than one subjects, and the files in the general directory just overwrite to the newest subject run. We have been working around this by running one subject at a time through the run_qc command and manually moving the files to the right location, but i am not sure if this is something that could be fixed? Thank you!
Call:
# -- NIFI QC
# -- run 2021-10-26 for 1 session as a test (pb11065) -> qunex said 'failed', but it created the files and data looks good, said "QC generation did not complete correctly"
# -- run 2021-10-29 for 1 session as a test (pb11115) -> got same error as above, but data was generated, but it overwrote the data from the previous subject, always saves in this location: /gpfs/project/fas/n3/Studies/TRANSCENDS.D1/slicesdir and it should save here, based on the script: ${SessionsFolder}/${CASE}/nii/slicesdir/
# -- run 2021-10-29 for 1 session as a test (pb11115) with outpath specified directly -> still did not work, saved in old location and overwrote previous files
# -- run 2021-10-29 for 1 session as a test (pb11115) with no outpath specified, then manually moved output -> success
# run 2021-11-8 for 7 sessions (pb11065, pb11156, pb11702, pb11089, pb11138, pb11567, pb11724) -> data got overwritten after each session, need to run one at a time
# run 2021-11-8 for pb11065 -> manually moved to correct location -> successful
# run 2021-11-8 for pb11156 -> manually moved to correct location -> successful
# run 2021-11-8 for pb11702 -> manually moved to correct location -> successful
# run 2021-11-8 for pb11089 -> manually moved to correct location -> successful
# run 2021-11-8 for pb11138 -> manually moved to correct location -> successful
# run 2021-11-8 for pb11567 -> manually moved to correct location -> successful
# run 2021-11-8 for pb11724 -> manually moved to correct location -> successful
sshcpu
qunexsource
/gpfs/project/fas/n3/software/qunexdev/bin/qunex_container run_qc \
--sessionsfolder="$my_study_folder/sessions" \
--sessions="pb11065,pb11115,pb11156,pb11702,pb11089,pb11138,pb11567,pb11724" \
--modality='rawNII' \
--container="$qunex_container"
mv /gpfs/project/fas/n3/Studies/TRANSCENDS.D1/slicesdir /gpfs/project/fas/n3/Studies/TRANSCENDS.D1/sessions/pb11115/nii/slicedir
Logs:
this is one example log, there are many but they are all similar
/gpfs/project/fas/n3/Studies/TRANSCENDS.D1/processing/logs/comlogs/error_run_qc_pb11156_2021-11-08_12.46.0888564112.log
# Generated by QuNex 0.91.11 on 2021-11-08_12.46.0888564112
#
Overwrite value not explicitly specified. Using default: no
---> Specified folder contains no scenes: /opt/qunex/qx_library/data/scenes/qc
---> Reverting to defaults: /opt/qunex/qx_library/data/scenes/qc
---> Suffix not manually set. Setting default: 2021-11-08_12.44.0542153543
---> hcp_suffix flag not explicitly provided. Using defaults:
-- qunex.sh: Specified Command-Line Options - Start --
Study Folder: /gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1
Session Folder: /gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions
Sessions: pb11156
QC Modality: rawNII
QC Output Path: /gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/QC/rawNII
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: 2021-11-08_12.44.0542153543
Zip Scene File: yes
-- qunex.sh: Specified Command-Line Options - End --
------------------------- Start of work --------------------------------
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/101
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/111
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/11
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/121
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/12
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/131
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/13
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/141
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/151
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/161
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/171
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/181
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/191
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/201
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/211
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/21
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/221
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/231
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/241
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/251
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/261
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/271
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/281
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/291
Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to first volume, but this functionality is deprecated and will be removed in a future release.
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/301
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/31
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/32
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/33
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/34
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/41
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/42
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/43
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/51
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/52
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/53
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/61
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/62
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/63
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/71
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/81
/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/sessions/pb11156/nii/91
Finished. To view, point your web browser at
file:/gpfs/loomis/pi/n3/Studies/TRANSCENDS.D1/slicesdir/index.html
------------------------- ERROR --------------------------------
QC generation did not complete correctly.
Check outputs: /QC_pb11156_UserRunQUEUE_rawNII_2021-11-08_12.44.0542153543.log
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