On XNAT, we are getting errors when processing on XNAT specifically if we use containers newer than v0_48_20. Below are detailed our tests we did with the test subject HCPA001: XNAT_MED
1. Up to hcp1 included = qunex-init
- D(escription):
qunex-init ran successfully on XNAT, with all containers versions: v0_48_20; v0_48_35 and v0_49_01. Example provided for v0_49_01
- C(all):
/opt/qunex/connector/functions/RunTurnkey.sh --bolds="" --xnathost=https://xnat.med.yale.edu --xnatuser=0590e894-b4e1-4d16-8cd3-db828f59de3f --xnatpass=DOBFYLAP5TGXZosGtSH8AUZk6hR50Mu0HcfzW9iU62GgkCfPd8NFF4gaRbBdol5J --batchfile=HCPA001_batch_parameters.txt --overwritestep=yes --overwriteprojectxnat=no --mappingfile=HCPA001_mapping.txt --xnataccsessionid=YALE_XNAT18_E00007 --xnatsessionlabels=HCPA001 --xnatprojectid=Upload_Test --xnatsubjectid=YALE_XNAT18_S00658 --subjects="HCPA001" --turnkeysteps="createStudy,mapRawData,processInbox,getHCPReady,setupHCP,createBatch,hcp1" --subjid=""
Build location: /Volumes/YaleStorage/XNAT/build/dc44aae3-db68-43e9-a013-99860e71c3c0
- L(ogs):
/Volumes/YaleStorage/XNAT/build/dc44aae3-db68-43e9-a013-99860e71c3c0/Upload_Test/processing/logs/comlogs/done_runTurnkey_HCPA001_2020-05-11_18.38.0346835905.log
qunex_init_successful_v0_49_01_done_runTurnkey_HCPA001_2020-05-11_18.38.0346835905.log (54.3 KB)
2. hcp2 > hcp5
- D(escription):
Steps hcp2 to hcp5 are successfully run only with v0_48_20 but error with and v0_49_01 and v0_48_35 to not use because multiple syntax errors. In addition, the status is marked complete on XNAT. Example provided for v0_49_01
- C(all):
/opt/qunex/connector/functions/RunTurnkey.sh --bolds="" --xnathost=https://xnat.med.yale.edu --xnatuser=ee2e3d25-dfee-42df-b853-479f3b9fdca9 --xnatpass=zJLkM5Tejp9VjrGeqEt7fZSCCjGlvmWENocobyJzEOjuq33Gli6ZFNgMKp1t2pLZ --batchfile=HCPA001_batch_parameters.txt --overwritestep=no --overwriteprojectxnat=no --mappingfile=HCPA001_mapping.txt --xnataccsessionid=YALE_XNAT18_E00007 --xnatsessionlabels=HCPA001 --xnatprojectid=Upload_Test --xnatsubjectid=YALE_XNAT18_S00658 --subjects="HCPA001" --turnkeysteps="hcp2,hcp3,runQC_T1w,runQC_T2w,runQC_Myelin,hcp4,hcp5,runQC_BOLD,BOLDParcellation" --subjid=""
Build: /Volumes/YaleStorage/XNAT/build/f6bf00fe-e94e-430b-9489-1eb7b82283f4
- L(ogs):
/Volumes/YaleStorage/XNAT/build/f6bf00fe-e94e-430b-9489-1eb7b82283f4/Upload_Test/processing/logs/comlogs/error_runTurnkey_HCPA001_2020-05-12_02.01.0081361616.log
Potential error: no rsync of the T2w folder in the build directory when running hcp2>hcp5. This does not happen with v0_48_20.
Outputs:
rsync to build
[32m -- Running rsync: rsync -avzH --include='/processing' --include='scenes/**' --include='specs/*' --include='/subjects' --include='HCPA001' --include='.txt' --include='hcp/' --include='T1w/**' --exclude='' /input/RESOURCES/qunex_study/ /output/Upload_Test [0m
error from hcp2
=================================================================
gmri hcp2 \
--subjid="" \
--logfolder="/output/Upload_Test/processing/logs" \
--subjectsfolder="/output/Upload_Test/subjects" \
--overwrite="no" \
--sessions="/output/Upload_Test/processing/HCPA001_batch_parameters.txt" \
=================================================================
Starting multiprocessing sessions in /output/Upload_Test/processing/HCPA001_batch_parameters.txt with a pool of 16 concurrent processes
---- Running local
Adding processing of session HCPA001 to the pool at Tuesday, 12. May 2020 02:03:54
---------------------------------------------------------
Session id: HCPA001
[started on Tuesday, 12. May 2020 02:03:54]
Running HCP FreeSurfer Pipeline [HCPStyleData] ...
---> PreFS results present.
---> ERROR: The requested HCP processing mode is 'HCPStyleData', however, not T2w image was specified!
Consider using LegacyStyleData processing mode.
---> FREESURFER_HOME set to: /opt/freesurfer/freesurfer-6.0
---> Subject can not be processed.
HCP FS completed on Tuesday, 12. May 2020 02:03:55
---------------------------------------------------------
===> Final report for command hcp2
... HCPA001 ---> FS can not be run
===> Not all tasks completed fully!
error_v0_49_01_hcp2-hcp5_error_runTurnkey_HCPA001_2020-05-12_02.01.0081361616.log (77.8 KB)