[RESOLVED] mapRawData error when dicom names identical for each acquisition

Issues
1

Description:

mapRawData step returns an error when the dicom names are identical for each acquisition

Issue identified on XNAT [example session below]:
https://xnat.med.yale.edu/app/action/DisplayItemAction/search_element/xnat%3AmrSessionData/search_field/xnat%3AmrSessionData.ID/search_value/YALE_XNAT21_E00003/popup/false/project/USChina

Tested on Grace - resulted in the same issues. Path to data on Grace: /gpfs/project/fas/n3/Studies/XNATTest/subjects/USChinaTEST

RawData:
/gpfs/project/fas/n3/Studies/XNATTest/subjects/USChinaTEST/RawData
Results:
/gpfs/project/fas/n3/Studies/XNATTest/subjects/USChinaTEST/Results
Specs:
/gpfs/project/fas/n3/Studies/XNATTest/subjects/USChinaTEST/specs

Tree output (example) in /gpfs/project/fas/n3/Studies/XNATTest/subjects/USChinaTEST/RawData/NDAR_INVR87KXM5R/NIH-HC037-0W/inbox:

├── 8-x-SpinEchoFieldMap_RL_BIC_v2-x-SpinEchoFieldMap_RL_BIC_v2
│ ├── DICOM
│ │ ├── 00001.dcm
│ │ └── 00002.dcm
│ └── SNAPSHOTS
│ ├── NIH-HC037-0W_8_qc.gif
│ └── NIH-HC037-0W_8_qc_t.gif
└── 9-x-SpinEchoFieldMap_LR_BIC_v2-x-SpinEchoFieldMap_LR_BIC_v2
├── DICOM
│ ├── 00001.dcm
│ └── 00002.dcm
└── SNAPSHOTS
├── NIH-HC037-0W_9_qc.gif
└── NIH-HC037-0W_9_qc_t.gif

Call:

StudyName="USChina"
InputFolder="/gpfs/project/fas/n3/Studies/XNATTest/subjects/USChinaTEST/RawData"
SpecFolder="/gpfs/project/fas/n3/Studies/XNATTest/subjects/USChinaTEST/specs"
StudyFolder="/gpfs/project/fas/n3/Studies/XNATTest/subjects/USChinaTEST/Results"

SUBJECTS="NDAR_INVR87KXM5R_NIH-HC037-0W"

qx runTurnkey \
  --rawdatainput="${InputFolder}" \
  --dataformat="DICOM" \
  --batchfile="${SpecFolder}/batch_parameters.txt" \
  --mappingfile="${SpecFolder}/hcp_mapping.txt" \
  --workingdir="${StudyFolder}" \
  --projectname="${StudyName}" \
  --path=${StudyFolder} \
  --sessions=${SUBJECTS} \
  --subjid=${SUBJECTS} \
  --turnkeytype="local" \
  --bolds="all" \
  --overwritestep="no" \
  --turnkeysteps="createStudy,mapRawData,processInbox,getHCPReady,setupHCP,createBatch"

Logs:
Linking step during the mapRawData step returns on 415/3643 files:

  --> Batch file transfer check: pass
  --> Mapping file transfer check: pass
  --> DICOM file count in input folder /input/SCANS: 3643
  --> DICOM file count in output folder /output/USChina/subjects/NDAR_INVR87KXM5R/inbox: 415
  --> DICOM mapping check: fail

Error. Something went wrong.

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2

Hi Clara, we’ve informed the developers about this issue. We will let you know once it is resolved.

3

Please use the latest public release is now out officially to check if this issue is resolved. You can download it here:

https://qunex.yale.edu/qunex-registration/

Go ahead and register for the latest stable version and check if the issue above is now resolved. If not, please send us the logs and we will investigate.