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Data sharing case study: OPDC

How to use Docker containers in XNAT

The OPDC project used the DPUK XNAT Node so that it could share imaging date the DPUK data portal.

XNAT Upload instructions using .csv file

To upload (Assuming you have already an xnat-project).

  1. Organise the DICOMs you want to upload into a structure like: mymaindirectory/
    • DICOMdir1
    • DICOMdir2
    • DICOMdirN

Where DICOMdir contains the DICOM data for a specific session for a certain subject (subject_ID)

  1. Create a .csv file (e.g. myproject.csv) with 3 columns:

|subject_ID | DICOMdir | scan_date | |————-|————|—————|

  • subject_ID is uniquely associated with the participant
  • directory is the name of the directory containing the DICOM files to upload. If more sessions of a certain subject exist, they have the code of the session (e.g. Calpendo ID)
  1. Run the csvupload.sh script:

E.g. usage ./csvupload.sh myproject.csv <xnat-username> <xnat-project_id> mymaindirectory > output_log.txt

This script calls uploaddcmtk.sh so make sure you have both.