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XNAT2012 - Image Session Validation



At the end of this session, attendees should be able to:

  • Create a schematron rule file
  • Launch image session validation



  • Working knowledge of XML and XPATH

Tasks during the talk:

Step 1: Adding a pipeline to a site

We would add the pipeline /opt/xnat/pipeline_1_6/catalog/validation_tools/Validate.xml to the site

  • Login to XNAT as Admin.
  • Navigate to Administer -> Pipelines
  • Click on Add Pipeline to Repository
  • Input:
    • Enter Path to Pipeline descriptor xml:   /opt/xnat/pipeline_1_6/catalog/validation_tools/Validate.xml
    • Enter Name of the custom webpage to launch this pipeline: PipelineScreen_protocolcheck.vm
    • Click on Add
    • You will get a message "... was added successfullyā€¯
    • If you did everything correct, you will see ProtocolCheck listed in the pipeline repository.

 Step 2: Upload the schematron file as a resource to project BOGUS_OUA


  • cd /opt/xnat/workshop2012/d2s1-validation
  • /opt/xnat/pipeline_1_6/xnat-tools/XNATRestClient -host http://localhost:8080/xnat -u admin -p admin -m PUT -remote "/data/archive/projects/BOGUS_OUA/resources/validation_xnat_mrSessionData"
  • /opt/xnat/pipeline_1_6/xnat-tools/XNATRestClient -host http://localhost:8080/xnat -u admin -p admin -m PUT -remote "/data/archive/projects/BOGUS_OUA/resources/validation_xnat_mrSessionData/files?content=v1.0" -local /opt/xnat/workshop2012/d2s1-validation/mrsession_rules.sch
  • ALTERNATIVELY: curl  -i -u admin:admin -X PUT -T mrsession_rules.sch http://localhost:8080/xnat/data/archive/projects/BOGUS_OUA/resources/validation_xnat_mrSessionData/files?content=v1.0&inbody=true

 Step 3: Setting up the pipeline for the project BOGUS_OUA

            Navigate to BOGUS_OUA project as project owner

    • Click on Pipelines tab.
    • Click on Add More Pipelines
    • Click on Add (for Validate.xml pipeline)
    • Select Is this pipeline to be launched automatically while archiving?
    • Set the value of Experiment Type to xnat:mrSessionData
    • Set the value of Content attribute set within the validation catalog to v1.0
    • Click on Submit

     Step 4: Setup the datatype

    • As Admin, click on Administer -> Data types
    • Select xnat:mrSessionData
    • Under Available Report Actions, enter
      • Name:  PipelineScreen_launch_pipeline,
      • Display Name: Build,
      • Popup: always,
      • Secure Access: edit
      • (leave other columns empty)

     Step 5: Launching the pipeline (via Action -> Build)

    • Navigate to project BOGUS_OUA
    • Select an MRSession
    • Click on Action -> Build
    • Select ProtocolCheck
    • Click on Submit

     Step 6: Launching the pipeline automatically

    • Upload a MR Session
    • Archive the session
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