XW2021 Town Hall: XNAT Integrations with Other Applications

Time: Day 2, 10:00 – 10:30 am CDT

Host: Dan Marcus, Washington University in St Louis

Panelists: Tim Olsen (Radiologics / Flywheel)

Other Participants: Marc Modat (Kings College London), Chris Battiston (Women's College Hospital), Ajay Kurani (Northwestern), and Daniel Beasley (University College London)

Questions and Answers

When possible and as time permitted, questions that were brought up in the Q&A module during each talk were addressed in real time by the presenter. Other responses were entered in the Q&A interface itself. Those written responses are included below.

Will there be a GUI at some point for defining the BIDS mapping? Right now I have to tell users "Well you gotta run this weird curl command," and they don't even know what curl is.
  • From Kate: "I agree! Radiologics is interested in adding this. Would you want to upload a mapping file each time you launch the BIDS conversion? Upload it at project level and then select it when you launch? Something else?"
    • I wouldn't want to upload a mapping file at all - I'd want the user to be able to fill out e.g. a two-column table mapping series names to BIDS names.
      • Ok, great feedback! They could set a default at the project level to avoid having to retype
Is there an ongoing effort to integrate XNAT with OpenHIM (open health information mediator) from the OpenHIE developer community?
  • No ongoing efforts but interested to hear more Samson.
After the import with SlicerDicer, how is the non-imaging data organised in XNAT?(Answered live in session)
Will the jupyter notebooks be launched via container, and if so how will the notebooks be stored persistently? i.e. docker volumes, XNAT resources, etc?
  • Yes, launched by container. As for persistence‚ I'm not sure.  Perhaps Rick can jump in with details on that.
I'm the REDCap Admin at my hospital and would love integration for data (esp Demographics).  I'm also interested in any work people are doing in R to pull metadata / data from XNAT for real-time analysis purposes.(Answered live in session)
You mentioned Slicer Dicer, I'd like to speak about that for a moment
  • From the chat: "Hey Dan, I'd just like to mention that we've discovered some issues with Slicer Dicer and find that our users prefer to use TriNetX for cohort building - there are some issues with access levels in Slicer Dicer that TriNetX doesn't suffer from. I think the ability to integrate cohort building into XNAT (and being able to retrieve the relevant images) would be a huge step for research. Great workshop btw"
Is there a way to strip the metadata on the outbound to the HPC environment so that you have all complete data needed in XNAT but phi is stripped when going to the compute resource?(Answered live in session)
Have there been any integrations with Redcap?

(Answered live in session)

  • From Dan Beasley: "Hi Chris Batt, I have a thing to convert redcap dictionaries to XNAT plugins"