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XW2021 Talks: XNAT – Past, Present, and Future

Time: Day 1, 9:05

Presenter: Daniel Marcus, director of the Computational Imaging Laboratories at Washington University in St Louis, as well as the director of the XNAT Development Team

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.

Do you plan to support genomics data and synthetic data in XNAT for ML pipeline development?(Answered live in the session)
Is the DICOM Q/R native to XNAT ? I don't recall seeing this feature within XNAT. How do you enable this feature ?(Answered live in the session)
Is there a way to anonymize ecat files from XNAT?
what about de-facing capability?
  • I know Human Connectome currently runs de-facing in a pipeline.  Mike Hodge would be the best contact for more details.
  • Misha Milchenko in our lab has developed a face-masking algorithm that is available as a pipeline or container. 

    Misha is presenting tomorrow during the poster session, I'd recommend finding him there and asking for details.

Does XNAT integrate with Aria?(Answered live in the session)
I see support for all files format, DICOM, NIFTI, TIFF, etc. What about bruker?(Answered live in the session)
Are you able to load outside segmentation from DICOM-RT (Radiation Oncology) into XNAT for review ?(Answered live in the session)
Could you please give some comments on how XNAT supports studies in clinical trails vs studies in academic resaerch?(Answered live in the session)
Can you annotate landmark points as well as regions using ohif viewer?
  • That's definitely planned
Can we use Clara 4.0/MONAI with XNAT?
  • We are working to integrate these two soon, there was a conversion from tensorflow to pyrtoch for CLARA so some changes will be required to our current integration of CLARA v3.0. And we are working with MONAI‚Äôs team to hopefully add some integration soon.
Does the container service work with singularity images?
  • Container service works with Slurm or Docker server. Singularity is typical executed with Slurm.
Any plans to better support BIDs? It would be great if it was easy to download an entire project in BIDs format.
  • We have talked about supporting BIDS and NIFTI data importers, as well as downloading in BIDS format. We have plans for better support for data publishing on the roadmap and this could be a part of that.
Is the XNAT Rapid Reader part of XNAT web, web plugin, or standalone client ?
  • The Rapid Reader was originally developed as a stand-alone client, using the same Electron platform as the XNAT Desktop Client. However, a plugin version also exists. Support for worklists is built into the plugin as well. 

    There will be a poster on the Rapid Reader presented tomorrow.

Will the classical pipeline engine be continued to be supported? We have a number of projects which found pipeline engine to be excellent.
  • It will no longer be maintained. But it will still be available and I don't see why you couldn't continue using it.  But ongoing development will focus on container service. I think there will be good reason to consider migrating
Are there sessions that will cover Jupyter notebook integration today or tomorrow?
  • Tomorrow we will have a session on "XNAT Integrations With Other Applications". Jupyter notebooks will be a part of that.
Regarding the Python SDK, is it PyXNAT or is there a plugin that directly integrates with the XNAT server without the REST API?
  • Answered live
  • There are two external Python libraries for developing XNAT clients, pyxnat and xnatpy. XNAT supports Python internally through the automation service, but is limited to now deprecated Python 2.7.
One key problem in preclinical work is simultaneous multiple mouse imaging in PET for example - is there a (planned) mechanism for streamlining managing data where one image represents multiple subjects?
  • Yes. We have a preliminary version of this "session splitter" already coded, and are working to improve the UI and workflow. Andy Lassiter will be presenting a poster on this tomorrow.
Is there a slack we can join to seek you out?
  • We don't have a public Slack yet, but we have set up collaborative Slack channels with other institutions that we work closely with and find it very useful. Feel free to reach out via email and we can set something up!
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