XW2021 Town Hall: Image Viewing and Annotation

Time: Day 2, 9:00 – 9:30 am CDT

Host: Simon Doran, Institute for Cancer Research, London

Panelists: James D'Arcy (ICR UK), Mo Alsad (Imperial College London), Lorena Escudero (University of Cambridge) and special guest Kate Alpert (Radiologics)

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.

Would you please elaborate further on OHIF viewer integration with machine learning ?(Answered live in session)

Can the viewer display RTDOSE data?

Would it be possible to contribute to the work to make these RTDOSE data compatible with the OHIF viewer? We have many datasets for testing.

  • No, but we are looking into that.
  • Also addressed in session
  • From Eve: "Aditya Apte is our guru for all things RT, if you can please invite him too for RTDOSE discussion."
For the microscopy data, do you already know what file format might be supported?(Answered live in session)

Can the OHIF plugin be used to display nifti files? or does it just display dicom images?

Is NIFTI integration coming to the OHIF viewer?

What sort of technical problems exist with the visualization of NIFTI-formatted images?

  • Only DICOM data so far.
  • Also addressed in session
Any chance for a progress bar of sorts when loading datasets? Hitting the spinning circle drives my radiologists up the wall.
  • It is on our ToDo list, expected to be implemented soon.
You mentioned copying ROI across dataset - what is the motivation? Shouldn't that be in a container instead of in the viewer?
  • We will try to answer this question after the webinar or please seek out Simon or anyone from the OHIF team for more discussion!
One of the goals of the overall system is to minimize downloading data by allowing users to view directly on the system.  Freesufer is a common research pipeline so would surface viewing be something considered.  For instance a brainbrowser plugin or something along those lines for the OHIF viewer to see surface data (cortical or subcortical shape data).  Datatypes could be .mgh/.mgz or .gii or cifti as examples
  • Thank you for the question. We will try and get an answer to it after the webinar.
Hi All, I always get asked about dose cubes, are there any plans? Also, I cannot view ROIs in shared sessions unless I am a member of the original project. I have a json blob datatype somewhere
  • Hi Dan, the ROIs need to be shared along the session to be able to access them in the viewer.
    • Hi Mo, I know, but they are not visible unless you are also a member of the original project.
      • I am not sure about ypur project setup. Could we discuss the issue offline?
Will the microscopy viewing be compatible with tiled mosaic microscopy images? DICOM formats only? In my limited experience, our microscopy group seems to prefer using .tiff, and trying to convert to DICOM seemed quite tricky, re: creating the correct DICOM headers, mosaic tile metadata, etc
  • Hi there - in the interest of time, we will try and answer this question after the webinar
My question is regarding how ROIs are saved in OHIF Viewer. I don't have version 1.8, only 1.7 but if I'm correct ROIs are saved as .xml? Why are they not saved as DICOM? I believe 3D slider reads RSTRUCT from Enhanced DICOM files?
  • Hi Joao! ROIs drawn in the OHIF viewer are saved as RTSTRUCT or DICOMSEG (depending if you are using Contour or Mask tools to draw) in addition to AIM.
  • my "in addition to AIM" above applies only to Contours ;)
Will microscopy handle pyramidal/multi resolution file viewing/zooming?
  • Hi Dom, yes it will.
Is there any guidance on converting nifti, nrrd, analyze, etc. segmentations into the dicom format compatible with ROI in OHIF? I believe it’s multiframe? Perhaps when given the original dicom series as an input?
  • The option that seems to be the most widespread and reliable across manufacturers and modalities is dcm2niix (https://github.com/rordenlab/dcm2niix). That tends to handle the coorddnate system issues that James mentioned the best.
  • DICOM segmentations are essentially multiframe images, yes. Having the DICOM images that the segmentation refers to would be very useful when converting NIFTI to DICOM SEG.
Does OHIF handle multiframe dicom well? Could that reduce the number of individual requests per image?
  • Yes, it handles multiframe images. For the current setup, yes multiframe.enhanced DICOM format can reduce the requests.
Is it possible to save Mask-based ROIs as an AIM XML with coordinate measurements instead of a Dicom Seg?
  • No, exporting masks is only available in DICOM SEG.
Could we have a return or close button to return to the XNAT main interface? :D
  • Coming in the next release - v3.1.0