Example post: PyRadiomics (2017 Winter)

(Isaiah Norton) #1

(Based on http://wiki.na-mic.org/wiki/2017_Winter_Project_Week/PyRadiomics)

Objective: Introduce PyRadiomics to the community

Investigators:

  • Joost van Griethuysen
  • Hugo Aerts, Steve Pieper (@pieper)
  • Jean-Christophe Fillion-Robin (@jcfr)
  • Andrey Fedorov (@fedorov)

Approach:

  • Present, meet collaborators…
  • Discuss issues related to integration with Slicer: external packages, numpy version, Slicer module UI
  • Discuss issues related to enhancing performance using C code

Screenshots:

The radiomics concept of going from segmented images to heatmaps of features that can be correlated with other data such as genomics, demographics, or outcomes.

PyRadiomics allows processing of image data and an extensible set of image feature calculators.

The SlicerRadiomics extension makes it easy to test and apply PyRadiomics to medical imaging data.


Progress:

  • Introduced PyRadiomics to the community
  • There are still some issues with the packaging of the extension, SlicerRadiomics. Numpy issue is resolved, PyRadiomics works with numpy 1.9.2, adjusted minimum requirements. Once these issues are resolved, it will be made publicly available in the Github Radiomics Organisation.
  • C code performance enhancement is written, but is still causing some issues during compilation. Switch setup to use skbuild and cmake. Latest (offline) tests work with setup.py develop and setup.py test.
  • Issues related to building SlicerRadiomics have been fixed, extension can now be built and used in the built version in the basic form
  • Issues related to packaging SlicerRadiomics have been identified (limitations of Slicer infrastructure packaging external python packages); JC identified the solution approach, and the issue will be resolved soon, we expect the extension to be available publicly within a month

References:

GitHub Repository
Documentation

Project page:

https://Github.com/Radiomics/SlicerRadiomics

2017 Summer Project Week Projects
(Jean Christophe Fillion Robin) #2

Not sure what is best to list screenshot. Here is an approach:

What do you think @ihnorton ? We could also enable table html tag …

Option 1

Screenshots



Option 2

While visible right away … there are two smalls and its hard to get the correct ratio

Option 3

Look like this plugin would be useful https://discourse.pro/t/topic/34

(Steve Pieper) #3

Looks nice but it didn’t seem to work for me.

(Isaiah Norton) #4

@jcfr @pieper yeah, not sure what to do here. Detail expand works OK, but not ideal. I have no objection to allowing

We can’t install plugins in the hosted instance.

(Jean Christophe Fillion Robin) #5

Option 2 works great in fact. After few seconds after editing the page, it is possible to show the large size version and also use the right left arrow to see the images.

  • preview “widget”

  • previous / next

3 Likes
(Jean Christophe Fillion Robin) archived #6