# Example post: PyRadiomics (2017 Winter)

**URL:** <https://discourse.slicer.org/t/example-post-pyradiomics-2017-winter/434>\
**Category:** Project Week\
**Created:** [June 2, 2017, 7:58pm UTC](https://discourse.slicer.org/t/example-post-pyradiomics-2017-winter/434 "2017-06-02T19:58:58Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![ihnorton](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ihnorton/32/9_2.png) [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Post date:** [June 2, 2017, 7:58pm UTC](https://discourse.slicer.org/t/example-post-pyradiomics-2017-winter/434/1 "2017-06-02T19:58:58Z")

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_(Based on [2017 Winter Project Week/PyRadiomics - NAMIC Wiki](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** :

 ![](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/1X/5133e1b312d4c2f243efe27b7887f183fb6e8fa9.jpg)

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.

 ![](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/1X/30cfea399c66d1fc1bfea5a7bfa878f0c73ca7df.jpg)  
PyRadiomics allows processing of image data and an extensible set of image feature calculators.  
 ![](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/1X/8d3c540481799f4bf120ecdb12af81af31ce9816.png)  
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](https://github.com/Radiomics/pyradiomics)  
[Documentation](http://pyradiomics.readthedocs.io/)

**Project page** :

> **[GitHub - AIM-Harvard/SlicerRadiomics: A Slicer extension to provide a GUI...](https://github.com/AIM-Harvard/SlicerRadiomics)**
>
> A Slicer extension to provide a GUI around pyradiomics - GitHub - AIM-Harvard/SlicerRadiomics: A Slicer extension to provide a GUI around pyradiomics

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**Author:** ![jcfr](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jcfr/32/17825_2.png) [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Post date:** [June 2, 2017, 8:46pm UTC](https://discourse.slicer.org/t/example-post-pyradiomics-2017-winter/434/2 "2017-06-02T20:46:56Z")

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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**
>
> ![](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/1/5133e1b312d4c2f243efe27b7887f183fb6e8fa9.jpeg)  
> ![](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/0/30cfea399c66d1fc1bfea5a7bfa878f0c73ca7df.jpeg)  
> ![](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/d/8d3c540481799f4bf120ecdb12af81af31ce9816.png)

### Option 2

 ![](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/1X/5133e1b312d4c2f243efe27b7887f183fb6e8fa9.jpg) ![](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/1X/30cfea399c66d1fc1bfea5a7bfa878f0c73ca7df.jpg) ![](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/1X/8d3c540481799f4bf120ecdb12af81af31ce9816.png)

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 [«Gallery» plugin (version 3.1, 2016-12-11) - Discourse Plugins](https://discourse.pro/t/topic/34)

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [June 2, 2017, 9:05pm UTC](https://discourse.slicer.org/t/example-post-pyradiomics-2017-winter/434/3 "2017-06-02T21:05:52Z")

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> [@jcfr](#):
>
> Option 3
> 
> Look like this plugin would be useful [«Gallery» plugin (version 3.1, 2016-12-11) - Discourse Plugins](https://discourse.pro/t/topic/34)

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

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**Author:** ![ihnorton](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ihnorton/32/9_2.png) [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Post date:** [June 2, 2017, 9:09pm UTC](https://discourse.slicer.org/t/example-post-pyradiomics-2017-winter/434/4 "2017-06-02T21:09:58Z")

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

> [@jcfr](#):
>
> Look like this plugin would be useful

We can’t install plugins in the hosted instance.

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**Author:** ![jcfr](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jcfr/32/17825_2.png) [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Post date:** [June 2, 2017, 9:27pm UTC](https://discourse.slicer.org/t/example-post-pyradiomics-2017-winter/434/5 "2017-06-02T21:27:06Z")

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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”

 ![](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/1X/86ad7b2e7ece9c2d0ed972e16ff802ae4d39a82d.png)

- previous / next

 ![](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/1X/e0bebedf507b80a614a4ac5f5d9fc9645b88db61.jpg)

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**Author:** ![jcfr](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jcfr/32/17825_2.png) [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Post date:** [June 7, 2017, 3:36pm UTC](https://discourse.slicer.org/t/example-post-pyradiomics-2017-winter/434/6 "2017-06-07T15:36:28Z")

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