# Radiomics module not working?

**URL:** <https://discourse.slicer.org/t/radiomics-module-not-working/33382>\
**Category:** Support\
**Created:** [December 13, 2023, 4:17pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382 "2023-12-13T16:17:59Z")\
**Posts on this page:** 16\
**Page:** 1

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**Author:** ![ogdenk](https://avatars.discourse-cdn.com/v4/letter/o/bbe5ce/32.png) [@ogdenk](https://discourse.slicer.org/u/ogdenk)\
**Post date:** [December 13, 2023, 4:18pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/1 "2023-12-13T16:18:00Z")

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I have been using the Radiomics module for several years now and it has worked properly. The latest version for which it still works for me is 5.4.0. In newer versions it does not work, the output is blank. I have not changed my computer platform so it is not a hardware issue. Is this a known issue, or is there something else locally I might need to address? Any help is appreciated!

Kent

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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:** [December 13, 2023, 5:28pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/2 "2023-12-13T17:28:58Z")

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Yes, it’s not currently working on all platforms (mac is broken, others might work on the new 5.6.1). Using the older release is probably the best workaround for the time being.

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**Author:** ![ogdenk](https://avatars.discourse-cdn.com/v4/letter/o/bbe5ce/32.png) [@ogdenk](https://discourse.slicer.org/u/ogdenk)\
**Post date:** [December 13, 2023, 5:37pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/3 "2023-12-13T17:37:57Z")

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Ok, thank you for the information! As long as it is not my computer . . .

Kent

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**Author:** ![Numan\_Kutaiba](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/numan_kutaiba/32/13906_2.png) [@Numan\_Kutaiba](https://discourse.slicer.org/u/Numan_Kutaiba)\
**Post date:** [January 3, 2024, 8:00pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/4 "2024-01-03T20:00:50Z")

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It’s a problem because I can’t use Total Segmentator unless I use the newer version. So right now I don’t have a version with both radiomics and Total Segmentator both working at the same time!

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**Author:** ![ogdenk](https://avatars.discourse-cdn.com/v4/letter/o/bbe5ce/32.png) [@ogdenk](https://discourse.slicer.org/u/ogdenk)\
**Post date:** [January 3, 2024, 8:04pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/5 "2024-01-03T20:04:19Z")

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I agree, I have two versions of Slicer installed because of this issue. My original comment meant that I don’t have a computer issue, it’s a software issue.

Kent

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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:** [January 3, 2024, 9:41pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/6 "2024-01-03T21:41:21Z")

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There’s a fix for windows and linux that needs to be reviewed (I don’t have access to that repo to merge it but maybe @fedorov does?).

In the meantime, it would be great if people could be testing the fix. It should just be a matter of replacing the lines of code or the whole file:

> <https://github.com/AIM-Harvard/pyradiomics/pull/857>
>
> I recently found the SlicerRadiomics extension does not work in 3D Slicer and be…low is the issue that I decribed in.
> https://github.com/AIM-Harvard/SlicerRadiomics/issues/80
> 
> I tried to modify the code with the help of @pieper :
> 1. Add the code below to the top of the file:
> \`from ruamel.yaml import YAML\`
> 2. Add the code below before line 353:
> \`yaml = YAML(typ='safe', pure=True) \`
> 3. Change what was in line 353 to:
> \`settingsSchema = yaml.load(schema)\['mapping'\]\['setting'\]\['mapping'\]\`

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**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [January 3, 2024, 11:05pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/7 "2024-01-03T23:05:14Z")

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I’ve just merged it - hope this fixes it! Coincidentally, I also just today noticed the extension is missing from Slicer.

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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:** [January 3, 2024, 11:39pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/8 "2024-01-03T23:39:32Z")

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Thanks Andrey 👍

The extension built on windows and linux but there was a runtime error. On mac there’s a build error so no extension is available.

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**Author:** ![miklontzas](https://avatars.discourse-cdn.com/v4/letter/m/d26b3c/32.png) [@miklontzas](https://discourse.slicer.org/u/miklontzas)\
**Post date:** [January 14, 2024, 6:13pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/9 "2024-01-14T18:13:06Z")

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Any update for Mac users? is the extension back? if not which is the latest working version of slicer that we can use to have a working radiomics plugin?

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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:** [January 14, 2024, 6:43pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/10 "2024-01-14T18:43:11Z")

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I don’t think there’s any progress on the mac version of pyradiomics. The build system needs work. Unless someone else knows off the top of their head you’ll need to test to see when there was a working version and report back if you can.

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**Author:** ![miklontzas](https://avatars.discourse-cdn.com/v4/letter/m/d26b3c/32.png) [@miklontzas](https://discourse.slicer.org/u/miklontzas)\
**Post date:** [January 14, 2024, 7:16pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/11 "2024-01-14T19:16:34Z")

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Thanks @pieper! I tried building Slicer 5.4.0 from source but I cannot install the extension… @fedorov is there a plan for a future fix for the most recent version of slicer?

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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:** [January 14, 2024, 9:43pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/12 "2024-01-14T21:43:39Z")

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It may be hard to build older slicers, but you should still be able to get the application and install extensions for released binaries at this link: [https://slicer-packages.kitware.com/#collection/5f4474d0e1d8c75dfc70547e/folder/5f4474d0e1d8c75dfc705482](https://slicer-packages.kitware.com/#collection/5f4474d0e1d8c75dfc70547e/folder/5f4474d0e1d8c75dfc705482)

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<div class="post-metadata">

**Author:** ![miklontzas](https://avatars.discourse-cdn.com/v4/letter/m/d26b3c/32.png) [@miklontzas](https://discourse.slicer.org/u/miklontzas)\
**Post date:** [January 14, 2024, 9:56pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/13 "2024-01-14T21:56:17Z")

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Thanks @pieper! Managed to download and install version 5.0.3 from the link you gave. I also downloaded the radiomics extension for this version which seems to work perfect. will stick there until a new version of the plugin is released to work with the latest version of slicer

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<div class="post-metadata">

**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [January 15, 2024, 3:19pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/14 "2024-01-15T15:19:58Z")

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> @fedorov is there a plan for a future fix for the most recent version of slicer?

The error seems to be in pyradiomics, not in the SlicerRadiomics extension itself. I submitted an issue, but I am not sure if pyradiomics is being maintained. I suggest following up in that issue.

> <https://github.com/AIM-Harvard/pyradiomics/issues/865>
>
> pyradiomics build fails on mac as part of Slicer preview build
> 
> https://slicer….cdash.org/viewBuildError.php?buildid=3271763
> 
> !\[image\](https://github.com/AIM-Harvard/pyradiomics/assets/313942/e8798f80-dd0c-4213-9da8-06416b18667b)

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<div class="post-metadata">

**Author:** ![jamesobutler](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jamesobutler/32/7511_2.png) [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Post date:** [January 15, 2024, 3:41pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/15 "2024-01-15T15:41:32Z")

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@fedorov is there a reason for SlicerRadiomics to build pyradiomics from source?

Latest pyradiomics (3.1.0) does have a Python whl file for macOS. [pyradiomics · PyPI](https://pypi.org/project/pyradiomics/#files). This seems to indicate that it isn’t so much a problem with pyradiomics as it was possible for it to build a whl file successfully and upload to PyPI for macOS.

Therefore SlicerRadiomics could instead install from whl instead of build from source.

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<div class="post-metadata">

**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [January 15, 2024, 8:42pm UTC](https://discourse.slicer.org/t/radiomics-module-not-working/33382/16 "2024-01-15T20:42:13Z")

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That’s a great idea! I don’t remember why we are building it from source in SlicerRadiomics, but indeed I should experiment with switching to pip install. Thank you!