# ROI markup is not filled with color in coronal view in Slicer 5.6.0

**URL:** <https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341>\
**Category:** Support\
**Created:** [December 11, 2023, 3:52pm UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341 "2023-12-11T15:52:10Z")\
**Posts on this page:** 12\
**Page:** 1

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**Author:** ![Maya\_Kiperwas\_Gal](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/maya_kiperwas_gal/32/68661_2.png) [@Maya\_Kiperwas\_Gal](https://discourse.slicer.org/u/Maya_Kiperwas_Gal)\
**Post date:** [December 11, 2023, 3:52pm UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341/1 "2023-12-11T15:52:10Z")

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Problem report for Slicer 5.6.0 win-amd64: ROI markup is not filled with color in coronal view

5.6.0 (revision 32390 / 0a13b9c) win-amd64 - installed release  
Windows / Professional / (Build 19045, Code Page 65001) - 64-bit

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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 11, 2023, 4:28pm UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341/2 "2023-12-11T16:28:58Z")

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Thanks for the report. That is odd.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/a/0ad6018b830648be25aca2217556311538f7d269.jpeg)

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**Author:** ![shai-ikko](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/shai-ikko/32/15765_2.png) [@shai-ikko](https://discourse.slicer.org/u/shai-ikko)\
**Post date:** [September 12, 2024, 8:00am UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341/3 "2024-09-12T08:00:24Z")

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I’m seeing the same thing here, Linux (Ubuntu 20.04), on both 5.6.2 and 5.4.0. I’ve only recently started to play with ROIs.

I was under the impression that it didn’t start this way, so I tried moving aside `.config/slicer.org/Slicer.ini` and removing `.slicerrc.py` (just to be on the safe side, as it was only comments anyway), but it didn’t change anything.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/d/cd0af014c751cd45ab3cc4d42188adaad7e1ba02.jpeg)

I’ve also tried to see if this was related to the slice view being Green or the fact that it’s coronal – by switching the viewers’ slice orientations – and it is, indeed, the coronal.

(I’m wondering if this could somehow be related to locale or timezone, @Maya_Kiperwas_Gal seems to be in Israel like me; starting the app with `LANG=en_US LANGUAGE=en_US LC_ALL=en_US TZ=UTC` didn’t change anything either)

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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:** [September 12, 2024, 1:47pm UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341/4 "2024-09-12T13:47:38Z")

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It’s not timezone related since it happens to me too in the US. It seems to just be a bug that someone will need to investigate.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [September 12, 2024, 2:45pm UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341/5 "2024-09-12T14:45:54Z")

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Please test with the latest Slicer Preview Release, too.

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**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:** [September 12, 2024, 3:01pm UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341/6 "2024-09-12T15:01:34Z")

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Latest Slicer preview (as of [d803d34](https://github.com/Slicer/Slicer/commit/d803d347e0dbd0ea825ddd4afa551deb7676e9d5)):

```python
slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
roi_node = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsROINode")
roi_node.SetSize([100, 100, 100])

```

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/5/f59bb51faed4f624e5df7a0ac6259ee545cc246e.png)

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**Author:** ![shai-ikko](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/shai-ikko/32/15765_2.png) [@shai-ikko](https://discourse.slicer.org/u/shai-ikko)\
**Post date:** [September 18, 2024, 2:58pm UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341/7 "2024-09-18T14:58:17Z")

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Right, I somehow misread the December messages. Sorry.

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**Author:** ![shai-ikko](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/shai-ikko/32/15765_2.png) [@shai-ikko](https://discourse.slicer.org/u/shai-ikko)\
**Post date:** [September 18, 2024, 3:08pm UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341/8 "2024-09-18T15:08:28Z")

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I don’t see this reported as an issue on Github – will reporting it there help, or is it just noise?

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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:** [September 18, 2024, 4:07pm UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341/9 "2024-09-18T16:07:05Z")

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I think and issue on github makes sense. I just tested and it’s still an issue on my local build.

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**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:** [September 18, 2024, 4:38pm UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341/10 "2024-09-18T16:38:39Z")

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I’ve added this to the Slicer issue tracker:

> <https://github.com/Slicer/Slicer/issues/7944>
>
> \## Summary
> 
> As originally reported at https://discourse.slicer.org/t/roi-marku…p-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341:
> 
> A Markups ROI object with a visible 2D fill opacity shows that there an issue with the display of that fill when the slice orientation is "Coronal". 
> 
> \## Steps to reproduce
> \`\`\`python
> slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
> roi\_node = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsROINode")
> roi\_node.SetSize(\[100, 100, 100\])
> \`\`\`
> !\[image\](https://github.com/user-attachments/assets/a73761e2-9e34-4eef-a4e6-168fc309b9d1)
> 
> 
> \## Environment
> \- Slicer version: Slicer-5.7.0-2024-09-17 (as of https://github.com/Slicer/Slicer/commit/114731d5f71167f1a2da81ed2494c8201d6a1654)
> \- Operating system: Windows, an issue on Linux and likely on macOS as well

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**Author:** ![mikebind](https://avatars.discourse-cdn.com/v4/letter/m/71e660/32.png) [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Post date:** [September 18, 2024, 4:47pm UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341/11 "2024-09-18T16:47:10Z")

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I did a little checking, and if you rotate the ROI, it appears that 2 of the 6 faces of the ROI show as unfilled. The appearance of unfilled ROI shapes is not limited to the coronal/green slice, and rotates with the ROI, and can therefore show up in any of the slice views. Just FYI for anyone who might start taking a look at debugging this.

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**Author:** ![shai-ikko](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/shai-ikko/32/15765_2.png) [@shai-ikko](https://discourse.slicer.org/u/shai-ikko)\
**Post date:** [November 4, 2024, 9:20am UTC](https://discourse.slicer.org/t/roi-markup-is-not-filled-with-color-in-coronal-view-in-slicer-5-6-0/33341/12 "2024-11-04T09:20:05Z")

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This has been fixed; the fix is already included in the latest preview release.

Thanks a lot to everyone involved!