# Problem with segment editor paint

**URL:** <https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [June 7, 2018, 12:00pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109 "2018-06-07T12:00:58Z")\
**Posts on this page:** 17\
**Page:** 1

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**Author:** ![Ash\_Alarfaj](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ash_alarfaj/32/3327_2.png) [@Ash\_Alarfaj](https://discourse.slicer.org/u/Ash_Alarfaj)\
**Post date:** [June 7, 2018, 12:00pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/1 "2018-06-07T12:00:58Z")

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Operating system:Windows

 ![paint%20problem%20disable](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/a/6a506de6ab74bfd650d5104a7e54f2a6e8d67c03.jpeg)  
Slicer version:4.9  
Expected behavior: apply paint  
Actual behavior: doesn’t work!

Hi could please help me, I start segmentation by applying the threshold, then correct it by paint and eras, but now, paint doesn’t work with me, in the middle of my segmentation I went to volume rendering and I can’t undo the volume rendering so does it affect the paint?

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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:** [June 7, 2018, 1:04pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/2 "2018-06-07T13:04:30Z")

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Volume rendering should not affect Segment editor.

Do you see any errors or warnings in the logs? (red icon in the lower-right corner)

Make sure you disabled all special options:

- Color smudge: off
- Editable area: Everywhere
- Editable intensity range: off
- Overwrite other segments: All segments

If you still have problems, try these:

- Save the scene, restart Slicer, and load the scene and see if you can paint.
- If still does not work, restart Slicer and load just the saved segmentation and volume and see if you can paint.
- Install the latest nightly build and try the two steps above.

Let us know which solution worked.

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**Author:** ![szhang](https://avatars.discourse-cdn.com/v4/letter/s/bc8723/32.png) [@szhang](https://discourse.slicer.org/u/szhang)\
**Post date:** [February 18, 2021, 7:19pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/3 "2021-02-18T19:19:04Z")

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Unfortunately it happens in the stable version 4.11.20200930 as well… In the middle of segment editing, the brush just cannot paint anymore…  
I tried to follow your instructions and restarted, but still cannot make the paint to brush in the segment editor. It didn’t work in nightly build of 20200818 either.  
Here are two “Warning” messages in “Log messages”  
QLayout::addChildLayout: layout “” already has a parent  
ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 100 1

Greatly appreciate your help!

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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:** [February 18, 2021, 7:21pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/4 "2021-02-18T19:21:40Z")

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Can you share the scene that demonstrates this issue (upload it somewhere and post the link here)?

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**Author:** ![szhang](https://avatars.discourse-cdn.com/v4/letter/s/bc8723/32.png) [@szhang](https://discourse.slicer.org/u/szhang)\
**Post date:** [February 18, 2021, 7:28pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/5 "2021-02-18T19:28:46Z")

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> **[2021-02-05-Scene.mrml](https://www.dropbox.com/s/k7tqphvvou0jvgm/2021-02-05-Scene.mrml?dl=0)**
>
> Shared with Dropbox

Would this work?

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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:** [February 18, 2021, 7:31pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/6 "2021-02-18T19:31:33Z")

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Please save the scene as a bundle (.mrb) so that the actual data files are included as well.

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**Author:** ![szhang](https://avatars.discourse-cdn.com/v4/letter/s/bc8723/32.png) [@szhang](https://discourse.slicer.org/u/szhang)\
**Post date:** [February 18, 2021, 8:29pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/7 "2021-02-18T20:29:07Z")

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> **[2021-02-05-Scene.mrb](https://www.dropbox.com/s/1qs0d0powtk7grg/2021-02-05-Scene.mrb?dl=0)**
>
> Shared with Dropbox

I see, please take a look at this one. Thank you.

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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:** [February 18, 2021, 9:31pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/8 "2021-02-18T21:31:34Z")

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All I had to do to display segmentations was to go to Data module and click on the eye icon of the segmentation node.

However, I’ve noticed that the segmentation was shifted down by about 10cm. I’m not sure how this offset could have occurred (maybe there was a transform applied on the master volume earlier?), but I removed it by editing the segmentation header file so that its geometry matches exactly the CT’s geometry. You can download the updated scene from [here](https://1drv.ms/u/s!Arm_AFxB9yqHxYcA91v9yZbA1681Kg?e=r4Yog1).

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**Author:** ![szhang](https://avatars.discourse-cdn.com/v4/letter/s/bc8723/32.png) [@szhang](https://discourse.slicer.org/u/szhang)\
**Post date:** [February 18, 2021, 10:28pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/9 "2021-02-18T22:28:47Z")

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Thank you, @lassoan !  
Now I noticed the shift, but when I was editing previous two segments they both looked fine on the master volume, until the 3rd one that I could not paint anymore…  
I experienced “paint brush stop working” before as well, and it seems other people had similar issue…  
Perhaps it was due to transformation drop-off while using segment editor?

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<div class="post-metadata">

**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:** [February 18, 2021, 11:49pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/10 "2021-02-18T23:49:58Z")

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It is hard to tell now what caused the shift. I think we fixed all the reported errors but if you can reproduce either shifting or paint strokes not appearing with latest stable or preview release then let us know.

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**Author:** ![Fullcalf42](https://avatars.discourse-cdn.com/v4/letter/f/b2d939/32.png) [@Fullcalf42](https://discourse.slicer.org/u/Fullcalf42)\
**Post date:** [May 26, 2023, 6:46pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/11 "2023-05-26T18:46:25Z")

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Was this resolved for you?

I am having the same issue yesterday and today. When I try to apply paint in a segment it doesn’t leave a mark. I saved my scene as .mrb but cannot upload it here.

[https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/2/e231c1b039874c31695ba70c0820f1edae61a17d.mp4](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/2/e231c1b039874c31695ba70c0820f1edae61a17d.mp4)

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<div class="post-metadata">

**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:** [May 28, 2023, 12:30am UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/12 "2023-05-28T00:30:45Z")

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It’s great if you can provide a scene that reproduces the unexpected behavior. You can upload the mrb file anywhere (dropbox, onedrive, google drive, etc.) and post the link here.

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**Author:** ![Ash\_Alarfaj](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ash_alarfaj/32/3327_2.png) [@Ash\_Alarfaj](https://discourse.slicer.org/u/Ash_Alarfaj)\
**Post date:** [May 28, 2023, 8:38am UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/13 "2023-05-28T08:38:13Z")

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Hello  
I did not have any issues currently, I did not asked any questions from long time.  
Thanks

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**Author:** ![Marcin\_Wczysla](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/marcin_wczysla/32/70219_2.png) [@Marcin\_Wczysla](https://discourse.slicer.org/u/Marcin_Wczysla)\
**Post date:** [April 26, 2024, 9:00pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/14 "2024-04-26T21:00:08Z")

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Hello, I am very new to 3D slicer, I began learning with the tools paint and thresholding, everything worked fine and then it stopped. When I try to paint it does not remain a trace, the boxes editable areas: everywhere, editable intensity range: not ticked, modify other segments: overwrite all,

same happens with thresholding… please help how I can solve this

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [April 27, 2024, 12:18am UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/15 "2024-04-27T00:18:54Z")

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Please start from scratch and try again. Chances are either you have change editable area settings and masking, or trying to segment something different than the master volume you have.

I encourage you to look this tutorial in detail if you are new to Slicer: [Tutorials/Segmentation at main · SlicerMorph/Tutorials · GitHub](https://github.com/SlicerMorph/Tutorials/tree/main/Segmentation)

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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:** [April 28, 2024, 12:03pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/16 "2024-04-28T12:03:52Z")

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It would be useful to know why the Segment Editor does not work as expected. Do you see any errors or warnings in the application log? Do you have multiple segmentations in the scene, are you editing the correct one? If you could join or weekly meeting on Tuesday and show it on your computer then we can guide you in how to make it work.

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**Author:** ![MedPhys2004](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/medphys2004/32/68746_2.png) [@MedPhys2004](https://discourse.slicer.org/u/MedPhys2004)\
**Post date:** [July 5, 2024, 5:02pm UTC](https://discourse.slicer.org/t/problem-with-segment-editor-paint/3109/17 "2024-07-05T17:02:43Z")

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This helped me, thank you!