# Setting segment opacity to \< 1.0 hides segments

**URL:** <https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800>\
**Category:** Support\
**Created:** [April 21, 2026, 5:23pm UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800 "2026-04-21T17:23:31Z")\
**Posts on this page:** 13\
**Page:** 1

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**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [April 21, 2026, 5:23pm UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/1 "2026-04-21T17:23:31Z")

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If the opacity of a segment is reduced from the default 1.0, either for the whole segmentation or for the selected segment, the 3D representation does not persist. It appears again if set to 1.0.

This is seen in Linux builds on 2 machines (5.10, today’s preview, self-built), all of them using Qt5.

It does not seem to have been reported yet, though it is observed in 5.10 stable.

May be some users might report if it’s a systemic issue.

Thank you.

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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:** [April 21, 2026, 5:47pm UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/2 "2026-04-21T17:47:55Z")

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Can you provide an example? I’m not seeing what you describe.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/6/9693432063596c519ce2699e992be060d3488b9a.jpeg)

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**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [April 21, 2026, 6:34pm UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/3 "2026-04-21T18:34:24Z")

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> [@pieper](#):
>
> Can you provide an example?

This video in 5.10 is demonstrative.

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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:** [April 21, 2026, 7:34pm UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/4 "2026-04-21T19:34:06Z")

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I’m also unable to replicate using Slicer 5.10.0 on the Windows platform.

Therefore, this may be Linux specific? @chir.set Did this suddenly start happening or do you think it has been an issue for awhile? Do you know a version when it did work before? Just wondering if it is a graphics issue specific to your machine, or something more generally observed on the Linux platform you are using.

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**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [April 21, 2026, 8:32pm UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/5 "2026-04-21T20:32:13Z")

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I noticed that as from today. I can’t say if it existed a few days ago since I don’t tweak opacity of segments every day.

Both machines run Arch, regularly updated, and have a Ryzen GPU. AFAIU, the 3D representation of segments is not GPU rendered like Volume Rendering, the latter having no malfunction.

I’ll be attentive to this and report if it gets back to normal, magically.

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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:** [April 21, 2026, 8:49pm UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/6 "2026-04-21T20:49:21Z")

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Thanks for the video. I tried the exact same thing on a Ubuntu machine with an nvidia card and did not see the behavior (all worked as I expected). Maybe you can try on a different machine or boot a different OS, since it may be GPU or driver related.

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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 21, 2026, 11:21pm UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/7 "2026-04-21T23:21:54Z")

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5.10 is widely used and nobody has reported this so far, so most likely this is something specific to your system, such as a recent regression in a video card driver.

- Do you have the same issue with the official Kitware-build Slicer packages, too?
- Does disabling depth peeling make the problem go away?
- Does it occur if you change [`SLICER_OPENGL_PROFILE` environment variable](https://slicer.readthedocs.io/en/latest/user_guide/settings.html#runtime-environment-variables) to `no`, `core`, or `compatibility`?
- Does it occur with both wayland and x11?
- Does ParaView have the same issue?

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**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [April 22, 2026, 6:29pm UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/8 "2026-04-22T18:29:22Z")

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> [@lassoan](#):
>
> Do you have the same issue with the official Kitware-build Slicer packages, too?

Yes, with the builds from [download.slicer.org](http://download.slicer.org).

The 3D opacity is rightly applied in Ubuntu 24.04 booted as an ISO, and in a third Arch machine that has been updated about 3 weeks ago.

Else, it’s on or off with any tweak : SLICER\_OPENGL\_PROFILE, 5.10, latest preview, Wayland, X11, older kernel, disabling slicerrc.py, creating a new user… I could not test depth peeling as I don’t find it in settings.

Thanks all for your input, wait and see…

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**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [April 23, 2026, 6:18pm UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/9 "2026-04-23T18:18:43Z")

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The solution found [here](https://wiki.archlinux.org/title/OpenGL) is to use:

> export MESA\_LOADER\_DRIVER\_OVERRIDE=zink

The problem occurs similarly for `Models` and for surfaces rendered in the `ExtraMarkups` extension, i.e, for any transparent polydata surface.

The default driver for AMD GPUs is `radeonsi`, which seems to be in cause. But maybe `VTK` has some additional things to consider here.

The fallback `llvmpipe` driver works also.

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<div class="post-metadata">

**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [May 23, 2026, 4:04am UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/10 "2026-05-23T04:04:59Z")

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The fundamental fix has been applied in the [mesa](https://gitlab.freedesktop.org/mesa/mesa/-/work_items/15352) package.

To be complete, the `zink` driver (Vulkan) resolves the transparency problem, but is found bad for `Volume rendering`.

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**Author:** ![Karuruychi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/karuruychi/32/81758_2.png) [@Karuruychi](https://discourse.slicer.org/u/Karuruychi)\
**Post date:** [August 7, 2026, 7:20am UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/11 "2026-08-07T07:20:44Z")

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@chir.set Hi, after looking into your issue, I noticed an interesting similarity with a problem I’m experiencing on Linux.

When I set the segmentation opacity to anything below 1.0, the rendering also becomes incorrect. In your case, the segmentation disappears completely, while in my case it becomes fragmented/corrupted.

The symptoms are different, but both problems seem to start when the opacity goes below 1.0. Could you take a look and see if you can guess what might be happening in both cases, and whether they could be related somehow?  
Link to my issue: [Color display error on 3D Volume](https://discourse.slicer.org/t/color-display-error-on-3d-volume/46390)

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<div class="post-metadata">

**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [August 7, 2026, 10:08am UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/12 "2026-08-07T10:08:00Z")

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> [@Karuruychi](#):
>
> see if you can guess what might be happening

That’s a hard exercise 😄

Look for any messages in the application log and in the python console. Start from the command line and see if there are unusual output. Try to determine the changes in your machine since the last normal result. Tweak the application settings relevant to display and segmentation. …

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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:** [August 12, 2026, 1:24pm UTC](https://discourse.slicer.org/t/setting-segment-opacity-to-1-0-hides-segments/46800/13 "2026-08-12T13:24:28Z")

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You can try to use different OpenGL profile (by setting `SLICER_OPENGL_PROFILE` to `no`, `core`, or `compatibility` see [here](https://slicer.readthedocs.io/en/latest/user_guide/settings.html#runtime-environment-variables)) or disable depth peeling in the 3D view settings.