# Transparent segments viewed in 3D clipped by volume renderer?

**URL:** <https://discourse.slicer.org/t/transparent-segments-viewed-in-3d-clipped-by-volume-renderer/5982>\
**Category:** Support\
**Created:** [March 1, 2019, 1:04pm UTC](https://discourse.slicer.org/t/transparent-segments-viewed-in-3d-clipped-by-volume-renderer/5982 "2019-03-01T13:04:20Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![hherhold](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/hherhold/32/12199_2.png) [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Post date:** [March 1, 2019, 1:04pm UTC](https://discourse.slicer.org/t/transparent-segments-viewed-in-3d-clipped-by-volume-renderer/5982/1 "2019-03-01T13:04:20Z")

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Can transparent segments be viewed in 3D along with the volume renderer? I searched through similar topics but didn’t find anything exactly like this.

Quick list of steps:

1. Make a segment
2. Enable viewing in 3D
3. Turn on volume rendering
4. Crop volume in volume rendering so segment “sticks out”
5. Change segment opacity to something other than 1.0
6. Segment disappears, except where volume is not in background - if you rotate around, segment becomes visible.

This is on the latest nightly (Feb 28), on both Mac and PC, and I have depth peeling enabled.

Any ideas? Thanks!!

-Hollister

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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:** [March 1, 2019, 3:05pm UTC](https://discourse.slicer.org/t/transparent-segments-viewed-in-3d-clipped-by-volume-renderer/5982/2 "2019-03-01T15:05:10Z")

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For me it works as you describe (segment disappears) if depth peeling is disabled but works perfectly if depth peeling is enabled.

Could you show a screen capture video of what you do?

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**Author:** ![hherhold](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/hherhold/32/12199_2.png) [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Post date:** [March 1, 2019, 4:42pm UTC](https://discourse.slicer.org/t/transparent-segments-viewed-in-3d-clipped-by-volume-renderer/5982/3 "2019-03-01T16:42:10Z")

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Hmm. I just re-did my scene from scratch after turning on depth peeling and it works properly (with transparency). Is depth peeling a setting in the scene’s MRML file, and it’s not properly set in my original (not working) file?

Thanks for the help!

-Hollister

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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:** [March 13, 2019, 11:42pm UTC](https://discourse.slicer.org/t/transparent-segments-viewed-in-3d-clipped-by-volume-renderer/5982/4 "2019-03-13T23:42:28Z")

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Yes, UseDepthPeeling flag is saved in the scene. It might be possible that if you enable it later then not everything is initialized correctly.

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**Author:** ![hherhold](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/hherhold/32/12199_2.png) [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Post date:** [March 14, 2019, 10:51am UTC](https://discourse.slicer.org/t/transparent-segments-viewed-in-3d-clipped-by-volume-renderer/5982/5 "2019-03-14T10:51:59Z")

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Thanks, Andras.

Not to nit-pick, but that’s a little confusing - setting depth peeling is in “Application Settings”, which I would take to mean application-wide, not per-file. Would it make more sense to move depth peeling to Volume Rendering or Segment Editor?

I guess the problem is that it’s an application setting, not a module setting, so there isn’t one good place to put it. Maybe a note by the depth peeling check box saying the setting is saved in scene files? (I’m happy to add that if agreed upon.)

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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:** [March 14, 2019, 4:03pm UTC](https://discourse.slicer.org/t/transparent-segments-viewed-in-3d-clipped-by-volume-renderer/5982/6 "2019-03-14T16:03:08Z")

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You can set **default** view settings in application settings, which is applied to new views.

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/1/f185bde58392ae1e8f695b7af213529ea5d8ba52.png)

You can change the current settings in the view controller.

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/7/4/74a298bcba2e25616b5f7bddfaadc4a40e1078fc.png)

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<div class="post-metadata">

**Author:** ![hherhold](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/hherhold/32/12199_2.png) [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Post date:** [March 14, 2019, 4:41pm UTC](https://discourse.slicer.org/t/transparent-segments-viewed-in-3d-clipped-by-volume-renderer/5982/7 "2019-03-14T16:41:46Z")

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Got it, ok - that makes sense.

“Problem between chair and keyboard”, as they say.

Thanks!

-Hollister

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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:** [January 27, 2021, 9:13pm UTC](https://discourse.slicer.org/t/transparent-segments-viewed-in-3d-clipped-by-volume-renderer/5982/8 "2021-01-27T21:13:20Z")

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A post was split to a new topic: [Separate vessels from bones](https://discourse.slicer.org/t/separate-vessels-from-bones/15703)