# Segmenting goes across 3 slices

**URL:** <https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079>\
**Category:** Support\
**Created:** [February 13, 2018, 3:42pm UTC](https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079 "2018-02-13T15:42:09Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![tnguyen](https://avatars.discourse-cdn.com/v4/letter/t/6f9a4e/32.png) [@tnguyen](https://discourse.slicer.org/u/tnguyen)\
**Post date:** [February 13, 2018, 3:42pm UTC](https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079/1 "2018-02-13T15:42:09Z")

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Hi everyone,  
I was using Paint Effect in Segment Editor and I noticed that the area that I painted on 1 slice also appears on the next two adjacent slices (if I try to erase this area on these two slices, it will also erase the painted area on the first slice too)

Windows  
Version: 4.8.1  
Expected behavior: Area painted on one slice will be only on that slice  
Actual behavior: Area painted on one slice also appears on the next two adjacent slice

I appreciate any input on how to go about this issue, thank you!

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**Author:** ![cpinter](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cpinter/32/7995_2.png) [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Post date:** [February 13, 2018, 4:01pm UTC](https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079/2 "2018-02-13T16:01:13Z")

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I can imagine two reasons:

1. The image you segment is non-axis-aligned. After a quick search I found [this thread](https://discourse.slicer.org/t/display-issue-with-rt-structs-and-mr-volume/546). Please check if this is the case.
2. The Spere brush option is enabled and it also paints on adjacent slices

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**Author:** ![tnguyen](https://avatars.discourse-cdn.com/v4/letter/t/6f9a4e/32.png) [@tnguyen](https://discourse.slicer.org/u/tnguyen)\
**Post date:** [February 13, 2018, 4:14pm UTC](https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079/3 "2018-02-13T16:14:54Z")

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> [@cpinter](#):
>
> this thre

Thanks for response Csaba, could you link the thread again? I can’t click it for some reasons

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**Author:** ![JoostJM](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/joostjm/32/1091_2.png) [@JoostJM](https://discourse.slicer.org/u/JoostJM)\
**Post date:** [February 13, 2018, 4:55pm UTC](https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079/4 "2018-02-13T16:55:27Z")

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Additionally, it is also possible the master volume on which you are segmenting has different spacing than the volume currently selected in your viewer.

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**Author:** ![cpinter](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cpinter/32/7995_2.png) [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Post date:** [February 13, 2018, 5:26pm UTC](https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079/5 "2018-02-13T17:26:52Z")

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I fixed the link, sorry about that.

@JoostJM also has a good point. If you selected a master volume and then switched, the geometry of the original master volume is used. In that case create a new segmentation and choose the volume with the geometry you want to have.

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**Author:** ![tnguyen](https://avatars.discourse-cdn.com/v4/letter/t/6f9a4e/32.png) [@tnguyen](https://discourse.slicer.org/u/tnguyen)\
**Post date:** [February 13, 2018, 6:02pm UTC](https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079/6 "2018-02-13T18:02:14Z")

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After checking the images again per your suggestions, I found that it may be because my master image thickness is 3 mm and the slice thickness at the viewing panel was at 1 mm. After I reset the thickness to 3 mm, the painted area stays within 1 slice. Thank you for helping me solve this!

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**Author:** ![DAT\_Minh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dat_minh/32/9097_2.png) [@DAT\_Minh](https://discourse.slicer.org/u/DAT_Minh)\
**Post date:** [December 6, 2020, 2:43pm UTC](https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079/7 "2020-12-06T14:43:21Z")

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Hello. I have the same problem with you but I can’t imagine the steps you go through. Can you post screen shot on where to see and adjust master image thickness and slice thickness? Thank you.

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**Author:** ![manjula](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/manjula/32/80981_2.png) [@manjula](https://discourse.slicer.org/u/manjula)\
**Post date:** [December 6, 2020, 3:30pm UTC](https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079/8 "2020-12-06T15:30:58Z")

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Please check if this is the case and will resolve your problem with this,  
1.

> **[Overview](https://lassoan.github.io/SlicerSegmentationRecipes/ObliqueSliceSegmentation/)**
>
> Recipes for common medical image segmentation tasks using 3D Slicer

1. Check if the Sphere brush is on and that is not the effect you want.

2. View Slice thickness

 ![Screenshot from 2020-12-06 16-35-46](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/7/b/7b443b1e2a91e78c1e9974666eca4ce02510a03a.png)

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**Author:** ![DAT\_Minh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/dat_minh/32/9097_2.png) [@DAT\_Minh](https://discourse.slicer.org/u/DAT_Minh)\
**Post date:** [December 6, 2020, 4:57pm UTC](https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079/9 "2020-12-06T16:57:09Z")

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Thank you very much. That’s a very straightforward and detailed work flow. Nice to have your respond.