Segmenting goes across 3 slices

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)

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!

I can imagine two reasons:

  1. The image you segment is non-axis-aligned. After a quick search I found this thread. 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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Thanks for response Csaba, could you link the thread again? I can’t click it for some reasons

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


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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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!

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.

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

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

  2. View Slice thickness

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