# Brain CT segmentation - grow from seed leak - rectangle appears

**URL:** <https://discourse.slicer.org/t/brain-ct-segmentation-grow-from-seed-leak-rectangle-appears/46245>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [February 22, 2026, 8:03pm UTC](https://discourse.slicer.org/t/brain-ct-segmentation-grow-from-seed-leak-rectangle-appears/46245 "2026-02-22T20:03:15Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![mechanical\_orange](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mechanical_orange/32/81155_2.png) [@mechanical\_orange](https://discourse.slicer.org/u/mechanical_orange)\
**Post date:** [February 22, 2026, 8:03pm UTC](https://discourse.slicer.org/t/brain-ct-segmentation-grow-from-seed-leak-rectangle-appears/46245/1 "2026-02-22T20:03:15Z")

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Operating system: mac os  
Slicer version: 5.6.2  
Expected behavior: grow from seed only segments parts of the brain without the background  
Actual behavior: grow from seed segments the background in a rectangle form.

Hi!

Segmenting brain CT: painting then using grow from seed. I am surely not putting painted points in the background. And regardless this all, a rectangle appears in the color of one of my segments, or the whole background become part of my segment. Mostly of the darkest segment.

I set the background to -10000 but the issue persists. How could I resolve this issue?

Thank you,

ervin

 ![Screenshot 2026-02-22 at 21.58.10](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/3/f35ff5b9c3284d42f3178d96d6186882f3c1e92b.jpeg)

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**Author:** ![drnoorfatima](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/drnoorfatima/32/81980_2.png) [@drnoorfatima](https://discourse.slicer.org/u/drnoorfatima)\
**Post date:** [February 23, 2026, 1:55am UTC](https://discourse.slicer.org/t/brain-ct-segmentation-grow-from-seed-leak-rectangle-appears/46245/2 "2026-02-23T01:55:29Z")

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Hi Ervin!

This is a known issue with Grow from Seeds on brain CT, the algorithm leaks into the background because CT background intensities overlap with certain brain regions. Setting background to -10000 alone won’t fix it, the solution involves a specific masking step before running the segmentation.  
Completely fixable though. I work with Slicer segmentation professionally you can dm me.

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**Author:** ![mechanical\_orange](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mechanical_orange/32/81155_2.png) [@mechanical\_orange](https://discourse.slicer.org/u/mechanical_orange)\
**Post date:** [February 23, 2026, 4:05pm UTC](https://discourse.slicer.org/t/brain-ct-segmentation-grow-from-seed-leak-rectangle-appears/46245/3 "2026-02-23T16:05:32Z")

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Thank you very much for your offer! I solved the issue by painting(segmenting) the background too, then when I exported the segments as labels, set the background to invisible. It seems successful for my current task for now.

ty again

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**Author:** ![drnoorfatima](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/drnoorfatima/32/81980_2.png) [@drnoorfatima](https://discourse.slicer.org/u/drnoorfatima)\
**Post date:** [February 24, 2026, 9:39am UTC](https://discourse.slicer.org/t/brain-ct-segmentation-grow-from-seed-leak-rectangle-appears/46245/4 "2026-02-24T09:39:20Z")

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no problem, have a good day.

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**Author:** ![gaoyi.cn](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/gaoyi.cn/32/1422_2.png) [@gaoyi.cn](https://discourse.slicer.org/u/gaoyi.cn)\
**Post date:** [March 4, 2026, 12:26pm UTC](https://discourse.slicer.org/t/brain-ct-segmentation-grow-from-seed-leak-rectangle-appears/46245/5 "2026-03-04T12:26:41Z")

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Segmenting part of the image is a designed feature of the module, to reduce memory/computation. Roughly, after you draws the seeds (both target and background), the algorithm computes a bounding box of from those seeds and crop a box out from the original image. It only segment in the cropped image. If the more seeds are added later in the interaction step, the box can be enlarged.