# Heart segmentation problem

**URL:** <https://discourse.slicer.org/t/heart-segmentation-problem/33179>\
**Category:** Support\
**Created:** [December 2, 2023, 1:19pm UTC](https://discourse.slicer.org/t/heart-segmentation-problem/33179 "2023-12-02T13:19:10Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Isabel\_Smith](https://avatars.discourse-cdn.com/v4/letter/i/e5b9ba/32.png) [@Isabel\_Smith](https://discourse.slicer.org/u/Isabel_Smith)\
**Post date:** [December 2, 2023, 1:19pm UTC](https://discourse.slicer.org/t/heart-segmentation-problem/33179/1 "2023-12-02T13:19:10Z")

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Operating system: Windows 11  
Slicer version: 5.4.0.  
Expected behavior:  
Actual behavior:

Hi! I am having trouble with replicating this segmentation of the heart:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/8/8841876a1b624c7ab8424311a29e9bce8c69cb97.jpeg)

I would like to segment this sample (below picture) like this as well, but so far I couldn’t. If you could help me with the process, I would be grateful!

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/b/6bfccc630c0433900de01b839d62cdbd46e4e73b.jpeg)

Thank you!  
Esther

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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:** [December 3, 2023, 1:58am UTC](https://discourse.slicer.org/t/heart-segmentation-problem/33179/2 "2023-12-03T01:58:42Z")

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There does not seem to be a visible difference between the heart muscle regions, so you need to manually separate them. You can start with Threshold effect, specify the intensity range that highlights the myocardium, and click “Use for masking”. You can then try to segment a few axial slices and then use “Fill between slices” to create a 3D segmentation from them. You can also [use Scissors effect to split a segment into parts](https://lassoan.github.io/SlicerSegmentationRecipes/Craniotomy/).

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**Author:** ![Isabel\_Smith](https://avatars.discourse-cdn.com/v4/letter/i/e5b9ba/32.png) [@Isabel\_Smith](https://discourse.slicer.org/u/Isabel_Smith)\
**Post date:** [December 3, 2023, 4:27pm UTC](https://discourse.slicer.org/t/heart-segmentation-problem/33179/3 "2023-12-03T16:27:08Z")

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Thank you! I was able to do this way.