# Using 3D slicer to segment intramyocardial fat

**URL:** <https://discourse.slicer.org/t/using-3d-slicer-to-segment-intramyocardial-fat/37027>\
**Category:** Support\
**Tags:** heart\
**Created:** [June 26, 2024, 2:54am UTC](https://discourse.slicer.org/t/using-3d-slicer-to-segment-intramyocardial-fat/37027 "2024-06-26T02:54:57Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![kasun](https://avatars.discourse-cdn.com/v4/letter/k/4491bb/32.png) [@kasun](https://discourse.slicer.org/u/kasun)\
**Post date:** [June 26, 2024, 2:54am UTC](https://discourse.slicer.org/t/using-3d-slicer-to-segment-intramyocardial-fat/37027/1 "2024-06-26T02:54:57Z")

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Hello all,

I was hoping to get some help with a project I’m working on.

I have a series of cardiac gated CTs and I would like to segment out the intramyocardial fat (lipomatous metaplasia) as a 3d shell vtk file.

This lipmatous metaplasia (LM) would be defined as “a continuous minimal area (eg, \>1 mm2) … with attenuation between −180 and 0 Hounsefield Units HU”  
[https://doi.org/10.1161/CIRCIMAGING.123.014399](https://doi.org/10.1161/CIRCIMAGING.123.014399)

My plan would be to use TotalSegmentator Heart Chambers model to segment the endo and epicardial borders of the LV and RV.

Would be it possible to automatically segment out this range of Hounsfield Units from only within the myocardium i.e. exclude epicardial adipose tissue (and ideally include them if there is \>1mm2 of contiguous fat)? And create a 3D model that can be exported as a VTK. How could I do this?

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [June 27, 2024, 12:08pm UTC](https://discourse.slicer.org/t/using-3d-slicer-to-segment-intramyocardial-fat/37027/2 "2024-06-27T12:08:08Z")

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That sounds quite doable, either interactively using various tools in the Segment Editor or if you want by writing a script to automate parts if you have a lot of cases to do. I’m not sure there’s any specific recipe other than practice with the tools and review examples.

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**Author:** ![kasun](https://avatars.discourse-cdn.com/v4/letter/k/4491bb/32.png) [@kasun](https://discourse.slicer.org/u/kasun)\
**Post date:** [July 11, 2024, 1:03am UTC](https://discourse.slicer.org/t/using-3d-slicer-to-segment-intramyocardial-fat/37027/3 "2024-07-11T01:03:08Z")

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Hi Steve

Thanks for this. Is there a particular tool that I can use to select pixels with a particular hounsfield unit? What is the name of that tool / is there a video/written guide of using this?

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<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [July 11, 2024, 11:53am UTC](https://discourse.slicer.org/t/using-3d-slicer-to-segment-intramyocardial-fat/37027/4 "2024-07-11T11:53:50Z")

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The Threshold tool in the SegmentEditor can be used to set high/low masking thresholds for other tools (paint, draw, scissors…). You can find lots of videos and examples online - these features have been stable for many years, so even old videos about older versions work basically the same.