Using 3D slicer to segment intramyocardial fat

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”

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?

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.

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?

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.