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Segmenting a Heart with 3D Slicer (New Segment Editor)

This walkthrough, presented at the 2018 and 2019 Society for Imaging Informatics in Medicine (SIIM) conferences, aims to familiarize you with Slicer’s new segmentation tool. We’ll do this by segmenting a heart from a CTA. This task nicely demonstrates many of the powerful features available through Slicer’s Segment Editor.

Slicer is open-source software supported by the NIH that has been around for over 2 decades and is still under active development. It can perform numerous quantitative imaging tasks, but has gained popularity recently for its ability to create 3D models from imaging studies. Slicer version 4.8 added a new module called “Segment Editor” which is a vast improvement over the prior segmentation module. Features highlighted in this tutorial include:

  • Grow and shrink segmentations
  • Hollow out a segmentation
  • Smooth and fill holes
  • Logical operators (add, subtract)


If you want to follow along, you can access source files at Everything is there, including a completed segmentation and STL file. However, to get started you just need Slicer installed and the “cta.nii” file in the “slicer” folder. This is the imaging study we will segment.


Follow along on this YouTube video – it is mostly up-to-date, but be aware that some links have changed from what they are in the video:

Once you’ve created a 3D model, it’s time to: