This guide is part of the series on creating 3D medical models, from the scan stage to a production-ready model. Here I'll demonstrate semi-automatic segmentation of bone, which is usually the easiest to perform (as long as you're not dealing with complex fractures).

With soft tissue the stages are similar, but there's usually more manual work, because HU ranges overlap more between tissue types. I'll also show, briefly, full automatic segmentation using the TotalSegmentator extension.

One note: the principles shown here are nearly identical in every medical segmentation software. The main differences are the interface, the available tools, and the automation capabilities. The demo here uses 3D Slicer, a free, open-source program used by radiologists, medical engineers, and scientists worldwide. Download link at the end.

1. Open the DICOM file and set the display

Load the CT file into 3D Slicer. Go to Volume Rendering and choose a suitable preset (for example, CT Abdomen) to adjust the contrast. You can also change the contrast manually to a version that's more comfortable to work with.

Adding a DICOM CT volume in 3D Slicer
Add the DICOM CT volume.
Volume rendering preset adjusting CT contrast in 3D Slicer
Volume Rendering with a contrast preset.

2. Create a new segment and set a color

Go to the Segment Editor, create a new segment (Add), and choose a bold color that makes the structure easy to identify.

Creating a new segment in the 3D Slicer Segment Editor
Create a new segment.

3. Segment with Threshold

Select the Threshold tool to set HU values appropriate for bone (for example, from about +150 and up, depending on the case). Make sure you include most of the bone while minimizing noise from soft-tissue regions.

Thresholding bone by Hounsfield units in 3D Slicer
Threshold by HU value.

4. Clean up with Islands

Choose Islands > Keep Selected Island, then click the part of the bone you want to keep. This automatically removes unwanted objects.

Using Islands, Keep Selected Island, to clean the segmentation
Islands: keep the selected island.

5. Crop to the region of interest

Use the Scissors tool in Erase Outside mode. Outline the region you want (for example, the lumbar vertebrae) to remove everything else.

Scissors tool in Erase Outside mode isolating the region of interest
Scissors, Erase Outside, keeps only the region of interest.

6. Improve model quality with smoothing

Two smoothing operations help: Closing (small kernel) to close small holes, and Median smoothing (large kernel) for general smoothing and noise reduction.

Smoothing the segmented bone model in 3D Slicer
Smoothing: closing plus median.

7. Automatic segmentation with TotalSegmentator

When you need to segment many structures, you can use the TotalSegmentator extension: install it through the 3D Slicer Extension Manager, run it on a DICOM file, and the tool extracts dozens of anatomical structures automatically. Human medical review is always required for corrections and final approval.

Automatic multi-structure segmentation with the TotalSegmentator extension
TotalSegmentator: automatic multi-structure segmentation.

8. Export to STL

Go to Segmentations > Export and save the segment as an STL file, ready for printing or for editing in another program.

Exporting the segment to an STL file in 3D Slicer
Export the segment to STL.

Tips from the field

  • The more accurate the initial Threshold setup, the shorter the manual editing time.
  • For soft tissue, combine Threshold with slice-by-slice manual marking in complex regions.
  • Working with a radiologist or surgeon at this stage saves you from late-stage rework.

Relevant links