InVesalius, 3D Slicer and ITK-SNAP are the three free, open-source programs dental teams most often use to turn a CBCT scan into a 3D model. The short answer: use InVesalius when you want a quick threshold-based DICOM to STL conversion with almost no learning; use 3D Slicer when you need teeth, jaws and the mandibular canal separated automatically (with the DentalSegmentator extension); use ITK-SNAP when you want to trace one structure precisely in a small, focused tool. None of them plans implants or designs guides, and none is a certified diagnostic viewer.
Side by side
| Item | InVesalius | 3D Slicer | ITK-SNAP |
|---|---|---|---|
| Licence | Free, open source (GPL v2) | Free, open source (BSD-style) | Free, open source (GPL v3) |
| Developer | CTI Renato Archer, Brazil | 3D Slicer open-source community | PICSL, University of Pennsylvania |
| Latest stable | 3.1.99998 (April 2022), plus nightly builds | 5.12.4 (September 2026) | 4.4.0 (September 2025) |
| Platforms | Windows 64-bit, macOS (Intel and Apple Silicon), Linux (Flatpak) | Windows 11, macOS 14+, Linux | Windows 64-bit, macOS (Intel and Apple Silicon), Linux 64-bit |
| Automatic tooth segmentation | No | Yes, with DentalSegmentator | AI-assisted (nnInteractive), needs a GPU service; no dental models |
| Main segmentation tools | Threshold presets, region growing, watershed, brush editor | Segment Editor: threshold, paint, scissors, grow from seeds, islands | Paintbrush, polygon, active contour, slice interpolation |
| Mesh export | STL, PLY, OBJ, VRML | STL, OBJ | STL, VTK, VTP, BYU, VRML |
| Learning curve | Low | Steep | Moderate |
| Intended use | No regulatory claim on the official site | Research; not approved for clinical use | Not presented as a medical device |
Converting a CBCT to an STL model
This is the most common reason people search “invesalius dicom to stl”, and InVesalius is the fastest route. Import the DICOM folder, pick the series with the full slice count, choose the Bone or Compact Bone (Adult) preset, raise the lower threshold until the cortex looks continuous, keep the largest connected region, create the surface and export binary STL.
3D Slicer does the same through the Segment Editor (Threshold, then Islands to keep the largest part, then export from the Segmentations module), but you face a much larger interface to get there. ITK-SNAP can do it with an active contour seeded inside the bone, which gives a cleaner result on noisy scans but takes longer to set up. For a plain jaw or skull model, InVesalius wins on time.
Separating teeth, jaws and the mandibular canal
Here 3D Slicer is clearly ahead. Install DentalSegmentator from the Extension Manager, load the CBCT, select the volume and click Apply: it produces five segments — maxilla, mandible, upper teeth, lower teeth and mandibular canal. On first run it downloads PyTorch, nnU-Net and the model weights, and it is much faster on an NVIDIA GPU. Review each segment slice by slice, especially around crowns and implants, and fix errors in the Segment Editor.
InVesalius has an Enamel preset that picks up the densest structures, but CBCT grey values are not calibrated, so teeth merge with bone and metal artefacts leak into the mask. Expect manual cleanup. ITK-SNAP can separate teeth, but you guide every structure yourself.
Tracing one structure precisely
For a cyst, an impacted tooth, the airway or a single root, ITK-SNAP is the most comfortable. Draw the outline with the polygon tool on a few slices, fill the gaps with slice interpolation and read the volume under Tools > Volumes and Statistics. The three linked views make it easy to see where a contour leaks. Version 4.4 adds nnInteractive: click or scribble on the structure and the model proposes a 3D segmentation, but it needs the ITK-SNAP DLS service on a GPU, and for patient data that service should run locally or on your institution’s server.
3D Slicer can do the same with Paint, Scissors and Grow from seeds and has more tools overall; InVesalius’s brush editor works but is the least precise of the three.
Viewing and explaining the scan
InVesalius has good volume rendering presets, MIP and MinIP modes and a crop plane, which makes it a quick tool for showing root position or bone width to a patient or a class. 3D Slicer has GPU volume rendering, multiplanar reformatting and measurement markups. ITK-SNAP focuses on segmentation and has fewer visual tools. If you only need to look at a scan in 3D, a browser viewer such as VolView is simpler than all three; our free dental imaging software guide lists more viewers.
Installing and running them
- InVesalius: the stable Windows installer is labelled for Windows 7/10, so test it on Windows 11 with one of your own scans before relying on it. Newer code is available only as nightly builds.
- 3D Slicer: install to a path with only English ASCII characters on Windows, or Python-based extensions may fail. Install extensions from the Extension Manager of the same Slicer release. 8 GB RAM or more is strongly recommended.
- ITK-SNAP: separate builds for Intel and Apple Silicon Macs; version 4.4 uses a new OpenGL renderer with a software fallback, so update the graphics driver if it fails to start.
All three produce meshes that need cleanup before printing. Run them through MeshLab to remove fragments, close holes and decimate.
Which one should you use
- Dentist or technician who needs a printable jaw model today: InVesalius.
- Orthodontic lab, researcher or student who needs separated teeth, jaws and canal: 3D Slicer with DentalSegmentator, plus Automated Dental Tools for landmarks and registration.
- Anyone measuring a lesion or tracing one structure carefully: ITK-SNAP.
- Anyone planning implants and printing a guide: none of these. Use Blue Sky Plan, which is shareware (conditionally free), or your commercial planning software. Our free dental implant planning and CBCT software guide compares all the options, including the dormant Seg3D.
FAQ
InVesalius vs 3D Slicer: which is better?
InVesalius is better for fast, simple DICOM to STL work with little learning. 3D Slicer is more powerful, actively released and has dental AI extensions, but takes longer to master. Many users keep both.
ITK-SNAP vs 3D Slicer: which should I use?
ITK-SNAP is smaller and focused on segmentation, which makes it easier to learn. 3D Slicer is broader and the better choice for automatic tooth and jaw segmentation through DentalSegmentator.
How do I convert DICOM to STL in InVesalius?
Import the DICOM series, choose a threshold preset such as Bone, keep the largest connected region, create the 3D surface and export it as STL. Clean the mesh in a separate editor before printing.
Can InVesalius, 3D Slicer or ITK-SNAP plan dental implants?
No. None of them has implant libraries or surgical guide design. Use them for segmentation and models, and a dedicated planning program for implants.
Are they free for commercial use in a clinic or lab?
Yes. InVesalius (GPL v2) and ITK-SNAP (GPL v3) have no paid editions, and 3D Slicer’s BSD-style licence allows commercial use. 3D Slicer’s developers still describe it as intended for research, not clinical use.
Do they run on a Mac?
Yes. All three publish macOS builds, including Apple Silicon builds for InVesalius and ITK-SNAP; 3D Slicer requires macOS 14 or later.
Last updated: 26 September 2026 · DentIIT editorial team. Licence, version and platform details are checked against each developer's official documentation; none of the tools listed here should be treated as a certified medical device unless its vendor says so.
