3D Slicer for Dental CBCT: Free Workflow and Limits

The short answer: 3D Slicer is a free, open-source imaging platform that opens dental CBCT scans, shows them as slices and as a 3D volume, lets you segment bone and teeth, and exports the result as an STL or OBJ model. Its licence says it is designed for research only, has not been reviewed or approved by the FDA, and that clinical applications are neither recommended nor advised. Use it for research, teaching, lab work and case preparation, not for diagnosis.

This guide is for dental researchers, students, technicians and clinic IT staff. Status: Not tested yet. Facts come from the official 3D Slicer documentation and download page, the developers’ extension pages and our verified SlicerCMF page, checked on 23 October 2026. Prepared by the dentsoftpro editorial team.

3D Slicer at a glance

Full requirements are in the 3D Slicer getting started guide.

Step 1: Install 3D Slicer

1. Get the installer from the official 3D Slicer site. The stable release changes a few times a year and receives extension updates; the preview release is rebuilt daily.
2. Windows: run the installer. The installation path must contain only English ASCII characters, so avoid folders with accented or non-Latin names.
3. macOS: open the disk image and drag Slicer.app into Applications; it cannot run from the read-only image. Preview builds are unsigned and must be allowed under System Settings > Privacy & Security.
4. Linux: extract the archive, install the distribution packages listed in the documentation and start the Slicer executable.

Step 2: Import the CBCT scan

3D Slicer reads the DICOM folder from a patient disc through its DICOM module and a local database.

1. Copy the disc to a local drive first. The documentation recommends importing from local storage rather than network, cloud or virtual drives, and using short, ASCII-only paths.
2. Open the DICOM module. On first use, let Slicer create a new DICOM database.
3. Drag the folder onto the Slicer window and choose Load directory in DICOM database, or click Import and select the folder. Subfolders are scanned.
4. If you import straight from a CD, DVD or USB stick, turn on Copy imported files to DICOM database in the Import drop-down, so the data stays available after the media is removed.
5. Double-click the patient, study or series to load it, then switch back to the viewer.

If a scan loads wrongly, tick Advanced, click Examine and load the item from the list. Files anonymised with empty Patient Name, Patient ID or Series Instance UID may fail to load; the DICOM Patcher module can repair some of them. Before sharing scans with colleagues, see how to anonymise DICOM files.

Step 3: Look at the scan in 3D

The slice views show the axial, coronal and sagittal planes as soon as the volume is loaded. For a 3D view, right-click the eye icon of the volume in the Data module and choose Show in 3D views as volume rendering. In the Volume Rendering module, pick a preset for bone and use the Shift slider when the preset does not match the intensity range of your scanner. On a PC without a suitable graphics card, switch from GPU to CPU ray casting; it works everywhere but is slower.

Step 4: Segment bone or teeth

Segmentation turns voxels into labelled structures such as the mandible, maxilla or single teeth. In the Segment Editor the main tools are:

• Threshold to fill a segment with an intensity range, a fast start for bone;
• Islands to keep the largest connected region and drop loose fragments;
• Scissors to cut away the opposite jaw, the spine or the head rest;
• Paint and Erase for manual correction, with a brush size in millimetres;
• Grow from seeds to separate touching structures from at least two seed segments;
• Smoothing to fill small holes and remove spikes before export.

Manual segmentation of teeth on CBCT is slow because tooth and bone intensities overlap. Two free extensions automate part of the work:

• DentalSegmentator segments the maxilla and upper skull, mandible, upper teeth, lower teeth and mandibular canal. It needs 3D Slicer 5.8.0 or later and installs PyTorch and nnU-Net on first launch. Its developers warn that processing without a CUDA GPU can be very slow and that GPU acceleration is currently unavailable on macOS.
• Automated Dental Tools, from the same DCBIA group that made SlicerCMF, adds automatic CBCT segmentation (AMASSS), landmark identification (ALI), orientation (ASO) and registration (AReg) for CBCT and intraoral scans. Several modules need trained models that are downloaded separately from inside the module.

Both are installed through the Extensions Manager. Always review automatic results slice by slice; neither extension states clinical validation on its project page.

Step 5: Measure and compare scans with SlicerCMF

SlicerCMF is a bundle of 3D Slicer modules for orthodontic, oral surgery and TMJ research. It registers a follow-up CBCT to a baseline on a stable region such as the cranial base (CMFreg), computes 3D cephalometric angles and distances split into right-left, anterior-posterior and superior-inferior components (Q3DC), and shows colour-coded surface distance maps between models (ModelToModelDistance, ShapePopulationViewer). Measurements can be exported to CSV.

Install it from the Extensions Manager and restart Slicer; the old standalone packages are no longer maintained. The bundle’s code has not changed since April 2022, so treat it as dormant, although it is still built for 3D Slicer 5.12.4. Documentation lives on cmf.slicer.org.

Step 6: Export a 3D model

To send a jaw or tooth model to a printer, a CAD program or a mesh editor, open the Export to files section of the Segmentations module (also reachable from the Segmentations button in the Segment Editor), choose a folder and STL or OBJ, and click Export. The model can then be cleaned or trimmed in a mesh tool; see Meshmixer and the free 3D mesh and scanning software hub.

Limitations

• Not a medical device. The licence describes 3D Slicer as research software, not reviewed or approved by the FDA, and advises against clinical applications. It does not replace the certified software that comes with your CBCT unit.
• No implant planning or surgical guide design in 3D Slicer or SlicerCMF. Those workflows need dedicated dental planning software.
• Learning curve. The interface is built for researchers; expect time on import, segmentation and transforms.
• Hardware. Large CBCT volumes need plenty of memory, and AI segmentation is slow without a CUDA GPU.
• Extension versions. Extensions are built for a specific Slicer release; if one is missing, update to a current stable or preview build.

Simpler alternatives

3DimViewer is lighter, with threshold segmentation and STL export, but no longer developed (last release 3.1.1, 2017). MITK Workbench is actively developed, with AI-assisted segmentation and STL export but no dental modules. For plain viewing, see the free DICOM viewers hub. Platforms are compared in our open-source CBCT imaging platforms hub.

FAQ

Is 3D Slicer free for dental use?

Yes. It is free and open source under a BSD-style licence, with no fee for any use. The licence says it is intended for research and that clinical use is not recommended.

Can 3D Slicer open a dental CBCT scan?

Yes. Import the DICOM folder from the disc into the DICOM module, then load the series. Copy the disc to a local drive first for the most reliable import.

Is 3D Slicer FDA approved?

No. Its licence states that it has not been reviewed or approved by the FDA and is designed for research purposes only.

Does 3D Slicer run on a Mac?

Yes, on macOS 14 or later. On 23 October 2026 the stable release was built for Intel Macs, and a native Apple Silicon build was available in the preview release.

How do I convert DICOM to STL in 3D Slicer?

Load the CBCT, create a segment with the Segment Editor (Threshold, then Islands and Scissors to clean it), and export it from the Segmentations module with Export to files as STL.

MITK vs 3D Slicer: which is better for dental CBCT?

3D Slicer has dental extensions (SlicerCMF, Automated Dental Tools, DentalSegmentator); MITK has none. Choose MITK if you want a general, actively developed workbench from DKFZ Heidelberg and do not need dental modules.

Last updated: 23 October 2026 · DentSoftPro 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.