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Bone 3D View

The Bone 3D view renders a three-dimensional volume from the DICOM data, allowing you to visualise bony anatomy and plan in 3D space.

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Volume Rendering Controls

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Bone Density Cutoff

The Bone Density Cutoff slider controls the minimum density value (in Hounsfield Units) used to render the bone surface. Adjust it to isolate cortical bone, include cancellous bone, or reveal soft tissue.
  • Higher cutoff — shows only dense cortical bone
  • Lower cutoff — includes softer tissue and cancellous bone

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Bone Transparency

The Bone Transparency slider controls the transparency of the rendered volume. Increase transparency to see through the outer cortex and visualise internal structures or planned tunnels.

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Surface Detail

Toggle Surface Detail to sharpen the boundaries of the rendered bone. This improves visual clarity, especially when the density cutoff captures a range of densities.

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View Style

Select a View Style from the toolbar dropdown:

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Clip Region

Use the Clip Region sliders in the properties panel to cut away portions of the volume along any axis (Left/Right, Front/Back, Bottom/Top). This lets you isolate a specific region of anatomy.
Use a sagittal clip to expose the intercondylar notch when planning ACL femoral tunnels.

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Slice Plane

The slice plane indicator shows the position of the current Stack view slice in the 3D bone rendering. This links the 2D slice position to the 3D view.

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Controls

  • ⊞ Slice — toggle the slice plane on/off
  • ▲ / ▼ — move the slice position up or down by one increment
  • Slice counter — shows the current slice number (e.g. 89/267)

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Clip Above / Below

Use ✂ Above or ✂ Below to clip the volume at the slice plane position:
  • ✂ Above — hides everything above the slice, exposing anatomy from above (e.g. tibial plateau)
  • ✂ Below — hides everything below the slice, showing anatomy from below (e.g. femoral condyles)
Click the active button again to restore the full volume. The clip integrates with the Clip Region settings — both are applied together.
Use ✂ Above at the knee joint line to examine tunnel exit points on the tibial footprint. Orbit the clipped view to inspect placement from any angle.

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Anatomical Views

Quick-access buttons orient the camera to standard anatomical positions: A (Anterior), P (Posterior), L (Lateral), R (Right), S (Superior), I (Inferior)

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Camera Controls

  • Left-click drag — orbit around the model
  • Right-click drag — pan
  • Scroll wheel — zoom in/out
  • Right-click (short click) — opens the context menu for tunnel placement, measurements, eraser, and anchor point
Press S (Superior) or I (Inferior) for a top-down perspective, useful when placing tunnel exit points on exposed joint surfaces.

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Tool Persistence

When you switch between view modes, your active tool is preserved if it’s compatible with the new view. Tools that only work on 2D slices (Length, Angle, Window/Level, Arrow, Circle, Rectangle, Eraser) reset to Pointer when switching to a 3D view, and vice versa for 3D-only tools.

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AI Bone Labelling

Click Label Bones in the bottom toolbar to identify bone structures using AI. The AI analyses the 3D volume from multiple angles and labels each visible bone (e.g. Femur, Tibia, Patella, Fibula) with a confidence indicator.

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MRI Data & Synthetic CT

When MRI DICOM data is loaded, the Bone 3D view adapts to handle the differences between MRI and CT imaging.
MRI signal intensities are not standardised like CT Hounsfield Units. An amber banner in the viewport explains this when MRI data is detected.

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MRI Sequence Quality

When MRI data is loaded, NavNX detects the MRI sequence type (PD, T1, T2, STIR, ZTE, UTE, etc.) from the DICOM tags and displays a colour-coded quality indicator: For sequences with limited bone visibility, a recommendation appears: “For CT-level bone accuracy, request an isotropic 3D ZTE or UTE sequence from the imaging provider.”

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Generating a Synthetic Bone Model

Because MRI lacks reliable density values, NavNX can generate a synthetic CT volume server-side to enable bone rendering:
  1. In the MRI Bone view sidebar, click Generate Synthetic CT
  2. The server processes the MRI data to produce an AI-estimated bone model. GPU provisioning may take up to 15 minutes on first run
  3. Once ready, the view switches to Bone 3D (Synthetic CT) with a blue caveat banner noting that density values are AI-generated approximations
  4. The Bone Density Cutoff slider and density-based controls appear after synthetic CT generation

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sCT Confidence Score

When a synthetic CT volume is generated, a confidence score may be displayed in the Bone view sidebar. This score (0–100%) indicates how confident the AI model is in the quality of the synthetic CT output: The confidence bar only appears when the segmentation pipeline provides a confidence score.

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Synthetic CT Safety Labeling

Density values derived from synthetic CT are clearly labeled throughout NavNX to prevent confusion with real CT measurements:
  • Tunnel density profiles show “(synthetic)” and a warning: “AI-generated values — not for densitometry”
  • Min/Max values display “sCT” instead of “HU” as the unit
  • Pre-op reports include a prominent disclaimer banner and a diagonal watermark when density data comes from MRI-derived synthetic CT
Synthetic CT values are approximations and should not be used for clinical densitometry or quantitative bone density assessment. Clinical decisions regarding bone quality should be confirmed with direct CT imaging or intraoperative assessment.

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Dual-Path Cross-Check

When both a synthetic CT volume and MR-derived segmentation meshes are available, NavNX compares the two paths and flags any disagreement. This cross-check acts as a safety guardrail for synthetic data. The agreement panel appears in the Bone view sidebar below the synthetic CT banner: Expand the panel to see per-structure metrics:
  • Overlap — Dice coefficient (percentage of volumetric agreement)
  • MSD — Mean surface distance between the two surfaces (mm)
  • Level — Per-structure agreement rating
If the cross-check shows low agreement, the synthetic CT may be unreliable in the flagged regions. Consider acquiring a CT scan for confirmation, or use the MR segmentation meshes directly in the Segments view.

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Segmentation Processing

When you trigger bone segmentation, the processing status appears in the viewport:
  • A spinner with a timing estimate is displayed during processing
  • GPU provisioning may take up to 15 minutes on first run — subsequent runs are faster
  • If processing exceeds 20 minutes, a timeout state appears with a “Reload to check” button
  • If segmentation fails, an error message describes the issue and suggests next steps
If you see the timeout state, click “Reload to check” — the segmentation may have completed after the polling window. GPU cold-starts on first use are the most common cause of extended processing times.

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Range of Motion Simulation

The ROM panel appears in the properties sidebar when viewing bone data for knee cases. It simulates joint flexion to help assess tunnel placement and graft behaviour through a range of motion.

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Setting Up

ROM simulation requires a defined flexion axis. Place two points on the medial and lateral epicondyles of the femur to define the axis of rotation.

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Controls

  • Flexion angle slider — rotates the femur around the defined axis
  • Graft isometry — tracks the graft length change (ΔL) during flexion. A chart shows how length varies across the full range
  • Impingement detection — warns if the tunnel path intersects the tibial mesh at any flexion angle
  • Patella tracking — simulates the patella gliding along the trochlear groove during flexion
Use the isometry chart to verify that your tunnel placement keeps graft length change within acceptable limits across the full flexion range. Excessive ΔL may indicate suboptimal tunnel position.

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Export STL

Click Export STL in the toolbar to download the current bone rendering as an STL mesh file. The export respects the current Bone Density Cutoff setting. See Exporting for details.