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Measurements and Statistics

Quantitative analysis transforms visual observations into numeric data. This tutorial covers distance and angle measurements, statistical analysis of volumes and masks, and geometric primitive fitting for dimensional characterization.

Estimated time: 30 minutes

Prerequisites:

  • Completed basic segmentation and visualization tutorials
  • A project with volumes, masks, and/or surfaces
Medical Disclaimer

Measurements on medical imaging data should be interpreted by qualified professionals. Measurement accuracy depends on image resolution, segmentation quality, and proper calibration.

Understanding Measurements in Volvicon​

Volvicon provides several measurement categories:

CategoryPurpose
Geometric MeasurementsDistances, angles, areas, volumes
PrimitivesReference geometry (planes, spheres, cylinders)
StatisticsIntensity and shape analysis
AnalysisSpecialized tools (wall thickness, deviation)

All measurements use physical units (mm, mm², mm³) based on the volume's spatial calibration.

Point-Based Measurements​

Accessing the Measurements Tool​

  1. Navigate to Measure → Measurement Tools → Measurements.
  2. Select the measurement type from the dropdown.
  3. Pick points in 2D or 3D views.

Measurement Types​

TypePointsResult
Point1X, Y, Z coordinates
Distance2Linear distance
Angle3Angle at middle point
Diameter3Diameter through three points
ContourMultiplePerimeter and enclosed area
CircleCenter + edgesRadius and area
EllipseCenter + axesArea and dimensions
RectangleCenter + edgesArea and dimensions
BoxCenter + edgesVolume and dimensions
Caption1Text annotation at location

Creating a Distance Measurement​

  1. Select Distance from the Measurements dropdown.
  2. Left-click to place the first point.
  3. Left-click to place the second point.
  4. The distance appears:
    • Visually as a line with value label
    • In the Measurements panel with coordinates

Creating an Angle Measurement​

  1. Select Angle from the Measurements dropdown.
  2. Click to place three points.
  3. The angle is measured at the middle point (vertex).

Contour Measurements​

For measuring perimeter and area:

  1. Select Contour from the dropdown.
  2. Click to place points around the boundary.
  3. Close the contour by:
    • Clicking near the first point
    • Or right-clicking
  4. Results include:
    • Area (for closed contours)
    • Perimeter length
    • Centroid point [X, Y, Z]
    • Lmax
    • Mean (GV)
    • Std. Dev. (GV)

Managing Measurements​

Measurement Panel​

All measurements appear in the Measurements panel:

ColumnInformation
ShowVisibility control icon
LockLock/unlock user interaction
NameMeasurement identifier
MeasurementNumeric result with unit (mm, degrees, mm², etc.)
CoordinatesPoints in physical coordinates

Editing Measurements​

  • Rename — Double-click the name
  • Delete — Select and press Delete, or right-click
  • Move points — Drag the measurement points in views
  • Hide/Show — Toggle visibility in views

Exporting Measurements​

  1. Navigate to Measure → Measurement Tools → Measurements.
  2. Select measurements to export.
  3. Press Save button
  4. Select format:
    • TXT — Formatted tables
    • INI — Programmatic access
  5. Click Save.

Intensity Analysis​

Draw Profile Line​

Analyze intensity values along a path:

  1. Navigate to Measure → Measurement Tools → Draw Profile Line.
  2. Click to start the line in a slice view.
  3. Click to end the line.
  4. The Profile panel shows:
    • Intensity values along the path
    • Graph of intensity vs. distance

Use cases:

  • Identifying threshold boundaries
  • Measuring intensity gradients
  • Detecting intensity variations across structures

A profile line drawn across a slice with two materials and a small dense inclusion, and the sampled gray values along it showing a plateau, a sharp transition at the boundary and a spike at the inclusion

Histogram Analysis​

Generate intensity histograms:

  1. Navigate to Measure → Measurement Tools → Histogram.
  2. Select the target volume.
  3. Optionally restrict analysis to a mask region.
  4. The histogram displays:
    • Intensity distribution
    • Configurable bin count
    • Statistical summary (mean, std, min, max)

The same gray value distribution drawn with 256 bins, with 32 bins, and with 256 bins on a logarithmic frequency axis that keeps a small second peak visible

Volume and Mask Statistics​

Volume Statistics​

Analyze grayscale properties:

  1. Navigate to Measure → Statistics → Volume Statistics.
  2. Select the volume to analyze.
  3. Optionally select a mask to restrict analysis region.
  4. Results include:
StatisticDescription
Mean gray valueAverage gray value
Median gray valueMiddle value
Std. dev. of gray valuesGray value variation
Min. gray value / Max. gray valueGray value range
Voxel countNumber of analyzed voxels
Volume (mm³) / Volume fraction (%)Size of the analyzed region

A skewed gray value distribution with the mean, median, 5 and 95 percent quantiles and the standard deviation marked, and the statistics table computed from it

Mask Statistics​

Analyze segmentation properties:

  1. Navigate to Measure → Statistics → Mask Statistics.
  2. Select the mask to analyze.
  3. Statistics include:

Whole Mask Statistics:

StatisticDescription
VolumeTotal volume (mm³)
Surface AreaBoundary area (mm²)
Voxel CountNumber of voxels
CentroidCenter of mass
Bounding BoxEnclosing dimensions

A mask slice with its connected region, centroid and bounding box, and the slice statistics computed from it: pixel count, area from the pixel spacing, centroid and bounding box size and diagonal

Per-Region Statistics:

  • Statistics for each connected component
  • Region count
  • Individual region volumes

Grayscale Statistics:

  • Mean intensity within mask
  • Intensity distribution within mask

Compare Masks​

Compare two segmentations:

  1. Navigate to Measure → Statistics → Compare Masks.
  2. Select the reference mask and test mask.
  3. Comparison metrics:
MetricDescription
Dice CoefficientOverlap similarity (0-1)

A source mask over a target mask on a voxel grid, coloured by voxels in both, source only and target only, with the Dice coefficient, false negative error, false positive error and volume similarity computed from those counts

These metrics are useful for:

  • Validating segmentation accuracy
  • Comparing automatic vs. manual results
  • Assessing inter-observer variability

Geometric Primitives​

Primitives are idealized geometric shapes for reference, measurement, and CAD integration.

Creating Primitives​

  1. Navigate to Measure → Primitive Tools → Primitives.
  2. Select primitive type:
TypeParameters
PlanePoint + normal vector
SphereCenter + radius
CylinderAxis + radius
ConeApex + axis + angle
CircleCenter + normal + radius
PointX, Y, Z coordinates
LineTwo points or point + direction

Wireframes of the primitive types: point, line, circle, sphere, ellipsoid, cylinder, capsule, tube, cone, arrow, spline, plane, cube and cuboid

  1. Click Add, then pick points in the target view.
  2. Right‑click the primitive item and select Properties to configure its parameters.

Primitive Fitting​

Automatically fit primitives to geometry:

  1. Navigate to Measure → Primitive Tools → Primitive Fitting.
  2. Select the surface to fit.
  3. Choose the primitive type.
  4. Click Apply.

The fitted primitive appears in the vews and is added to the Primitives tool.

Scattered points with the best-fit circle through them and its radius, and scattered points with the best-fit line along their principal axis through the centroid

Measurement Between Primitives​

Measure relationships between primitives:

  1. Navigate to Measure → Primitive Tools → Measurement between Primitives.
  2. Select two primitives.
  3. Click Update.

Surface and Mesh Statistics​

Surface Statistics​

Analyze triangle mesh properties:

  1. Navigate to Measure → Statistics → Surface Statistics → Whole Surface Mesh Statistics.
  2. Select the target surface.
  3. Results include:
StatisticDescription
Vertex CountNumber of vertices
Triangle CountNumber of triangles
Surface AreaTotal area (mm²)
VolumeEnclosed volume (mm³)
BoundsSpatial extent
CenterGeometric center

Volume Mesh Statistics​

For tetrahedral meshes:

  1. Navigate to Measure → Statistics → Volume Mesh Statistics.
  2. Results include element count, volume, and quality metrics.

Mesh Quality Analyzer​

Evaluate mesh element quality:

  1. Navigate to Measure → Analysis → Mesh Quality Analyzer.
  2. Select the surface or volume mesh.
  3. Quality metrics visualized:
    • Aspect ratio — Element shape quality
    • Minimum angle — Smallest triangle angle
    • Jacobian — Element distortion
  4. Color mapping shows quality distribution.
  5. Statistics identify problematic elements.

A well-shaped, a stretched and a sliver triangle with their minimum and maximum angles, edge ratio and equiangle skew

Practical Exercise: Complete Measurement Workflow​

Part 1: Dimensional Measurements​

  1. Load a project with a segmented bone.
  2. Navigate to Measurements tool.
  3. Create three distance measurements at key anatomical points.
  4. Create an angle measurement.
  5. Rename measurements descriptively.

Part 2: Statistical Analysis​

  1. Run Mask Statistics on the bone mask.
  2. Record the volume and surface area.
  3. Run Volume Statistics on the original CT volume.
  4. Restrict analysis to the bone mask region.
  5. Compare mean intensity with literature values.

Part 3: Primitive Fitting​

  1. If you have a cylindrical structure (e.g., femur shaft):
  2. Navigate to Primitive Fitting.
  3. Fit a cylinder to the surface.
  4. Record the fitted radius and axis direction.
  5. Measure distance from other structures to the cylinder.

Part 4: Export Results​

  1. Export measurements to disk.
  2. Export statistics using copy-to-clipboard.
  3. Generate a screenshot with visible measurements.

Best Practices​

Measurement Accuracy​

  • Use appropriate zoom for precise point placement
  • Place points on clearly defined features
  • Consider image resolution limits
  • Validate with known dimensions when possible

Statistical Interpretation​

  • Report units with all values
  • Consider partial volume effects at boundaries
  • Document analysis regions (whole mask vs. subset)
  • Compare with established reference values

Documentation​

  • Name measurements descriptively
  • Export measurements for records
  • Include screenshots showing measurement locations
  • Document any manual adjustments

Troubleshooting​

Measurements not visible​

  • Check visibility in Measurements panel
  • Verify measurement scale (may be too small to see)
  • Ensure you're viewing the correct slice

Statistics seem incorrect​

  • Verify volume spacing is correct
  • Check mask includes intended region
  • Confirm units (some displays show mL vs. mm³)

Primitive fitting fails​

  • Ensure sufficient geometry for fitting
  • Try different fitting region
  • Check surface quality for defects

Next Steps​

Continue with advanced analysis:

See Also​