Mask Statistics
The Mask Statistics tools provide statistical analysis of mask objects in your workspace. This dropdown menu in the Measure ribbon tab contains five tools for analyzing masks from different perspectives.
If you're working with defect detection, see Void/Inclusion Analysis which provides the same measurements and report sections but with defect-oriented wording (for example, "voids", "inclusions", or "defects") instead of generic mask-label terms.
Accessing Mask Statistics
- Navigate to the Measure ribbon tab
- Click the Mask Statistics dropdown button
- Select the appropriate analysis tool
- Whole Mask/Slice: Analyze complete masks or slice-by-slice distribution
- Per-Region: Identify and analyze individual disconnected components in binary masks
- Per-Label: Analyze multi-label segmentation results (e.g., from AI segmentation)
- 3D Preview tools: Add surface mesh statistics to voxel-based analysis
Whole Mask/Slice Statistics
Compute statistics for the complete mask volume or analyze individual slices along any axis.
Description
This tool calculates shape and intensity statistics for entire mask objects or on a per-slice basis. Results are displayed in tabular format with options to select which statistics to compute.
Target Selection
| Option | Description |
|---|---|
| Active mask | Analyze only the currently selected mask |
| Visible masks | Analyze all masks that are currently visible |
Slice Analysis Mode
| Option | Description |
|---|---|
| Whole mask | Compute statistics for the entire 3D volume |
| X slices (Sagittal) | Compute statistics for each YZ slice |
| Y slices (Coronal) | Compute statistics for each XZ slice |
| Z slices (Axial) | Compute statistics for each XY slice |
Histogram Settings
| Control | Description |
|---|---|
| Number of bins | Number of histogram bins (10-1000, default: 100) |
Output Tables
| Table | Description |
|---|---|
| Information | General mask properties (name, dimensions, spacing) |
| Statistics | Selected statistics values for the mask |
| Individual visible mask statistics | Per-mask breakdown when analyzing visible masks |
Toolbar
| Button | Description |
|---|---|
| Edit Statistics... | Open dialog to select which statistics to compute |
| Export... | Export results to PDF or CSV |
Per-Region Mask Statistics
Analyze connected regions (components) within a mask with region-by-region statistics.
Description
Automatically detects and labels connected regions within a binary mask, then computes statistics for each individual region. Includes descriptive statistics summarizing all regions.
Target Selection
| Option | Description |
|---|---|
| Active mask | Analyze connected regions in the currently selected mask |
| Visible masks | Analyze connected regions in all visible masks |
Histogram Settings
| Control | Description |
|---|---|
| Y-axis mode | Frequency (linear) or Frequency (log scale) |
| Number of bins | Histogram resolution (10-1000, default: 100) |
Output Tables
This tool produces three separate results tables:
| Table | Description |
|---|---|
| Region Statistics | Individual statistics for each connected region |
| Descriptive Statistics | Min, Max, Mean, and Std Dev across all regions for each statistic |
| Whole Mask Statistics | Statistics computed for the entire mask (all regions combined) |
Region Table Columns
- Region ID: Unique identifier for each connected region
- Voxel Count: Number of voxels in the region
- Volume: Physical volume (mm³)
- Centroid X/Y/Z: Center of mass position
- Intensity statistics: Min, Max, Mean, Median, Standard Deviation
- Shape metrics: Roundness, Compactness, Elongation, Flatness
Histogram Display
Interactive histogram showing intensity distribution:
- Toggle between count and percentage mode
- Adjustable bin count for resolution control
- Visual display of intensity spread across regions
Annotation Feature
Each region can be annotated with a text label that appears in the 3D view.
Toolbar
| Button | Description |
|---|---|
| Edit Statistics... | Select which statistics to compute |
| Add Annotation | Add text annotation to selected region |
| Export... | Export results to PDF or CSV |
Per-Label Mask Statistics
Analyze multi-label segmentation masks with label-by-label statistics.
Description
Computes statistics for each unique label value in a multi-label mask. Ideal for analyzing AI segmentation results where different structures have different label values.
Target Selection
| Option | Description |
|---|---|
| Active mask | Analyze labels in the currently selected mask |
| Visible masks | Analyze labels in all visible masks |
Label Display
Each label is displayed with:
- Label ID: The numeric label value
- Color: Color from the lookup table (if assigned)
- Name: Label name from lookup table (if available)
Histogram Settings
| Control | Description |
|---|---|
| Y-axis mode | Frequency (linear) or Frequency (log scale) |
| Number of bins | Histogram resolution (10-1000) |
Output Tables
This tool produces three separate results tables:
| Table | Description |
|---|---|
| Label Statistics | Individual statistics for each label value |
| Descriptive Statistics | Min, Max, Mean, and Std Dev across all labels |
| Whole Mask Statistics | Statistics for the entire mask (all labels combined) |
Label Table Columns
- Label Value: The numeric ID of the label
- Label Name: Name from lookup table (if assigned)
- Voxel Count: Number of voxels with this label
- Volume: Physical volume (mm³)
- Volume Fraction: Percentage of total mask volume
- All selected statistics: Same as Per-Region analysis
Lookup Table Integration
When a lookup table is assigned to the mask:
- Labels display their assigned names
- Labels display their assigned colors
- Unknown labels show as "Unknown" with gray color
Annotation Feature
Each label can be annotated with a text label that appears in the 3D view.
Toolbar
| Button | Description |
|---|---|
| Edit Statistics... | Select which statistics to compute |
| Add Annotation | Add text annotation to selected label |
| Export... | Export results to PDF or CSV |
Per-Region Mask 3D Preview Statistics
Generate 3D surface meshes for connected regions and compute surface-based statistics.
Description
Creates a 3D surface mesh for each connected region in the mask and computes mesh-based statistics. Provides interactive 3D visualization with color-coded regions.
Target Selection
| Option | Description |
|---|---|
| Active mask | Analyze the currently selected mask |
Processing
- Automatically detects connected regions
- Generates a surface mesh for each region
- Computes mesh-based statistics
- Displays colored regions in 3D preview
3D Preview Features
| Feature | Description |
|---|---|
| Color coding | Each region displayed in a distinct color |
| Interactive rotation | Rotate, zoom, and pan the 3D view |
| Region selection | Click to select individual regions |
| Visibility toggle | Show/hide individual regions |
Surface Mesh Statistics
In addition to voxel-based statistics, surface mesh statistics include:
- Surface area (mm²)
- Mesh volume (mm³)
- Number of vertices
- Number of faces/triangles
- Surface-to-volume ratio
Toolbar
| Button | Description |
|---|---|
| Export Mesh... | Export selected region mesh as STL/OBJ |
| Export... | Export statistics to PDF or CSV |
Per-Label Mask 3D Preview Statistics
Generate 3D surface meshes for each label value and compute surface-based statistics.
Description
Creates a 3D surface mesh for each label in a multi-label mask and computes mesh-based statistics. Provides interactive 3D visualization with color-coded labels.
Target Selection
| Option | Description |
|---|---|
| Active mask | Analyze the currently selected mask |
Processing
- Extracts each unique label value
- Generates a surface mesh for each label
- Applies lookup table colors (if available)
- Displays labeled surfaces in 3D preview
3D Preview Features
| Feature | Description |
|---|---|
| Lookup table colors | Labels use colors from assigned lookup table |
| Interactive rotation | Rotate, zoom, and pan the 3D view |
| Label selection | Click to select individual labels |
| Visibility toggle | Show/hide individual labels |
| Label names | Display label names from lookup table |
Surface Mesh Statistics
Same as Per-Region 3D Preview:
- Surface area (mm²)
- Mesh volume (mm³)
- Number of vertices
- Number of faces/triangles
- Surface-to-volume ratio
Toolbar
| Button | Description |
|---|---|
| Export Mesh... | Export selected label mesh as STL/OBJ |
| Export... | Export statistics to PDF or CSV |
Available Statistics
All mask statistics tools can compute the following measurements. Use Edit Statistics... to select which statistics to include.
Default Statistics (Computed by Default)
| Statistic | Description |
|---|---|
| Voxel Count | Number of voxels in the region/label |
| Volume | Physical volume in mm³ |
| Volume Fraction | Percentage of total mask volume |
| Perimeter | Boundary perimeter length |
| Min Intensity | Minimum voxel intensity value |
| Max Intensity | Maximum voxel intensity value |
| Mean Intensity | Average intensity across voxels |
| Median Intensity | Middle intensity value |
| Standard Deviation | Intensity variation measure |
Shape Statistics
| Statistic | Description |
|---|---|
| Equivalent Diameter | Diameter of sphere with equivalent volume |
| Roundness | Circularity measure (0-1, 1 = perfect sphere) |
| Compactness | Shape compactness (0-1) |
| Elongation | Ratio of primary to secondary axis lengths |
| Flatness | Ratio of secondary to tertiary axis lengths |
| Shape Factor | Overall shape irregularity measure |
Position Statistics
| Statistic | Description |
|---|---|
| Centroid X | X-coordinate of center of mass |
| Centroid Y | Y-coordinate of center of mass |
| Centroid Z | Z-coordinate of center of mass |
| PCA Deviation X | Deviation along first principal axis |
| PCA Deviation Y | Deviation along second principal axis |
| PCA Deviation Z | Deviation along third principal axis |
| Projected Size X/Y/Z | Size projected onto each axis |
| Projected Area XY/XZ/YZ | Area projected onto each plane |
Intensity Percentiles
| Statistic | Description |
|---|---|
| Histogram 5% Quantile | 5th percentile intensity |
| Histogram 25% Quantile | 25th percentile (Q1) |
| Histogram 50% Quantile | 50th percentile (median) |
| Histogram 75% Quantile | 75th percentile (Q3) |
| Histogram 95% Quantile | 95th percentile intensity |
Descriptive Statistics Table
For Per-Region and Per-Label tools, the Descriptive Statistics table summarizes all regions/labels:
| Column | Description |
|---|---|
| Statistic | Name of the measured statistic |
| Min | Minimum value across all regions/labels |
| Max | Maximum value across all regions/labels |
| Mean | Average value across all regions/labels |
| Std Dev | Standard deviation across all regions/labels |
This table helps identify:
- Range of values (Min to Max)
- Typical values (Mean)
- Variation in the data (Std Dev)
Export Options
All statistics can be exported via the toolbar:
| Format | Description |
|---|---|
| PDF Report | Complete report with tables, charts, and optional 3D scene |
| CSV | Comma-separated values for spreadsheet import |
PDF Report Contents
When exporting to PDF, you can include:
- Analysis metadata and settings summary
- Requested metrics list
- All statistics tables
- Histogram visualizations
- Histogram data tables (per selected metric)
- 3D scene with labeled regions/labels
- Snapshots of views
- Custom header/footer and metadata
If the source workflow is Void/Inclusion analysis, the report uses defect-oriented wording (void/inclusion/defect) instead of mask-label terminology.
See PDF Report Generation for detailed export options.
Tips
- Per-Region is best for analyzing individual objects within a single binary mask
- Per-Label is ideal for multi-structure segmentations (e.g., AI segmentation results)
- 3D Preview tools add surface mesh statistics not available in voxel-based analysis
- Use the histogram to identify intensity distribution patterns
- The Descriptive Statistics table quickly shows data spread across regions/labels
- Export to Excel for further statistical analysis in spreadsheet software
- Use annotations to mark specific regions/labels of interest in 3D
Related Tools
- Compare Masks — Overlap statistics between two masks
- Volume Statistics — Statistics for volume datasets
- Surface Statistics — Statistics for surface meshes