Volume Statistics
The Volume Statistics tool calculates grayscale-based statistics for the active volume dataset and generates a histogram of pixel intensities. Statistics can be filtered by mask regions and computed for individual slices or the entire volume.
Accessing the Tool
- Navigate to the Measure tab in the ribbon
- Click the Volume Statistics button in the Statistics section
Overview
Calculate grayscale-based statistics for the active volume dataset and generate a histogram of pixel intensities, with an option to filter data by selecting corresponding masks.
An active volume dataset must be loaded in the project. Mask-based filtering requires at least one mask object.
User Interface
Description
Displays: "Calculate grayscale-based statistics for the active volume dataset and generate a histogram of pixel intensities, with an option to filter data by selecting corresponding masks."
Options
| Control | Description |
|---|---|
| Target | Select the data source for statistics calculation |
| Slice | Choose which slice(s) to analyze |
Target Options
| Option | Description |
|---|---|
| Active volume | Calculate statistics for all pixels in the active volume dataset |
| Active mask | Calculate statistics for pixels within the active mask only |
| Visible masks | Calculate statistics for pixels within the union of all visible masks |
Slice Options
| Option | Description |
|---|---|
| Current Plane 1 (YZ) slice | Analyze only the current Plane 1 (YZ) slice |
| Current Plane 2 (XZ) slice | Analyze only the current Plane 2 (XZ) slice |
| Current Plane 3 (XY) slice | Analyze only the current Plane 3 (XY) slice |
| All slices | Analyze the entire volume (default) |
Histogram Chart
The histogram is drawn in the Interactive Histogram Chart. Right-click the chart to reach its display options, its interval actions, and its export actions.
| Setting | Description |
|---|---|
| Scale | Linear or logarithmic frequency axis |
| Graph | Bars, line, or filled line |
| Binning | Groups the bins before they are drawn |
Drag across the chart to mark a gray value range. The marked range reports its borders, mean, standard deviation, total, and share of the analyzed data, which complements the tables below with a value for a region of the distribution.
Information Table
The group is titled Information and displays context about the analysis:
| Field | Description |
|---|---|
| Volume | Name of the active volume dataset |
| Mask | Name of the mask (if mask filtering is used) |
| Slice | Which slice or "All slices" |
Whole Volume Statistics Table
The group is titled Whole volume statistics and lists the calculated statistics for the analyzed region as Name and Value rows, in this order:
| Statistic | Description |
|---|---|
| Mean gray value | Average gray value |
| Median gray value | Middle value when the gray values are sorted |
| Std. dev. of gray values | Measure of gray value variation |
| Voxel count | Number of voxels analyzed |
| Volume (mm³) | Physical volume of the analyzed region |
| Volume fraction (%) | Analyzed volume relative to the total image volume |
| Min. gray value / Max. gray value | Lowest and highest gray value |
| Min. gray value index / Max. gray value index | Voxel index where each extreme occurs |
| Variance | Square of the standard deviation |
| RMS | Root mean square of the gray values |
| Skewness | Measure of distribution asymmetry |
| Kurtosis | Measure of distribution tail weight |
| Uniformity | Uniformity of the gray values |
| Entropy | Entropy of the gray value distribution |
| Mean of positive pixels | Mean over the positive gray values only |
| Uniformity of positive pixels | Uniformity over the positive gray values only |
| 5% / 25% / 50% / 75% / 95% quantile value | Gray value below which that share of the voxels falls |
A single slice has no volume, so Voxel count becomes Pixel count, Volume (mm³) becomes Area (mm²), and Volume fraction (%) becomes Area fraction (%).
Volume Statistics Within Individual Visible Mask
When the Visible masks target is selected, an additional table titled Volume statistics within individual visible mask shows the statistics for each visible mask separately.
Workflow
Basic Statistics Calculation
- Ensure a volume dataset is active
- Open the Volume Statistics tool
- Select Active volume as the target
- Choose All slices to analyze the complete volume
- Statistics are calculated and displayed automatically
- The histogram updates to show the intensity distribution
Masked Region Statistics
- Create or activate a mask covering the region of interest
- Open the Volume Statistics tool
- Select Active mask or Visible masks as the target
- Statistics are calculated only for voxels within the mask
Slice-Specific Statistics
- Navigate to the slice of interest
- Open the Volume Statistics tool
- Select the corresponding slice option
- Statistics reflect only that slice's pixel values
Export
Click the Export... button to save results. Export options include:
- CSV file: Tabular statistics data, followed by the histogram at its full resolution
- PDF Report: Formatted report with statistics, histogram, and optional snapshots
The PDF report includes:
- Analysis settings (target, slice, histogram binning, frequency axis scaling)
- Information table
- Statistics table
- Histogram visualization
- Histogram data table
The histogram picture in the report always shows the whole gray value range, so a zoom you set on screen does not change it. The histogram data table groups the gray values into as many rows as the chart draws bars, so that it fits into the report. Each row states the gray value range it covers, in a Grayvalue from and a Grayvalue to column, and the pixel count next to it is the exact number of pixels within that range.
The histogram in the CSV file and the Export as CSV... action in the chart context menu are both written at the full resolution of the analyzed region, not at the resolution the chart is drawn with. For an integer image this resolves every gray value, so each row carries one gray value and its pixel count. A floating point image has no gray value step, so each row covers a range of gray values and states it in a Grayvalue from and a Grayvalue to column. Use either file when the distribution is analysed further, and the report table when it documents what the chart shows. The chart can also be saved as a picture from the same menu; see Exporting the Chart.
If the active volume changes while the file dialog is open, the histogram can no longer be recomputed for the volume the chart shows. The export is then cancelled with a message instead of writing a file, so a report never carries a distribution measured on a different volume.
Use Cases
Image Quality Assessment
Analyze mean, standard deviation, and histogram shape to assess image quality and noise levels.
Tissue Characterization
Compare statistics across different masked regions to characterize tissue types.
Threshold Determination
Use histogram visualization and statistics to determine appropriate segmentation thresholds.
Comparative Analysis
Compare statistics between different volumes or time points for longitudinal studies.
Related Tools
| Page | Description |
|---|---|
| Interactive Histogram Chart | Reading, navigating, and evaluating the histogram chart |
| Histogram | Focused histogram visualization without statistics tables |
| Volume Similarity Statistics | Compare two volumes |
| Mask Statistics | Shape and intensity statistics for masks |