Iso-Threshold

The Iso-Threshold tool performs thresholding on the active volume object to create a new mask or update existing ones by specifying lower and upper threshold values. This tool also allows you to create a line on one of the slice views and visualize the intensity profile along that line.

Accessing the Tool

1. Navigate to the Segmentation tab in the ribbon.
2. Click Additional in the Create Mask section.
3. Select Iso-Threshold from the menu.

Parameters

Presets

• Description: Pre-configured threshold settings for common materials (available in the Presets group box)

Threshold Adjustment

• Description: Interactive histogram widget for setting minimum and maximum threshold values
• Features:
  • Visual histogram of intensity distribution
  • Adjustable lower and upper threshold markers
  • Real-time preview of thresholded region

Profile Line (Collapsible, Optional)

• Description: Create a line on one of the slice views to visualize the intensity profile (HU or grayscale values) along that line
• Purpose: Helps identify appropriate threshold values by examining intensity variations

Options (Collapsible)

Fill Cavities

• Description: If checked, internal gaps in resulting mask will be filled. If unchecked, no gap filling will be applied
• Type: Checkbox (unchecked by default)

Filter Regions

Checkable group box (unchecked by default) with two modes:

Keep the Largest Region (default):

• Retain only the largest region in the resulting mask, based on its volume

Remove Regions:

• Minimum region size (voxels): 1 to 9,999,999 (default: 2)
• Description: Remove regions that are smaller than the specified size in voxels

Result

Target Mask

• Description: Select the mask object where the segmentation result will be stored
• Type: LineEditComboBox (can create new or select existing mask)

Mode

• Replace: If enabled, the selected mask will be replaced with the segmentation calculated by the current operation (default)
• Merge: If enabled, the segmentation calculated by the current operation will be merged into the selected mask object

Workflow

1. Ensure you have an active volume object.
2. Open the Iso-Threshold tool from the Segmentation tab (under Additional).
3. Optional: Select a preset from the Presets section for common materials.
4. Use the Threshold Adjustment histogram to set lower and upper threshold values:
   • Drag the lower marker to set minimum intensity
   • Drag the upper marker to set maximum intensity
   • View the histogram to understand intensity distribution
5. Optional: Enable and use the Profile Line tool:
   • Draw a line on a slice view
   • Examine the intensity profile along the line
   • Use this information to refine threshold values
6. Configure Options (optional):
   • Enable Fill cavities to fill internal gaps
   • Enable Filter regions and choose:
     • "Keep the largest region" to retain only the biggest connected component
     • "Remove regions" and specify minimum size to filter small regions
7. Configure Result:
   • Select or create the Target Mask
   • Choose Replace or Merge mode
8. Click Apply to create the segmentation.
9. Review the result and adjust threshold values if needed.

How It Works

Iso-threshold (range threshold) applies binary classification based on intensity range:

$$M(x,y,z) = \begin{cases} 1 & \text{if } T_{min} \leq I(x,y,z) \leq T_{max} \\ 0 & \text{otherwise} \end{cases}$$

Where:

• $M(x,y,z)$ is the resulting mask value
• $I(x,y,z)$ is the intensity at voxel position
• $T_{min}$ is the lower threshold (minimum intensity)
• $T_{max}$ is the upper threshold (maximum intensity)

Use Cases

• Surface Extraction: Define the boundary for subsequent surface generation.
• Bone Segmentation: Isolate high-density bone tissue in CT scans.
• Material Boundaries: Identify material interfaces at specific density values.

Relationship to Other Threshold Tools

Tool	Description	Bounds
Iso-Threshold	Range-based thresholding with min/max values	Lower and upper bounds
Threshold	Basic range thresholding (same functionality)	Lower and upper bounds
Multilevel Thresholding	Automatic multi-threshold using Otsu or K-means	Multiple thresholds (N thresholds for N+1 regions)

Note: Iso-Threshold provides the same functionality as the basic Threshold tool, using lower and upper threshold bounds to define an intensity range.

Tips

• Histogram Analysis: Use the Threshold Adjustment histogram to visually identify intensity peaks and valleys
• Profile Line Tool: Use this feature to examine intensity variations along specific paths, helping you determine appropriate threshold values
• Presets: Start with presets for common materials, then fine-tune as needed
• Fill Cavities: Enable this to automatically close internal holes in the segmented region
• Filter Regions: Use "Keep the largest region" to quickly isolate the main object and remove noise
• Replace vs. Merge: Use Replace for new segmentation, Merge to add to existing mask
• Iterative Refinement: Adjust threshold values and reapply to refine the segmentation
• Combine with other tools like Region Growing or Dynamic Region Grow for more sophisticated segmentation

See Also

• Threshold — Range-based thresholding.
• Multilevel Thresholding — Automatic multi-threshold segmentation.
• Segmentation Tab Overview — Overview of all segmentation tools.