Getting Started

This guide walks you through using the Adaptive Brush for the first time.

Prerequisites

  • 3D Slicer 5.10 or later

  • A volume loaded (CT, MRI, etc.)

Tutorial

Step 1: Open Sample Data

Go to File → Download Sample Data or select the Sample Data module. This provides built-in datasets for practice.

Open Sample Data

Step 2: Volume Loaded

After clicking on a dataset (e.g., MRBrainTumor1), the volume loads and displays in the slice views. This brain MRI contains a visible tumor.

Volume Loaded

Step 3: Open Segment Editor

Navigate to the Segment Editor module using the module selector or by pressing the Segment Editor button in the toolbar.

Open Segment Editor

Step 4: Create Segment

Create a new segmentation and add a segment for the structure you want to segment. Click ‘Add’ to create a new segment.

Create Segment

Step 5: Select Adaptive Brush

Click on the Adaptive Brush effect in the effects toolbar. The options panel will show algorithm selection and brush settings.

Select Adaptive Brush

Step 6: Configure Settings

Preset: Select ‘MRI T1+Gd Tumor’ preset for contrast-enhanced tumors. Presets configure intensity thresholds automatically.

Algorithm: Select Watershed - a good general-purpose choice for tumors.

Brush Radius: Adjust with Shift + scroll wheel to match your target.

Threshold Zone: Inner circle where intensities are sampled. Smaller zone (30%) = stricter matching; larger zone (70%) = more variation. Adjust with Ctrl + Shift + scroll wheel.

Configure Settings

Step 7: Navigate to Region

Use the slice sliders or scroll wheel to navigate to the region you want to segment. The brush preview shows where painting will occur.

Navigate to Region

Step 8: Paint

Click on the slice view to paint. The adaptive brush automatically detects edges and segments the region based on intensity similarity. The red overlay shows the segmented area.

Paint

Step 9: Refine Segmentation

Building up: Click multiple times to extend the segmentation. Each click adds the adaptively-detected region.

Erase mode: Hold Ctrl (or Middle+Left-click) to remove areas you over-segmented. The brush will adaptively detect what to remove.

Sampling settings (in Advanced): Control how intensities are sampled:

  • Mean ± Std: Uses mean intensity with standard deviation range

  • Percentile: Uses intensity percentiles (more robust to outliers)

  • Gaussian weighting: Weights center pixels more heavily

Edge sensitivity: Higher values stop at weaker edges; lower values allow more permissive segmentation.

Refine Segmentation

Step 10: View in 3D

The 3D view (bottom-right) shows your segmentation as a surface. The segmented region appears as a colored surface that can be rotated and examined.

View in 3D

Tips for Best Results

Keyboard Shortcuts

Action

Shortcut

Adjust brush size

Shift + scroll wheel

Adjust threshold zone

Ctrl + Shift + scroll wheel

Erase mode

Ctrl + click or Middle + Left-click

Brush Size

  • Start with a brush slightly smaller than your target region

  • Use multiple smaller strokes for complex shapes

Edge Sensitivity

  • Higher sensitivity = stricter edge detection (stops at faint edges)

  • Lower sensitivity = more permissive (may leak beyond boundaries)

Algorithm Selection

  • Watershed: Good general-purpose choice for most tissues

  • Geodesic Distance: Fast, good for structures with clear edges

  • Threshold Brush: Fastest, simple intensity-based painting

Presets

  • Use presets to quickly configure settings for common tissue types

  • Presets set appropriate thresholds based on imaging modality

Next Steps

This documentation was auto-generated on 2026-01-31. Screenshots reflect the current UI.