# 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.

```{image} /_static/screenshots/workflows/getting_started_001_open_sample_data.png
:alt: Open Sample Data
:width: 100%
```

### 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.

```{image} /_static/screenshots/workflows/getting_started_002_volume_loaded.png
:alt: Volume Loaded
:width: 100%
```

### 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.

```{image} /_static/screenshots/workflows/getting_started_003_open_segment_editor.png
:alt: Open Segment Editor
:width: 100%
```

### 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.

```{image} /_static/screenshots/workflows/getting_started_004_create_segment.png
:alt: Create Segment
:width: 100%
```

### 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.

```{image} /_static/screenshots/workflows/getting_started_005_select_adaptive_brush.png
:alt: Select Adaptive Brush
:width: 100%
```

### 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**.

```{image} /_static/screenshots/workflows/getting_started_006_configure_settings.png
:alt: Configure Settings
:width: 100%
```

### 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.

```{image} /_static/screenshots/workflows/getting_started_007_navigate_to_region.png
:alt: Navigate to Region
:width: 100%
```

### 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.

```{image} /_static/screenshots/workflows/getting_started_008_paint.png
:alt: Paint
:width: 100%
```

### 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.

```{image} /_static/screenshots/workflows/getting_started_009_refine_segmentation.png
:alt: Refine Segmentation
:width: 100%
```

### 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.

```{image} /_static/screenshots/workflows/getting_started_010_view_in_3d.png
:alt: View in 3D
:width: 100%
```

## 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

- Explore different [algorithms](algorithms.md)
- Use the [Parameter Wizard](parameter_wizard.md) for optimization
- Create [recipes](recipes.md) for reproducible segmentation

---

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