Viewer
The Viewer tab displays reconstructed NIfTI volumes using NiiVue — a WebGL2-based medical image viewer. It opens automatically when a reconstruction stage completes.
Layout
The viewer shows four panes in a 2×2 grid:
- Axial (top-left)
- Coronal (top-right)
- Sagittal (bottom-left)
- 3D (bottom-right, when a volume is loaded)
Click any pane to bring it into focus. The crosshair updates across all views simultaneously.
Loading Volumes
Volumes are loaded automatically when:
- A reconstruction stage completes and the file watcher detects a new
.niior.nii.gzin the output directory. - You drag and drop a NIfTI file onto any viewer pane.
The sidebar on the right lists all loaded volumes. Click a volume name to select it, or use the Remove button to unload it.
Volume Controls
Each volume in the sidebar shows:
- Colormap — click to change. Common options:
gray,hot,cool,viridis,jet. - Display range — drag the min/max handles to adjust window/level.
- Opacity — slider to control overlay transparency (for overlays).
Slice Scrubber
A horizontal scrubber below each view shows the current slice position. Drag to scroll through slices, or use the keyboard:
| Key | Action |
|---|---|
↑ / ↓ | Move crosshair in the superior/inferior direction |
+ / - | Increase/decrease slice |
R | Reset to centre slice |
C | Toggle crosshairs visible |
Overlays
To add an overlay (e.g. a mask or sensitivity map):
- Click Add Overlay in the sidebar.
- Select a NIfTI file.
- Adjust opacity and colormap in the overlay's controls.
Overlays are layered above the base volume. Multiple overlays are supported.
View Modes
Use the view mode selector (top-right of the viewer) to switch between:
| Mode | Description |
|---|---|
| Multiplanar | 2×2 grid with axial, coronal, sagittal, and 3D |
| Axial only | Single large axial view |
| Coronal only | Single large coronal view |
| Sagittal only | Single large sagittal view |
Auto-Switch
The viewer tab is activated automatically when:
- A reconstruction job completes.
- The file watcher detects a new
.niior.nii.gzoutput file.
You can disable auto-switch in Settings → Viewer → Auto-switch to Viewer on Completion.