Mask Editor
The Mask Editor is an interactive stage that pauses the pipeline to let you review and optionally edit an automatically generated mask (typically a brain mask) before reconstruction continues.
The tab appears in the sidebar with an amber indicator when a gate is active.
When the Mask Editor Appears
A pipeline stage of type interactive generates a preliminary result (e.g. an auto brain mask) and then pauses. The sidebar shows an amber pulse dot on the brain icon, and the Monitor tab shows an amber gate banner.
Click Open Mask Editor in the gate banner to switch to the editor.
Editor Layout
┌────────────────────────────────────────────────────┐
│ Tool palette (left, 64 px) │
├─────────────────┬──────────────────────────────────┤
│ │ Properties panel (right, 220 px) │
│ NiiVue canvas │ │
│ (multiplanar │ Volume Info │
│ grid view) │ Mask Stats │
│ │ Brush Settings │
├─────────────────┤ │
│ Slice scrubber │ │
├─────────────────┴──────────────────────────────────┤
│ [Approve] [Reject] │
└────────────────────────────────────────────────────┘Tools
| Tool | Shortcut | Action |
|---|---|---|
| Brush | B | Paint mask voxels |
| Eraser | E | Erase mask voxels |
| Pan | P | Pan the view without drawing |
| Undo | Ctrl+Z | Undo last brush stroke |
| Zoom In | + | Zoom in |
| Zoom Out | - | Zoom out |
Select a tool from the left palette or use the keyboard shortcut.
Brush Controls
In the Brush Settings section of the properties panel:
- Size — slider to change the brush radius in voxels.
- Opacity — controls how the mask overlay is displayed (display only, does not affect the saved mask).
Slice Navigation
The amber scrubber below the canvas shows your position through the volume. Drag to move to a different slice. The crosshair in all four views updates simultaneously.
Properties Panel
Volume Info
| Field | Description |
|---|---|
| Filename | Source NIfTI filename |
| Dimensions | Voxel matrix size (Nx × Ny × Nz) |
| Voxel size | Physical voxel dimensions in mm |
Mask Statistics
- Masked voxels — total number of non-zero mask voxels.
- Coverage — masked voxels as a percentage of the total volume.
These update live as you paint or erase.
Approve
Click Approve to accept the mask (edited or not) and continue the pipeline. The mask is passed to the next stage as its input. If you edited the mask, the edited flag is set so downstream stages can record that the mask was manually modified.
Reject
Click Reject to fail the gate. The job is marked as failed with reason "Gate rejected by user". You can then retry the stage from the Monitor tab with different auto-mask parameters.
Auto-Approve (Batch Mode)
In batch mode, stages with auto_approve: true skip the mask editor entirely and accept the auto-generated mask without pausing. See Batch Mode →.