Docs › Menu reference
[Region Edit] Menu
The [Region Edit] menu refines binary region masks in place through 3D morphological cleanup, slice-intensity filtering, connected-component tools, and multi-region Boolean or parcellation operations. Single-region edits modify the highlighted row by default and can be reverted with [Regions][Undo] (Ctrl+Shift+Z), while the Regions menu, Region Move menu, and ROI-Based Fiber Tracking cover file management, spatial shifts, and tracking roles.
Checked regions
| Menu item | Behavior |
|---|---|
| Checkable toggle (off by default) that applies single-region edits to all checked regions instead of only the highlighted row. Separate still splits only the first checked region, and Region set operations always process all checked regions. |
Dilation and erosion
| Menu item | Behavior |
|---|---|
Shortcut: Ctrl+Shift+D. Expands the region mask outward by 1 voxel in 3D, thickening thin tracking barriers or bridging single-voxel boundary gaps. |
|
Expands the region mask outward in 3D by a chosen radius (1–100 voxels, default 10). Distance is measured in voxels rather than mm, so physical expansion scales with the region’s voxel size. |
|
Expands the region outward by 1 voxel only where boundary neighbors meet an intensity cutoff on the active slice (pre-filled with Otsu’s threshold). Positive values grow into brighter voxels; negative values grow into darker voxels. |
|
Shrinks the region inward by 1 voxel only along borders that meet an intensity cutoff on the active slice (pre-filled with Otsu’s threshold; positive for brighter voxels, negative for darker voxels). (Spelled Erosioin By Threshold... in the menu.) |
|
Shortcut: Ctrl+Shift+E. Shrinks the region mask inward by 1 voxel in 3D. Thin 1–2 voxel sheets or small islands can vanish completely; use [Regions][Undo] if over-eroded. |
Opening and closing
| Menu item | Behavior |
|---|---|
| Shortcut: Ctrl+Shift+O. Removes thin exterior protrusions, narrow bridges, and stray boundary spurs while preserving the main mask shape without uniform shrinkage. | |
| Shortcut: Ctrl+Shift+C. Fills small internal holes, narrow gaps, and boundary clefts without uniformly expanding the outer mask surface. |
Smoothing and mask structure
| Menu item | Behavior |
|---|---|
| Shortcut: Ctrl+Shift+S. Smooths jagged, stair-stepped 3D boundaries on the region mask. Because Ctrl+Shift+S is shared with [Regions][Save Checked Regions to one 4D NIFTI…], click this menu item directly if the shortcut conflicts. | |
| Shortcut: Ctrl+Shift+F. Keeps only the single largest connected 3D piece of the region and deletes all smaller disconnected islands. Avoid using on bilateral or multi-part masks unless smaller pieces should be discarded. | |
Shortcut: Ctrl+Shift+P. Splits disconnected 3D pieces into up to 256 new checked regions (<Name>_1, <Name>_2, …) while leaving the original region intact. Even with Modify All Checked enabled, only the first checked region is split. |
|
| Shortcut: Ctrl+Shift+N. Inverts the region mask across the full 3D volume, turning background voxels into foreground and vice versa. Intersect the result with a brain mask (via [Region Edit][All Intersect First]) to exclude outer background. |
Threshold
| Menu item | Behavior |
|---|---|
| Shortcut: Ctrl+Shift+T. Filters existing voxels inside the region by active-slice intensity (pre-filled with Otsu’s threshold; positive values keep brighter voxels, negative values keep darker voxels). Never adds exterior voxels; use [Regions Misc][New Region From Thresholding…] for whole-slice thresholding. |
Region set operations
All five operations require at least two checked regions and process them in top-to-bottom table order on the topmost checked region’s voxel grid (resampling any lower region on a different grid and clearing its undo history).
| Menu item | Behavior |
|---|---|
| Shortcut: Ctrl+Shift+1. Replaces each lower checked region in place with its overlap against the topmost checked region, leaving the topmost region unchanged. Requires at least 2 checked regions. | |
| Shortcut: Ctrl+Shift+2. Subtracts the topmost checked region from each lower checked region in place, leaving the topmost region unchanged. Requires at least 2 checked regions. | |
| Shortcut: Ctrl+Shift+3. Subtracts all lower checked regions from the topmost checked region in place (for example, to carve out ventricles or lesions), leaving lower regions unchanged. Requires at least 2 checked regions. | |
| Shortcut: Ctrl+Shift+4. Clips, expands, and smooths all lower checked regions into a gap-free, non-overlapping parcellation filling the topmost checked region (lower rows take precedence where masks overlap; topmost stays unchanged). Requires at least 2 checked regions. | |
| Shortcut: Ctrl+Shift+5. Adjusts shared borders across all checked regions (including the topmost) to follow local tissue intensities on the active slice, producing non-overlapping masks. Requires at least 2 checked regions and an active slice. |