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Dilate Atlas Parcellation Boundaries

Source: R/dilate_parcels.R
dilate_atlas.Rd

Expands the boundaries of brain atlas parcels by dilating them into adjacent unassigned voxels within a specified mask. This is useful for filling small gaps between parcels or extending parcels into neighboring regions.

Usage

dilate_atlas(atlas, mask, radius = 4, maxn = 50)

Arguments

atlas

An object of class "atlas" containing the parcellation to be dilated

mask

A binary mask (NeuroVol object) specifying valid voxels for dilation. Dilation will only occur within non-zero mask values. May also be a TemplateFlow space identifier (string) or list of `get_template()` arguments, which will be resolved to a NeuroVol via `.resolve_template_input()`.

radius

Numeric. The maximum distance (in voxels) to search for neighboring parcels when dilating. Default: 4

maxn

Integer. Maximum number of neighboring voxels to consider when determining parcel assignment. Default: 50

Value

A ClusteredNeuroVol object containing the dilated parcellation. The object maintains the original label mappings but may include additional voxels in existing parcels.

Details

The dilation process:

  • Identifies unassigned voxels that lie within the mask

  • For each unassigned voxel, finds assigned voxels within radius (Euclidean distance, in voxel units)

  • Assigns the voxel to a parcel by inverse-distance-weighted voting over those neighbours (up to maxn of them)

  • Leaves a voxel unassigned when no parcel lies within radius, so distant in-mask voxels (e.g. cerebellar grey matter for a cortical atlas) are not absorbed

  • Respects mask boundaries to prevent dilation into unwanted regions

The function uses a k-d tree implementation (via Rnanoflann) for efficient nearest neighbor searches in 3D space.

References

The algorithm uses efficient k-d tree based nearest neighbor searches for spatial queries in 3D voxel space.

See also

get_template_brainmask for creating appropriate masks from TemplateFlow

Examples

if (FALSE) { # \dontrun{
# Load an atlas
atlas <- get_aseg_atlas()

# Create or load a brain mask
mask <- get_template_brainmask()

# Dilate the atlas within the mask
dilated <- dilate_atlas(atlas, mask, radius = 4)

# More conservative dilation with fewer neighbors
dilated_conservative <- dilate_atlas(atlas, mask, radius = 2, maxn = 20)
} # }