neuroim2 (version 0.8.5)

searchlight_shape_functions: Convenience shape generators for resampled_searchlight()

Description

Helpers that return ready-to-use shape_fun callbacks for resampled_searchlight(), covering a few sensible non-spherical defaults.

Usage

ellipsoid_shape(scales = c(1, 1, 1), jitter = 0)
cube_shape()
blobby_shape(drop = 0.3, edge_fraction = 0.7)

Value

A function suitable for the shape_fun argument of

resampled_searchlight().

Arguments

scales

Length-3 positive numeric vector scaling the x/y/z axes relative to a sphere (for ellipsoid_shape). Values >1 stretch; <1 compress.

jitter

Non-negative numeric; standard deviation of multiplicative Gaussian noise applied to scales each draw (ellipsoid).

drop

Numeric in [0,1]; probability of dropping a voxel (blobby).

edge_fraction

Numeric in (0,1]; fraction of farthest voxels (by Euclidean distance from the center, in voxel units) considered "edge" and eligible for random dropping (blobby).

Details

Each returned function has signature function(mask, center, radius, iter, nonzero) and should return an \(n \times 3\) integer coordinate matrix. The coordinates are later converted to a ROIVolWindow internally.

Examples

mask <- read_vol(system.file("extdata", "global_mask_v4.nii", package="neuroim2"))

# Ellipsoid stretched along z with modest per-iteration jitter
sl_ellip <- resampled_searchlight(mask, radius = 6,
                                   shape_fun = ellipsoid_shape(scales = c(1, 1, 1.4),
                                                              jitter = 0.1))

# Simple axis-aligned cube (Chebyshev ball)
sl_cube <- resampled_searchlight(mask, radius = 5, shape_fun = "cube")

# Blobby sphere with 40% dropout on boundary voxels
sl_blob <- resampled_searchlight(mask, radius = 6,
                                 shape_fun = blobby_shape(drop = 0.4, edge_fraction = 0.6))