neuroim2 (version 0.8.5)

cgb_filter: Correlation-guided bilateral filtering (convenience wrapper)

Description

High-level interface that builds a correlation-guided bilateral (CGB) graph with sensible defaults (similar to the bilateral filter interface) and immediately applies it to smooth the data.

Usage

cgb_filter(
  runs,
  mask = NULL,
  spatial_sigma = 2,
  window = NULL,
  corr_map = c("power", "exp", "soft"),
  corr_param = 2,
  topk = 16L,
  passes = 1L,
  lambda = 1,
  leave_one_out = FALSE,
  run_weights = NULL,
  add_self = TRUE,
  time_weights = NULL,
  confounds = NULL,
  robust = c("none", "huber", "tukey"),
  robust_c = 1.345,
  return_graph = FALSE
)

Value

If leave_one_out=FALSE, a smoothed NeuroVec. If

leave_one_out=TRUE, a list of smoothed NeuroVec. When

return_graph=TRUE, returns a list with elements result and

graph (single object or lists accordingly).

Arguments

runs

A NeuroVec or a list of NeuroVec.

mask

Optional LogicalNeuroVol/NeuroVol or logical array for spatial masking. Defaults to in-mask voxels.

spatial_sigma

Spatial Gaussian sigma in mm. Used both for weighting and, when window is NULL, to auto-choose the neighborhood size.

window

Integer half-width of the cubic neighborhood. If NULL, it is computed as ceiling(2 * spatial_sigma / min(spacing)) and at least 1.

corr_map

Mapping from pooled correlation to affinity; one of "power", "exp", or "soft". Defaults to "power".

corr_param

Parameter for corr_map (gamma/tau/r0 respectively).

topk

Keep strongest k neighbors (0 keeps all). Defaults to 16.

passes

Number of smoothing passes (>=1). Defaults to 1.

lambda

Blend factor in [0,1] per pass. Defaults to 1 (pure diffusion).

leave_one_out

If TRUE and multiple runs are supplied, builds LORO graphs and returns a list of smoothed runs.

run_weights

Optional numeric weights per run for Fisher-z pooling.

add_self

Logical; add a tiny self-edge before normalization.

time_weights

Optional list (or single vector) of per-run time weights.

confounds

Optional list (or single matrix) of per-run confounds.

robust

One of "none", "huber", or "tukey".

robust_c

Tuning constant for robust weights.

return_graph

Logical; if TRUE, also return the graph(s) alongside the smoothed data.

Details

This is a convenience front-end to cgb_make_graph and cgb_smooth with a bilateral-like interface: - If window is NULL, it is chosen as ceiling(2 * spatial_sigma / min(spacing)) (at least 1). Larger windows allow correlations over more distant neighbors, at the cost of extra compute and memory. - spatial_sigma (in mm) controls how quickly spatial weights fall with distance. Small values emphasize very local structure; larger values mix information over a wider spatial footprint. - corr_map and corr_param set how pooled correlations are turned into edge weights: * "power": a(r) = r^gamma for r > 0. Larger gamma (e.g., 3-4) strongly emphasizes high correlations and produces more edge-preserving, patchy smoothing; smaller values (e.g., 1-2) behave more like standard correlation-weighted smoothing. * "exp": Gaussian on 1 - r with scale tau. Small tau keeps only very similar time-series; larger tau makes the filter closer to a spatial Gaussian while still respecting sign. * "soft": a(r) = max(r - r0, 0). Increasing r0 discards more weak correlations and tends to sharpen edges but can make the result more piecewise-constant. - topk limits each voxel to at most k strongest neighbors. Smaller topk yields sparser, more anisotropic graphs (cheaper but sometimes less smooth); larger topk increases mixing and memory. - passes and lambda control diffusion strength. With lambda = 1, each pass applies pure graph diffusion; multiple passes compound smoothing. Choosing lambda < 1 blends each pass with the identity and can prevent over-smoothing when using more passes. - Setting leave_one_out = TRUE for multi-run inputs builds a separate graph for each run that excludes its own correlations, which reduces information leakage in cross-validation or decoding workflows. - time_weights, confounds, and robust/robust_c adjust how time-points contribute to the correlation estimates. Down- weighting high-motion/high-DVARS frames (via make_time_weights and robust != "none") will typically yield smoother, less noisy graphs but can also reduce effective temporal degrees of freedom. - Use return_graph = TRUE when you plan to reuse the constructed graph(s) with cgb_smooth or inspect their sparsity pattern.

Examples

# \donttest{
vec <- read_vec(system.file("extdata", "global_mask_v4.nii", package = "neuroim2"))
mask <- read_vol(system.file("extdata", "global_mask_v4.nii", package = "neuroim2"))

# Auto window from spatial_sigma and spacing, single pass
out <- cgb_filter(vec, mask, spatial_sigma = 3, window = NULL, topk = 16)

# Stronger diffusion with two passes and lambda < 1
out2 <- cgb_filter(vec, mask, spatial_sigma = 4, window = NULL,
                   passes = 2, lambda = 0.7)
# }