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fmrismooth_mppca_pipeline: MP-PCA denoising followed by bilateral filtering

fmrismooth_mppca_pipeline.Rd

Denoises 4D fMRI with MP-PCA in overlapping patches, then applies a joint-bilateral lattice filter with optional guides.

Usage

fmrismooth_mppca_pipeline(
  vec,
  t1 = NULL,
  probs = NULL,
  mask = NULL,
  design = NULL,
  motion = NULL,
  sigma_mode = c("patch", "global", "fixed"),
  sigma_value = NULL,
  sigma_sp = 2.5,
  sigma_t = 0.5,
  sigma_r = 15,
  sigma_d = 1,
  lattice_blur_iters = 1L
)

Arguments

vec

4D fMRI array or `NeuroVec`.

t1

Optional 3D structural guide.

probs

Optional list of 3D guides (e.g., tissue probabilities).

mask

Optional 3D logical/0-1 mask.

design

Optional per-frame design regressor.

motion

Optional per-frame motion matrix used by some stages.

sigma_mode

MP-PCA noise mode: 'patch', 'global', or 'fixed'.

sigma_value

Noise sigma when `sigma_mode='fixed'`.

sigma_sp

Spatial sigma (voxels) for joint bilateral.

sigma_t

Temporal sigma (frames) for joint bilateral.

sigma_r

Range sigma(s) for joint bilateral guidance.

sigma_d

Sigma for design regressor feature.

lattice_blur_iters

Number of lattice blur iterations.

Value

Smoothed 4D data, wrapped like `vec` when possible.