neuroim2 (version 0.8.5)

ClusteredNeuroVec: ClusteredNeuroVec: Cluster-aware 4D neuroimaging data

Description

`ClusteredNeuroVec` creates a 4D array-like object where voxels are grouped into clusters, with one time-series per cluster. All voxels within a cluster share the same time-series, making it ideal for parcellated analyses (e.g., Schaefer-Yeo parcellations).

Usage

ClusteredNeuroVec(x, cvol, FUN = mean, weights = NULL, label = "")

Value

A ClusteredNeuroVec object containing:

cvol

The input ClusteredNeuroVol defining cluster structure

ts

A TxK matrix of cluster time-series (T=timepoints, K=clusters)

cl_map

Integer vector mapping linear voxel indices to cluster IDs

label

Character label for the object

Arguments

x

Either a `NeuroVec` object to be reduced by clusters, or a pre-computed numeric matrix of cluster time-series (T x K, where T=time points, K=clusters)

cvol

A `ClusteredNeuroVol` object defining the cluster assignments

FUN

Reduction function to aggregate voxels within clusters (default: mean). Common choices include mean, median, or custom functions.

weights

Optional numeric vector of per-voxel weights for weighted aggregation. Must have length equal to the number of non-zero voxels in the mask.

label

Optional character label for the object (default: "")

Details

This class implements array-like 4D access while storing data efficiently as a TxK matrix instead of the full voxel x time representation. Each cluster's time-series is computed by applying the aggregation function (FUN) to all voxels within that cluster.

The object supports standard NeuroVec operations:

• Indexing: x[,,,t] to extract 3D volumes at time t

• Series extraction: series(x, i, j, k) for time-series at voxel (i,j,k)

• Matrix conversion: as.matrix(x) to get the TxK cluster matrix

Single-voxel clusters are handled efficiently without aggregation overhead.

See Also

ClusteredNeuroVol for creating cluster assignments, cluster_searchlight_series for cluster-based searchlight analysis, series for extracting time-series

Examples

# Create synthetic 4D data (10x10x10 volume, 20 timepoints)
sp4 <- NeuroSpace(c(10,10,10,20), c(1,1,1))
arr <- array(rnorm(10*10*10*20), dim=c(10,10,10,20))
vec <- NeuroVec(arr, sp4)

# Create a mask covering the central region
sp3 <- NeuroSpace(c(10,10,10), c(1,1,1))
mask_arr <- array(FALSE, dim=c(10,10,10))
mask_arr[3:8, 3:8, 3:8] <- TRUE
mask <- LogicalNeuroVol(mask_arr, sp3)

# Assign voxels to 5 random clusters
n_voxels <- sum(mask_arr)
clusters <- sample(1:5, n_voxels, replace=TRUE)
cvol <- ClusteredNeuroVol(mask, clusters)

# Create clustered representation
cv <- ClusteredNeuroVec(vec, cvol)

# Access like a regular NeuroVec
vol_t1 <- cv[,,,1]  # 3D volume at time 1
ts <- series(cv, 5, 5, 5)  # time-series at voxel (5,5,5)

# Get cluster time-series matrix
cluster_matrix <- as.matrix(cv)  # T x K matrix
dim(cluster_matrix)  # 20 x 5