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Calculate user-defined connectivity

calc_conn.Rd

General-purpose connectivity calculator for user-defined ROI or network connections. Computes mean connectivity between a source (from) and one or more targets (to) using raw cell average.

Usage

calc_conn(conn_array, indices, from, to)

Arguments

conn_array

3D numeric array of connectivity values with dimensions (ROI x ROI x subjects)

indices

Named list of integer vectors mapping network/ROI names to index positions

from

Character. Name of the source ROI or network. Must match a name in indices

to

Character vector. One or more target names. Each must match a name in indices. Connectivity is calculated from from to each target separately

Value

A data frame with one row per subject and one column per target, named {from}_{to}.

Details

Connectivity is computed using raw cell average: for each subject, the function extracts conn_array[from_idx, to_idx, subj] and takes the mean of all values. When both from and to resolve to single ROIs, the direct connection value is returned (no averaging needed).

Supports any combination of ROIs and networks:

  • ROI-to-network: e.g., from = "ahip", to = "default"

  • ROI-to-ROI: e.g., from = "ahip", to = "phip"

  • Network-to-network: e.g., from = "default", to = "cont"

Names in from and to reference entries in indices, including any manual groupings.

See also

calc_within for within-network connectivity. calc_between for between-network connectivity. get_indices for generating the indices input.

Examples

# ROI-to-network
indices <- get_indices(ex_conn_array)
ahip_default <- calc_conn(ex_conn_array, indices,
                          from = "ahip", to = "default")

# ROI-to-multiple-networks
ahip_nets <- calc_conn(ex_conn_array, indices,
                       from = "ahip",
                       to = c("default", "cont", "vis"))

# ROI-to-ROI
ahip_phip <- calc_conn(ex_conn_array, indices,
                       from = "ahip", to = "phip")

if (FALSE) { # \dontrun{
# Full workflow with manual grouping
z_mat <- load_matrices("data/conn.mat", type = "zmat", exclude = c(3, 5))
indices <- get_indices(z_mat,
  manual_assignments = list(ahip = "hippocampus", phip = "hippocampus"))

hip_nets <- calc_conn(z_mat, indices,
                      from = "hippocampus",
                      to = c("default", "cont", "limbic",
                             "salventattn", "dorsattn", "sommot", "vis"))
} # }