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Get ROI indices organized by network

get_indices.Rd

Extracts ROI index positions and organizes them by network or region name. Schaefer ROIs are automatically grouped by functional network. Other ROIs are preserved individually unless grouped via manual_assignments.

Usage

get_indices(
  x,
  roi_include = c("all", "schaefer"),
  reorder_networks = TRUE,
  manual_assignments = NULL
)

Arguments

x

Input source for ROI names. Can be:

  • A file path to a CONN toolbox .mat file (requires NetworkToolbox)

  • A 3D connectivity array with ROI names in dimnames

  • A character vector of ROI names

roi_include

Character. "all" (default) processes all ROIs; "schaefer" processes only Schaefer-labeled ROIs.

reorder_networks

Logical. If TRUE (default), reorder Schaefer networks as: default, cont, limbic, salventattn, dorsattn, sommot, vis. Non-Schaefer ROIs always appear at the end.

manual_assignments

Named list to override groupings. Format: list(roi_name = "group_name"). Matching is case-insensitive.

Value

A named list where names are network/ROI labels and values are integer vectors of ROI indices.

Details

Schaefer ROIs are grouped by network (e.g., all visual ROIs become "vis"). Non-Schaefer ROIs are preserved individually with lowercase names (e.g., "AHIP" becomes "ahip"). Attention network naming variations across atlas versions (ventatt, salventattn, dorsatt, etc.) are automatically normalized for consistency.

See also

load_matrices for loading connectivity data. calc_within, calc_between, calc_conn for connectivity calculations using indices. plot_heatmap for visualizing connectivity matrices using indices.

Examples

# From character vector of ROI names
indices <- get_indices(ex_roi_names)
names(indices)
#> [1] "default"     "cont"        "limbic"      "salventattn" "dorsattn"   
#> [6] "sommot"      "vis"         "ahip"        "phip"       

# Access specific network indices
indices$vis
#> [1] 1 2 3 4 5
indices$default
#> [1] 25 26 27 28
indices$ahip
#> [1] 29

# From connectivity array with dimnames
indices <- get_indices(ex_conn_array)
names(indices)
#> [1] "default"     "cont"        "limbic"      "salventattn" "dorsattn"   
#> [6] "sommot"      "vis"         "ahip"        "phip"       

# Extract Schaefer ROIs only
indices_schaefer <- get_indices(ex_roi_names, roi_include = "schaefer")
names(indices_schaefer)
#> [1] "default"     "cont"        "limbic"      "salventattn" "dorsattn"   
#> [6] "sommot"      "vis"        

# Manual grouping of ROIs
indices_grouped <- get_indices(
  ex_roi_names,
  manual_assignments = list(ahip = "hippocampus", phip = "hippocampus")
)
indices_grouped$hippocampus
#> [1] 29 30

# Preserve original matrix order
indices_original <- get_indices(ex_roi_names, reorder_networks = FALSE)

if (FALSE) { # \dontrun{
# From CONN .mat file
indices <- get_indices("path/to/conn.mat")

# From connectivity array loaded with NetworkToolbox
conn_mats <- NetworkToolbox::convertConnBrainMat("path/to/conn.mat")
indices <- get_indices(conn_mats$rmat)
} # }