brainGraph (version 0.48.0)

dti_create_mats: Create connection matrices for tractography analysis

Description

This function will take a vector of filenames which contain connection matrices (e.g. the fdt_network_matrix files from FSL) and create arrays of this data. You may choose to normalize these matrices by the waytotal or region size (which both require a character vector of filenames), or not at all.

Usage

dti_create_mats(A.files, Nv, divisor = c("none", "waytotal", "size",
  "rowSums"), div.files, mat.thresh = 0, sub.thresh = 0.5, groups = NULL)

Arguments

A.files

A character vector of the filenames with connection matrices

Nv

Integer representing the number of vertices (rows/columns)

divisor

A character string indicating how to normalize the connection matrices; either 'none', 'waytotal', 'size', or 'rowSums'

div.files

A character vector of the filenames with the data to normalize by (e.g. a list of waytotal files)

mat.thresh

A numeric (vector) for thresholding connection matrices

sub.thresh

A numeric (between 0 and 1) for thresholding by subject numbers

groups

A character vector of group names

Value

• A list containing:
• A
  A 3-d array of the raw connection matrices
• A.norm
  A 3-d array of the normalized connection matrices
• A.bin
  A 3-d array of binarized connection matrices
• A.bin.sums
  A list of 2-d arrays of connection matrices, with each entry signifying the number of subjects with a connection present; the number of list elements equals the length of mat.thresh
• A.inds
  A list of arrays of binarized connection matrices, containing 1 if that entry is to be included
• A.norm.sub
  A list of 3-d arrays of the normalized connection matrices for all given thresholds
• A.norm.mean
  A list of 2-d arrays of the normalized connection matrices averaged for each group

Details

The argument mat.thresh allows you to choose a numeric threshold, below which the connections will be replaced with 0; this argument will also accept a numeric vector. The argument sub.thresh will keep only those connections for which at least X% of subjects have a positive entry (the default is 0.5, or 50%).

Examples

thresholds <- seq(from=0.001, to=0.01, by=0.001)
my.mats <- dti_create_mats(f.A, Nv, 'waytotal', f.way, thresholds,
  sub.thresh=0.5, groups)
my.mats <- dti_create_mats(f.A, Nv, 'size', f.size, thresholds,
  sub.thresh=0.5, groups)