brainGraph (version 0.72.0)

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, divisor = c("none", "waytotal", "size", "rowSums"), div.files = NULL, mat.thresh = 0, sub.thresh = 0.5, inds, algo = c("probabilistic", "deterministic"), P = 5000)

Arguments

A.files

A character vector of the filenames with connection matrices

divisor

A character string indicating how to normalize the connection matrices; either 'none' (default), '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) (default: NULL)

mat.thresh

A numeric (vector) for thresholding connection matrices (default: 0)

sub.thresh

A numeric (between 0 and 1) for thresholding by subject numbers (default: 0.5)

inds

A list (length equal to number of groups) of integers; each list element should be a vector of length equal to the group sizes

algo

Character string of the tractography algorithm used (default: 'probabilistic')

P

Number of samples generated using FSL (default: 5000)

Value

A list containing: A list containing:

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

## Not run: 
# thresholds <- seq(from=0.001, to=0.01, by=0.001)
# my.mats <- dti_create_mats(f.A, 'waytotal', f.way, thresholds,
#   sub.thresh=0.5, inds)
# my.mats <- dti_create_mats(f.A, 'size', f.size, thresholds,
#   sub.thresh=0.5, inds, P=5000)
# ## End(Not run)