brainGraph (version 1.0.0)

create_mats: Create connection matrices for tractography or fMRI data

Description

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

Usage

create_mats(A.files, modality = c("dti", "fmri"), divisor = c("none",
  "waytotal", "size", "rowSums"), div.files = NULL, threshold.by = c("raw",
  "density"), mat.thresh = 0, sub.thresh = 0.5, inds,
  algo = c("probabilistic", "deterministic"), P = 5000)

Arguments

A.files

Character vector of the filenames with connection matrices

modality

Character string indicating data modality (default: dti)

divisor

Character string indicating how to normalize the connection matrices; either 'none' (default), 'waytotal', 'size', or 'rowSums' (ignored if modality equals fmri)

div.files

Character vector of the filenames with the data to normalize by (e.g. a list of waytotal files) (default: NULL)

threshold.by

Character string indicating how to threshold the data; choose density if you want all resulting matrices in a subject group to have the same density (default: raw)

mat.thresh

Numeric (vector) for thresholding connection matrices (default: 0)

sub.thresh

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

inds

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

Integer; number of samples generated using FSL (default: 5000)

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

## Not run: ------------------------------------
# thresholds <- seq(from=0.001, to=0.01, by=0.001)
# my.mats <- create_mats(f.A, modality='fmri', threshold.by='raw',
#   mat.thresh=thresholds, sub.thresh=0.5, inds=inds)
# dti.mats <- create_mats(f.A, divisor='waytotal', div.files=f.way,
#   mat.thresh=thresholds, sub.thresh=0.5, inds=inds)
## ---------------------------------------------