R/getNetwork.R

In stnava/itkImageR: Examples using Rcpp to interface R and ITK

# getNetwork
getNetwork <- function(tmat, mask, labels, timeStep = 1) {
  labelmat <- labels2matrix(labels, mask)
  regions <- tmat %*% labelmat
  
  sums <- colSums(regions)
  for (i in c(1:length(sums))) {
    if (sums[i] != 0) {
      regions[, i] <- regions[, i]/sums[i]
    }
  }
  corrs <- cor(regions)
  corrs[is.na(corrs)] <- 0
  corrs[is.nan(corrs)] <- 0
  
  corimg <- as.antsImage(as.matrix(corrs))
  for (i in c(1:dim(corrs)[1])) {
    corimg[i, i] <- 0
  }
  
  # view all average time series plot in a single window labelID <- rep( 1:max(as.array(labels)),
  # each=dim(tmat)[1] ) times <- rep( timeStep*c(0:(dim(regions)[1]-1)), dim(regions)[2] ) dat <- data.frame(
  # signal=as.vector(regions), time=times, id=factor(as.vector(labelID)) ) ggplot( data=dat, aes(x=time,
  # y=signal, group=id, colour=id) ) + geom_line() + ylab('regional cbf') + xlab( 'time (ms)' )
  
  return(corimg)
}