antsBOLDNetworkAnalysis.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/antsBOLDNetworkAnalysis.R
\name{antsBOLDNetworkAnalysis}
\alias{antsBOLDNetworkAnalysis}
\title{a basic framework for network analysis that produces graph metrics}
\usage{
antsBOLDNetworkAnalysis(
  bold = NULL,
  mask = NULL,
  labels = NULL,
  motion,
  gdens = 0.2,
  threshLo = 1,
  threshHi = 90,
  freqLo = 0.01,
  freqHi = 0.1,
  winsortrim = 0.02,
  throwaway
)
}
\arguments{
\item{bold}{input 4D image}

\item{mask}{antsImage defines areas of interest}

\item{labels}{antsImage defines regions of interest ie a parcellation}

\item{motion}{motion parameters - if missing, will estimate from data}

\item{gdens}{graph density applied to network covariance matrix}

\item{threshLo}{lower threshold for the label image}

\item{threshHi}{upper threshold for the label image}

\item{freqLo}{lower frequency cutoff}

\item{freqHi}{upper frequency cutoff}

\item{winsortrim}{winsorize the bold signal by these values eg 0.02}

\item{throwaway}{this number of initial bold volumes}
}
\value{
list of outputs
}
\description{
An implementation of a network analysis framework for BOLD data. We expect
that you mapped a label image ( e.g. aal ) to the 3D BOLD space. We build a
network and graph metrics from this image and these labels based on the
user-defined graph density level.
}
\examples{
# none yet - this is not very well tested with recent ANTsR
\dontrun{
myimg <- antsImageRead(getANTsRData("ch2"), 3)
mylab <- antsImageRead(getANTsRData("ch2a"), 3)
boldfn <- getANTsRData("pcasl")
bold <- antsImageRead(boldfn, 4)
avgbold <- getAverageOfTimeSeries(bold)
breg <- antsRegistration(avgbold, myimg, typeofTransform = c("AffineFast"))
warpedParcellation <- antsApplyTransforms(avgbold, mylab,
  transformlist = breg$fwdtransforms, interpolator = "NearestNeighbor"
)
mask <- getMask(avgbold)
warpedParcellation <- maskImage(warpedParcellation, img.mask = mask)
old <- NA
labels <- warpedParcellation
gdens <- 0.2
threshLo <- 1
threshHi <- 90
freqLo <- 0.01
freqHi <- 0.1
winsortrim <- 0.02
result <- antsBOLDNetworkAnalysis(bold = bold, mask = mask, warpedParcellation)
}
}
\author{
BB Avants
}