filterfMRIforNetworkAnalysis: Basic pre-processing for BOLD or ASL-based network analysis.

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

Basic pre-processing for BOLD or ASL-based network analysis.

Description

This function works for either raw BOLD time-series data, ASL-based BOLD time-series data or ASL-based CBF time series data. In all 3 cases, this function performs motion-correction, factoring out motion and compcor nuisance paramters, frequency filtering and masking. The output contains the filtered time series (matrix form), the mask and a vector of temporal signal variance. Some ASL MR sequences allow network analysis of either BOLD or ASL signal. See "Implementation of Quantitative Perfusion Imaging Techniques for Functional Brain Mapping using Pulsed Arterial Spin Labeling" by Wong et al, 1997 for an overview. This function employs "surround" techniques for deriving either CBF or BOLD signal from the input ASL. This is a WIP.

Usage

filterfMRIforNetworkAnalysis(
  aslmat,
  tr,
  freqLo = 0.01,
  freqHi = 0.1,
  cbfnetwork = "ASLCBF",
  mask = NULL,
  labels = NULL,
  graphdensity = 0.5,
  seg = NULL,
  useglasso = NA,
  nuisancein = NA,
  usesvd = FALSE,
  robustcorr = FALSE
)

Arguments

aslmat	The filename to an antsr image or pointer to an antsr image
tr	The sequence's TR value , typically 3 or 4.
freqLo	The lower frequency limit, e.g. 0.01 in band-pass filter
freqHi	The higher frequency limit, e.g. 0.1 in band-pass filter
cbfnetwork	"ASLCBF" A string dictating whether to do nothing special (standard BOLD) or get CBF (ASLCBF) or BOLD (ASLBOLD) signal from ASL
mask	the mask image
labels	the label image
graphdensity	desired density
seg	a segmentation image
useglasso	use sparse inverse covariance for network estimation
nuisancein	nuisance variable data frame
usesvd	bool, to reduce nuisance variables
robustcorr	bool

Value

output is a list containing "filteredTimeSeries" "mask" "temporalvar"

or

1 – Failure

Author(s)

Avants BB

Examples

## Not run: 
if (!exists("fn")) fn <- getANTsRData("pcasl")
img <- antsImageRead(fn)
mask <- getMask(getAverageOfTimeSeries(img))
fmat <- timeseries2matrix(img, mask)
myres <- filterfMRIforNetworkAnalysis(fmat, tr = 4, 0.01, 0.1, cbfnetwork = "BOLD", mask = mask)

## End(Not run)

stnava/ANTsR documentation built on April 16, 2024, 12:17 a.m.