preprocessfMRI: Preprocess BOLD fMRI image data.

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

Preprocess BOLD fMRI image data.

Description

Preprocess fMRI data by performing compcor/motion correction, nuisance regression, band-pass filtering, and spatial smoothing.

Usage

preprocessfMRI(
  boldImage,
  maskImage = NULL,
  maskingMeanRatioThreshold = 0.75,
  initialNuisanceVariables,
  numberOfCompCorComponents = 6,
  doMotionCorrection = TRUE,
  useMotionCorrectedImage = FALSE,
  motionCorrectionAccuracyLevel = 1,
  meanBoldFixedImageForMotionCorrection = NULL,
  frequencyLowThreshold = NA,
  frequencyHighThreshold = NA,
  spatialSmoothingType = "none",
  spatialSmoothingParameters = 0,
  residualizeMatrix = TRUE,
  num_threads = 1,
  seed = NULL
)

Arguments

boldImage	4-D ANTs image fMRI data.
maskImage	3-D ANTs image defining the region of interest.
maskingMeanRatioThreshold	If mask image is not specified, a mask image is created using the specified threshold which is in terms of the mean of the average image ie 0.8 means threshold at 0.8 of the mean.
initialNuisanceVariables	Optional initial nuisance variables.
numberOfCompCorComponents	Numer of CompCor nuisance components.
doMotionCorrection	Boolean indicating whether motion correction should be performed and used in nuisance regression.
useMotionCorrectedImage	Boolean indicating whether or not the motion corrected image should be used in the rest of the pipeline. This is off by default to avoid additional interpolation.
motionCorrectionAccuracyLevel	Accuracy for the motion correcting registration: 0 = fast/debug parameters, 1 = intrasession parameters, or 2 = intersession/intersubject parameters.
meanBoldFixedImageForMotionCorrection	Optional target fixed image for motion correction.
frequencyLowThreshold	Lower threshold for bandpass filtering.
frequencyHighThreshold	Upper threshold for bandpass filtering.
spatialSmoothingType	Either none, gaussian (isotropic) or perona-malik (anisotropic) smoothing.
spatialSmoothingParameters	For gaussian smoothing, this is a single scalar designating the smoothing sigma (in mm). For perona-malik, a vector needs to be specified with the conductance parameter and the number of iterations, e.g. c(0.25, 5).
residualizeMatrix	boolean
num_threads	will execute Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = num_threads) before running to attempt a more reproducible result. See https://github.com/ANTsX/ANTs/wiki/antsRegistration-reproducibility-issues for discussion. If NULL, will not set anything.
seed	will execute Sys.setenv(ANTS_RANDOM_SEED = seed) before running to attempt a more reproducible result. See https://github.com/ANTsX/ANTs/wiki/antsRegistration-reproducibility-issues for discussion. If NULL, will not set anything.

Value

List of:

• cleanBOLDImage: Cleaned BOLD image.

• maskImage: mask image.

• DVARS: Framewise change in BOLD signal, as in Powers et al.

• DVARSPostCleaning: DVARS after cleaning image.

• FD: Framewise displacement.

• globalSignal: Global signal.

• nuisanceVariables: Nuisance variables used in denoising.

Author(s)

Tustison NJ, Avants BB

References

Power et al. 2012, "Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion." NeuroImage 59, 2142-2154.

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