preprocessfMRI.Rd
Preprocess fMRI data by performing compcor/motion correction, nuisance regression, band-pass filtering, and spatial smoothing.
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
)
4-D ANTs image fMRI data.
3-D ANTs image defining the region of interest.
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.
Optional initial nuisance variables.
Numer of CompCor nuisance components.
Boolean indicating whether motion correction should be performed and used in nuisance regression.
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.
Accuracy for the motion correcting registration: 0 = fast/debug parameters, 1 = intrasession parameters, or 2 = intersession/intersubject parameters.
Optional target fixed image for motion correction.
Lower threshold for bandpass filtering.
Upper threshold for bandpass filtering.
Either none
, gaussian
(isotropic) or
perona-malik
(anisotropic) smoothing.
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)
.
boolean
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.
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.
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.
Power et al. 2012, "Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion." NeuroImage 59, 2142-2154.