Description Usage Arguments Value Author(s) References Examples
View source: R/preprocessRestingBOLD.R
Preprocess resting fMRI by performing compcor/motion correction, nuisance regression, band-pass filtering, and spatial smoothing.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | preprocessRestingBOLD(
boldImage,
maskImage = NULL,
maskingMeanRatioThreshold = 0.75,
initialNuisanceVariables,
denseFramewise = FALSE,
numberOfCompCorComponents = 6,
doMotionCorrection = TRUE,
useMotionCorrectedImage = FALSE,
motionCorrectionAccuracyLevel = 1,
motionCorrectionIterations = 1,
meanBoldFixedImageForMotionCorrection = NULL,
frequencyLowThreshold = NA,
frequencyHighThreshold = NA,
spatialSmoothingType = "none",
spatialSmoothingParameters = 0,
residualizeMatrix = TRUE,
num_threads = 1,
seed = NULL
)
|
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. |
denseFramewise |
boolean for dense framewise stats |
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. |
motionCorrectionIterations |
number of iteration for motion correction |
meanBoldFixedImageForMotionCorrection |
Optional target fixed image for motion correction. |
frequencyLowThreshold |
Lower threshold for bandpass filtering. |
frequencyHighThreshold |
Upper threshold for bandpass filtering. |
spatialSmoothingType |
Either |
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. |
residualizeMatrix |
boolean |
num_threads |
will execute
|
seed |
will execute
|
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.
Tustison NJ, Avants BB
Power et al. 2012, "Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion." NeuroImage 59, 2142-2154.
1 2 3 4 5 6 7 | set.seed(123)
n=8
nvox <- n*n*n*6
dims <- c(n,n,n,6)
boldImage <- makeImage(dims, rnorm(nvox) + 500) %>% iMath("PadImage", 2)
# for real data: boldImage <- antsImageRead(getANTsRData('pcasl'))
cleanfMRI <- preprocessRestingBOLD(boldImage)
|
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