ANTsR (version 1.0)

antsPreprocessfMRI: Preprocess BOLD fMRI image data.

Description

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

Usage

antsPreprocessfMRI <- function( boldImage,
  maskImage = NA,
  maskingThreshold = 0.75,
  initialNuisanceVariables = NA,
  numberOfCompCorComponents = 6,
  doMotionCorrection = TRUE,
  useMotionCorrectedImage = FALSE,
  motionCorrectionAccuracyLevel = 1,
  meanBoldFixedImageForMotionCorrection = NA,
  spatialSmoothingType = c( "none", "gaussian", "perona-malik" ),
  spatialSmoothingParameters = 0.0,
  frequencyLowThreshold = 0.01,
  frequencyHighThreshold = 0.1 )

Arguments

boldImage

4-D ANTs image fMRI data.

meanBoldFixedImageForMotionCorrection

Optional target fixed image for motion correction.

maskImage

3-D ANTs image defining the region of interest.

maskingThreshold

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

Booelan 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.

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 ).

Value

Output is the "clean" fMRI bold image and mask. Quality assurance output includes the framewise displacement (FD) and DVARS. "DVARS is the root mean squared (RMS) change in BOLD signal from volume to volume (D referring to temporal derivative of time courses and VARS referring to RMS variance over voxels.)" --- Power et. al 2012, Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion. Neuroimage 59, 2142-2154. The globalSignal is also returned.

Examples

# NOT RUN {
boldImage <- antsImageRead( "fmri.nii.gz", dim = 4, pixeltype = "float" )
cleanfMRI <- antsPreprocessfMRI( boldImage )
cleanBoldImage <- cleanfMRI$cleanBoldImage
maskImage <- cleanfMRI$maskImage
framewiseDisplacement <- cleanfMRI$FD
dtRMS <- cleanfMRI$DVARS
# }