aslDenoiseR: WIP: data-driven denoising for ASL MRI

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

WIP: data-driven denoising for ASL MRI

Description

Denoises regression based reconstruction of CBF from arterial spin labeling

Usage

aslDenoiseR(
  boldmatrix,
  targety,
  covariates = NA,
  selectionthresh = 0.1,
  maxnoisepreds = 2:12,
  polydegree = "loess",
  crossvalidationgroups = 4,
  scalemat = F,
  noisepoolfun = max,
  usecompcor = F,
  verbose = F
)

Arguments

boldmatrix	input bold matrix
targety	target to predict
covariates	motion or other parameters / nuisance variables
selectionthresh	e.g. 0.1 take 10 percent worst variables for noise estimation
maxnoisepreds	integer search range e.g 1:10
polydegree	eg 4 for polynomial nuisance variables or 'loess'
crossvalidationgroups	prior defined or integer valued
scalemat	boolean
noisepoolfun	function to help select noise pool e.g. max
usecompcor	boolean
verbose	boolean

Value

matrix is output

Author(s)

Avants BB

Examples

# asl<-antsImageRead( getANTsRData("pcasl") )
set.seed(1)
nvox <- 10 * 10 * 10 * 20
dims <- c(10, 10, 10, 20)
asl <- makeImage(dims, rnorm(nvox) + 500)
aslmean <- getAverageOfTimeSeries(asl)
aslmask <- getMask(aslmean)
aslmat <- timeseries2matrix(asl, aslmask)
for (i in 1:10) aslmat[, i * 2] <- aslmat[, i * 2] * 2
asl <- matrix2timeseries(asl, aslmask, aslmat)
tc <- as.factor(rep(c("C", "T"), nrow(aslmat) / 2))
dv <- computeDVARS(aslmat)
dnz <- aslDenoiseR(aslmat, tc,
  covariates = dv, selectionthresh = 0.1,
  maxnoisepreds = c(1:2), polydegree = 2, crossvalidationgroups = 2
)
testthat::expect_equal(dnz$R2atBestN, 7, tolerance = 0.5)

## Not run: 
# a classic regression approach to estimating perfusion
# not recommended, but shows the basic idea.
# see ?quantifyCBF for a better approach
perfmodel <- lm(aslmat ~ tc + dnz$noiseu)
perfimg <- antsImageClone(aslmask)
perfimg[aslmask == 1] <- bigLMStats(perfmodel)$beta[1, ]
m0 <- getAverageOfTimeSeries(asl)
ctl <- c(1:(nrow(aslmat) / 2)) * 2
m0[aslmask == 1] <- colMeans(aslmat[ctl, ])
pcasl.parameters <- list(sequence = "pcasl", m0 = m0)
cbf <- quantifyCBF(perfimg, aslmask, pcasl.parameters)

# default mode network example

if (!exists("bold")) {
  bold <- antsImageRead(getANTsRData("rsbold"))
  meanbold <- getAverageOfTimeSeries(bold)
  boldmask <- getMask(meanbold)
  # map to mni
  mni <- antsImageRead(getANTsRData("mni"))
  mniaal <- antsImageRead(getANTsRData("mnia"))
  mymap <- antsRegistration(meanbold * boldmask, mni,
    typeofTransform = "SyNBold",
    verbose = 1
  )
  aalimg <- antsApplyTransforms(meanbold, mniaal, mymap$fwdtransforms,
    interpolator = "NearestNeighbor"
  )
  data("aal", package = "ANTsR")
  timeselect <- 10:dim(bold)[4]
  if (!exists("moco")) {
    moco <- antsMotionCalculation(bold, boldmask)
  }
  sbold <- smoothImage(moco$moco_img, 3.0)
  antsImageWrite(boldmask, "boldmask.nii.gz")
  antsImageWrite(meanbold, "boldmean.nii.gz")
  antsImageWrite(aalimg, "boldaal.nii.gz")
  boldmask <- boldmask * thresholdImage(aalimg, 1, Inf)
}
postcing <- aal$label_num[grep("Cingulum_Post", aal$label_name)]
postCingMask <- maskImage(boldmask, aalimg,
  level = as.numeric(postcing), binarize = T
)
mpostCingMask <- antsImageClone(postCingMask) * 0
mpostCingMask[postCingMask == 0] <- 1
boldmat <- timeseries2matrix(sbold, boldmask * mpostCingMask)
boldmat <- boldmat[timeselect, ]
boldmat <- frequencyFilterfMRI(boldmat, tr = antsGetSpacing(bold)[4], opt = "trig")
dmnvec <- (timeseries2matrix(sbold, postCingMask)[timeselect, ])
dmnvec <- rowMeans(
  frequencyFilterfMRI(dmnvec, tr = antsGetSpacing(bold)[4], opt = "trig")
)
dmnmat <- matrix(dmnvec, ncol = 1)
mocpar <- moco$moco_params[timeselect, 3:14]
dnz <- aslDenoiseR(boldmat, dmnvec,
  covariates = mocpar, selectionthresh = 0.2,
  maxnoisepreds = c(2:10), polydegree = "loess",
  crossvalidationgroups = 8
)
boldmat <- timeseries2matrix(sbold, boldmask)
boldmat <- boldmat[timeselect, ]
boldmat <- frequencyFilterfMRI(boldmat, tr = antsGetSpacing(bold)[4], opt = "trig")
mdl <- bigLMStats(lm(boldmat ~ dmnvec + dnz$covariates + dnz$noiseu), 0.001)
betas <- mdl$beta.t[1, ]
betaImg <- makeImage(boldmask, betas)
antsImageWrite(betaImg, "dmnBetas.nii.gz")
# this should give default mode network around beta = 12

## End(Not run)

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