rftResults: RFT Statistical Results

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

RFT Statistical Results

Description

Returns RFT based statistical results for a single statistical image

Usage

rftResults(
  x,
  resels,
  fwhm,
  df,
  fieldType,
  RPVImg = NULL,
  k = 1,
  threshType = "pRFT",
  pval = 0.05,
  pp = 0.001,
  n = 1,
  statdir = NULL,
  verbose = FALSE
)

Arguments

x	statistical field image of class antsImage
resels	resel values for the mask
fwhm	full width at half maxima
df	degrees of freedom expressed as df = c(degrees of interest, degrees of error)
fieldType	T: T-field F: F-field X: Chi-square field' Z: Gaussian field
RPVImg	resels per voxel image
k	minimum desired cluster size (default = 1)
threshType	a numeric value to threshTypeold the statistical field or a character of the following methods: cRFT: computes a threshTypeold per expected cluster level probability pRFT: uses the mask and pval calculates the minimum statistical threshTypeold cFDR: uses an uncorrected threshTypeold at the alpha level and then computes and FDR threshTypeold based on cluster maxima pFDR: computes the fdr threshTypeold for the entire field of voxels
pval	the p-value for estimating the threshTypeold (default = .05)
pp	the primary (initial) p-value for threshTypeolding (only used for FDR methods; default = .001)
n	number of images in conjunction
statdir	directory where output is saved (if not specified images are not saved)
verbose	enables verbose output

Details

rftPval is used to compute all family-wise error (FWE) corrected statistics while p.adjust is used to compute all false-discovery rate based statistics. All statistics herein involve implementation of random field theory (RFT) to some extent.

Both cluster-level and peak-level statistics are described by the uncorrected p-value along with the FDR and FWE corrected p-values for each cluster. Peak-level statistics are described by the maximum statistical value in each cluster and the comparable Z statistic. The ClusterStats table also contains coordinates for each cluster and the number of voxels therein. By default threshType = "pRFT" and pval=.05. Alternatively, the user may use a specific numeric value for threshTypeolding the statistical field. statFieldThresh more fully describes using appropriate threshTypeolds for statistical fields and how pp plays a role in FDR threshTypeolding.

Value

Outputs a statistical value to be used for threshTypeold a statistical field image

• SetStats: set-level statistics and number of clusters

• ClusterStats: cluster-level statistics and descriptors

• PeakStats: peak-level statistics and descriptor"

• LabeledClusters: image of labeled clusters

• threshTypeold: the threshTypeold used

Author(s)

Zachary P. Christensen

References

Chumbley J., (2010) Topological FDR for neuroimaging

Friston K.J., (1996) Detecting Activations in PET and fMRI: Levels of Inference and Power

Worsley K.J., (1992) A Three-Dimensional Statistical Analysis for CBF Activation Studies in Human Brain.

Examples

## Not run: 
mnit1 <- antsImageRead(getANTsRData("mni"))
mask <- getMask(mnit1)
ilist <- list()
for (i in 1:10) {
  ilist <- lappend(ilist, antsImageClone(mnit1) * rnorm(1))
}
response <- rnorm(10)
imat <- imageListToMatrix(ilist, mask)
residuals <- matrix(nrow = nrow(imat), ncol = ncol(imat))
tvals <- matrix(nrow = nrow(imat), ncol = ncol(imat))
for (i in 1:ncol(imat)) {
  fit <- lm(response ~ imat[, i])
  tvals <- coefficients(fit)[2]
  residuals[, i] <- residuals(fit)
}
myfwhm <- estSmooth(residuals, mask, fit$df.residual)
res <- resels(mask, myfwhm$fwhm)
timg <- makeImage(mask, tvals)

# threshold to create peak values with p-value of .05 (default)
results1 <- rftResults(timg, res, myfwhm$fwhm, df,
  fieldType = "T",
  threshType = "pRFT", pval = .05
)

# threshold to create clusters with p-value of .05
results2 <- rftResults(timg, res, myfwhm$fwhm, df,
  fieldType = "T",
  threshType = "cRFT", pval = .05
)

# initial threshold at p-value of .001 followed by peak FDR threshTypeold at
# p-value of .05
results3 <- rftResults(timg, res, myfwhm$fwhm, df,
  fieldType = "T",
  threshType = "pFDR", pval = .05, pp = .01
)

# initial threshold at p-value of .001 followed by cluster FDR threshold at
# p-value of .05
results4 <- rftResults(timg, res, myfwhm$fwhm, df,
  fieldType = "T",
  threshType = "cFDR", pval = .05, pp = .01
)

# correcting for non-isotropic
results5 <- rftResults(timg, res, myfwhm$fwhm, df,
  fieldType = "T",
  fwhm$RPVImg
)

## End(Not run)

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