rftResults.Rd
Returns RFT based statistical results for a single statistical image
rftResults(
x,
resels,
fwhm,
df,
fieldType,
RPVImg = NULL,
k = 1,
threshType = "pRFT",
pval = 0.05,
pp = 0.001,
n = 1,
statdir = NULL,
verbose = FALSE
)
statistical field image of class antsImage
resel values for the mask
full width at half maxima
degrees of freedom expressed as df = c(degrees of interest, degrees of error)
T: T-field
F: F-field
X: Chi-square field'
Z: Gaussian field
resels per voxel image
minimum desired cluster size (default = 1)
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
the p-value for estimating the threshTypeold (default = .05)
the primary (initial) p-value for threshTypeolding (only used for FDR methods; default = .001)
number of images in conjunction
directory where output is saved (if not specified images are not saved)
enables verbose output
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
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.
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.
if (FALSE) { # \dontrun{
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
)
} # }