Nothing
## fMRI data as prefiltered by FSL : read all time series in slice
## niislicets: slice time-series
## mask: slice mask
## X: design matrix
## nvar: n. of regression vars
## nobs: n. of observations
read.design <-
function(fsldesign="design.mat")
{
g1 <- paste("grep NumWaves", fsldesign, " | awk '{ print $2 }'")
nevs <-as.integer(system(g1, intern=TRUE))
stopifnot(!is.na(nevs))
g2 <- paste("grep NumPoints", fsldesign," | awk '{ print $2 }'")
npts <- as.integer(system(g2, intern=TRUE))
stopifnot(!is.na(npts))
## cat("npts=",npts,"\n")
## cat("nevs=",nevs,"\n")
dsgn <- numeric(nevs*npts)
model <- .C("readmodel",
fsldesign=as.character(fsldesign),
nevs=as.integer(nevs),
npts=as.integer(npts),
dsgn=as.double(dsgn) )
invisible(model)
}
read.fmrislice <-
function (fbase=NULL, slice=NULL, swap=FALSE)
{
if(!is.null(fbase)) {
fsl.filtered <- system.file(paste("extdata/", fbase,
"_filtered_func_data.nii.gz", sep = ""), package = "cudaBayesregData")
fsl.mask <- system.file(paste("extdata/", fbase, "_mask.nii.gz",
sep = ""), package = "cudaBayesregData")
## Design matrix (FSL-like)
fsl.design <- system.file(paste("extdata/", fbase, "_design.mat",
sep = ""), package = "cudaBayesregData")
}
else {
fsl.filtered <- "filtered_func_data.nii.gz"
fsl.mask <- "mask.nii.gz"
fsl.design <- "design.mat"
}
stopifnot(file.exists(fsl.design))
img.nifti <- readNIfTI(fsl.filtered)
mask.nifti <- readNIfTI(fsl.mask)
img <- img.nifti@.Data
mask <- mask.nifti@.Data
dimg <- img.nifti@dim
if(is.null(slice)) ## default slice n.
slice <- floor(dimg[3]/2)
cat("Using slice n.", slice,"\n")
X <- nrow(img)
Xm <- nrow(mask)
if (swap) { ## swap=T to be represented as in fslview
niislicets <- img[X:1, , slice, ]
mask <- mask[Xm:1, , slice]
}
else {
niislicets <- img[, , slice, ]
mask <- mask[, , slice]
}
model <-read.design(fsldesign=fsl.design)
dsgn <- matrix(model$dsgn, ncol=model$nevs, byrow=T)
nobs <- nrow(dsgn)
X0 <- as.matrix(dsgn)
X <- cbind(rep(1, nobs), X0) ## with intercept
nvar <- ncol(X)
invisible(list(fbase=fbase, slice = slice, niislicets = niislicets, mask = mask,
X = X, nvar = nvar, nobs = nobs, swap = swap))
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.