#' @title Wrapper for Camino \code{dt2nii} function
#' @description Performs the Camino \code{dt2nii} function
#' @param infile Output from \code{\link{camino_modelfit}}
#' @param header NIfTI image with header information
#' @param inputmodel model used for tensors
#' @param outputroot Output file root. If there is one component, or output is to a vector,
#' the output image is called root.ext, otherwise output is numbered by component.
#' @param outputdatatype Specifies the data type of the output image.
#' The data type can be any of the following strings:
#' "byte", "short", "int", "long", "float" or "double".
#' @param maxcomponents Maximum tensor components, for use with input model "multitensor".
#' @param gzip Set gzip compression for the output image, if supported by the image format.
#' @param verbose print diagnostic messages
#' @export
camino_dt2nii = function(infile,
header,
inputmodel = c("dt", "twotensor", "threetensor", "multitensor"),
outputroot = NULL,
outputdatatype = NULL,
maxcomponents = NULL,
gzip = TRUE,
verbose = TRUE
) {
infile = checkimg(infile)
header = checkimg(header)
inputmodel = match.arg(inputmodel)
if (inputmodel != "multitensor") {
maxcomponents = NULL
} else {
if (is.null(maxcomponents)) {
stop('If inputmodel = "multitensor", maxcomponents must be specified!')
} else {
if (maxcomponents < 1) {
stop('If inputmodel = "multitensor", maxcomponents must be > 0')
}
}
}
#########################
# Fixing types
#########################
if (!is.null(outputdatatype)) {
outputdatatype = match.arg(outputdatatype,
choices = c("float", "byte", "short",
"int", "long", "double"))
}
if (is.null(outputroot)) {
outputroot = tempfile(fileext = "_")
}
opts = c( "-inputfile" = infile,
"-header" = header,
"-inputmodel" = inputmodel,
"-outputroot" = outputroot,
"-outputdatatype" = outputdatatype,
"-maxcomponents" = maxcomponents
)
ext = ".nii"
if (gzip) {
opts = c(opts, "-gzip" = "")
ext = ".nii.gz"
}
opts = collapse_opts(opts)
cmd = camino_cmd("dt2nii")
cmd = paste(cmd, opts)
if (verbose) {
message(cmd)
}
res = system(cmd)
#########################################
# Construction output filenames
#########################################
out_suff = c("exitcode", "lns0")
if (inputmodel == "dt") {
out_suff = c(out_suff, "dt")
} else {
n_comp = switch(inputmodel,
"twotensor" = 2,
"threetensor" = 3,
"multitensor" = maxcomponents)
add_suffs = c(sapply(seq_along(n_comp), function(x){
paste0(c("dt", "mix"), x)
}))
out_suff = c(out_suff, add_suffs)
}
outfiles = paste0(outputroot, out_suff, ext)
return(outfiles)
}
# .B voxel2image -outputroot <root> -header <header> -components <N> [options]
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.