#' @title FSL Motion Correction
#' @description This function calls \code{mcflirt}
#' @param file (character) image to be manipulated
#' @param outfile (character) resultant image name (optional)
#' @param retimg (logical) return image of class nifti
#' @param reorient (logical) If \code{retimg}, should file be reoriented when read in?
#' Passed to \code{\link{readnii}}.
#' @param intern (logical) to be passed to \code{\link{system}}
#' @param opts (character) operations to be passed to \code{mcflirt}. Cannot use
#' \code{-o} or \code{-verbose}, as output file should be specified in \code{outfile}.
#' @param verbose (logical) print out command before running
#' @param ... additional arguments passed to \code{\link{readnii}}.
#' @return If \code{retimg} then object of class nifti. Otherwise,
#' it will have additional attributes in the \code{additional_files} field.
#' @export
mcflirt = function(
file,
outfile = NULL,
retimg = TRUE,
reorient = FALSE,
intern = FALSE,
opts = "",
verbose = TRUE,
...){
outfile = check_outfile(outfile = outfile, retimg = retimg)
opts = paste(opts, "-verbose", as.numeric(verbose), "-o")
file = checkimg(file)
file = path.expand(file)
res = fslcmd(func = "mcflirt",
file = file,
outfile = outfile,
retimg = retimg,
reorient = reorient,
intern = intern,
opts = opts,
verbose = verbose,
... = ...,
frontopts = "-in",
samefile = FALSE)
output_files = c(
mat = ".mat",
par = ".par",
abs_rms = "_abs.rms",
abs_mean_rms = "_abs_mean.rms",
rel_rms = "_rel.rms",
rel_mean_rms = "_rel_mean.rms")
output_files = paste0(nii.stub(outfile),
output_files)
output_files = output_files[file.exists(output_files)]
if (retimg) {
outfile = readnii(outfile)
}
if (length(output_files) > 0) {
L = as.list(output_files)
names(L) = names(output_files)
attr(outfile, "additional_files") = L
}
return(outfile)
}
#' @title MCFLIRT help
#' @description This function calls \code{mcflirt}'s help
#' @return Prints help output and returns output as character vector
#' @export
#' @examples
#' library(fslr)
#' if (have.fsl()){
#' mcflirt.help()
#' }
mcflirt.help = function(){
return(fslhelp("mcflirt", help.arg = "-help"))
}
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