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#' @title FSL Robust Field of View
#' @description This function calls \code{robustfov} to
#' automatically crop the image
#' @param file (character) image to be manipulated
#' @param brain_size size of brain in z-dimension (default 150mm)
#' @param mat_name matrix output name
#' @param roi_name ROI volume output name
#' @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 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,
#' Result from system command, depends if intern is TRUE or FALSE.
#' @export
fslrobustfov = function(
file,
brain_size = NULL,
mat_name = NULL,
roi_name = NULL,
retimg = TRUE,
reorient = FALSE,
intern = FALSE,
verbose = TRUE,
...){
opts = ""
if (!is.null(brain_size)) {
opts = paste(opts, "-b", brain_size)
}
if (!is.null(mat_name)) {
opts = paste(opts, "-m", shQuote(mat_name))
}
if (!is.null(roi_name)) {
opts = paste(opts, "-m", shQuote(roi_name))
}
if (verbose) {
opts = paste(opts, "--verbose")
}
res = fslcmd(func = "robustfov",
file = file,
outfile = NULL,
retimg = retimg,
reorient = reorient,
intern = intern,
opts = opts,
frontopts = "-i",
verbose = verbose,
... = ...,
samefile = TRUE,
no.outfile = TRUE)
return(res)
}
#' @rdname fslrobustfov
#' @export
fsl_robustfov = function(
retimg = FALSE,
...){
res = fslrobustfov(..., retimg = retimg)
return(res)
}
#' @title FSL Robust Field of View Help
#' @description This function calls \code{robustfov} help
#' @export
fslrobustfov.help = function(){
fslhelp(func_name = "robustfov")
}
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