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#' @title FSL Copy Geometry
#' @description This function calls \code{fslcpgeom}
#' @param file (character) image to be manipulated
#' @param file_with_header image with header to be copied over
#' @param retimg (logical) return image of class nifti
#' @param reorient (logical) If 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{fslmaths}
#' @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
fslcpgeom = function(
file,
file_with_header,
retimg = TRUE,
reorient = FALSE,
intern = FALSE,
opts = "",
verbose = TRUE,
...){
file_with_header = checkimg(file_with_header, ...)
all.opts = paste(shQuote(file), opts, collapse = " ")
### need to switch up file and file_with_header
### first file is the one copying information from
res = fslcmd(func="fslcpgeom",
file= file_with_header,
outfile = NULL,
retimg = retimg,
reorient = reorient,
intern = intern,
opts = all.opts,
verbose = verbose,
... = ...,
samefile = TRUE)
return(res)
}
#' @title fslcpgeom help
#' @description This function calls \code{fslcpgeom}'s help
#' @return Prints help output and returns output as character vector
#' @export
#' @examples
#' if (have.fsl()){
#' fslcpgeom.help()
#' }
fslcpgeom.help = function(){
return(fslhelp("fslcpgeom", help.arg=""))
}
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