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#' MRI Defacer
#'
#' @param file input file image to remove face/ears
#' @param brain_mask brain mask of file. If \code{NULL}, \code{\link{fslbet}}
#' will be applied
#' @param bet_opts options to pass to \code{\link{fslbet}} if applied
#' @param search_radius search radius option to pass to \code{\link{flirt}}
#' @param opts additional options to pass to \code{\link{flirt}}
#' @param template_brain template brain image, may be \code{NULL}
#' @param template_brain_weight template brain weight image, used
#' for registration may be \code{NULL}
#' @param template_biometric_mask template biometric mask. Everything that
#' is wanted should be \code{1}, may be \code{NULL}
#' @param verbose print diagnostic messages. If \code{> 1}, more verbose
#' @param ... not used
#'
#' @note Adapted from
#' \url{https://github.com/mih/mridefacer}
#'
#' @return A character filename of the output image
#' @export
#'
#' @examples
#' if (have_fsl()) {
#' file = "~/Downloads/sample_T1_input.nii.gz"
#' if (file.exists(file)) {
#' res = mridefacer(file)
#' }
#' }
mridefacer = function(file, ..., verbose = TRUE) {
outfile = get_mridefacer_mask(file = file, verbose = verbose, ...)
if (verbose) {
message("Masking the image with mridefacer mask")
}
res = fsl_mask(file, mask = outfile, verbose = verbose > 1)
outfile = as.character(outfile)
attr(res, "mask") = outfile
return(res)
}
#' @export
#' @rdname mridefacer
get_mridefacer_mask = function(
file,
brain_mask = NULL,
bet_opts = "-f 0.5",
search_radius = 90,
opts = NULL,
template_brain = NULL,
template_brain_weight = NULL,
template_biometric_mask = NULL,
verbose = TRUE) {
null_brain = is.null(template_brain)
null_weight = is.null(template_brain_weight)
null_mask = is.null(template_biometric_mask)
res = sum(null_brain, null_weight, null_mask)
if (!res %in% c(0, 3)) {
stop("template information must all be NULL or all be specified")
}
dl_file = function(fname, filename) {
url = "https://raw.githubusercontent.com/mih/mridefacer/master/data/"
if (is.null(fname)) {
fname = tempfile(fileext = paste0("_", filename))
in_url = paste0(url, filename)
dl = download.file(in_url, destfile = fname,
quiet = verbose < 2)
stopifnot(dl == 0)
}
fname = checkimg(fname)
return(fname)
}
if (verbose & res == 3) {
message("Downloading template images")
}
template_brain = dl_file(template_brain,
"head_tmpl_brain.nii.gz")
template_brain_weight = dl_file(template_brain_weight,
"head_tmpl_weights.nii.gz")
template_biometric_mask = dl_file(template_biometric_mask,
"face_teeth_ear_mask.nii.gz")
if (verbose) {
message("Reorienting File")
}
rpi_img = rpi_orient_file(file, verbose = verbose > 1)
file = rpi_img$img
if (is.null(brain_mask)) {
# brain extract
if (verbose) {
message("Running Brain extraction")
}
brain_image = fsl_bet(file, opts = bet_opts,
verbose = verbose > 1)
bm = rpi_img
} else {
bm = rpi_orient_file(brain_mask, verbose = verbose > 1)
brain_mask = bm$img
brain_image = fsl_mask(file = file,
mask = brain_mask, verbose = verbose > 1)
}
# XXX SOME LIKE IT, SOME NOT
flirt_opts = c("-bins 256", "-cost corratio",
paste("-searchrx", -1*search_radius, search_radius),
paste("-searchry", -1*search_radius, search_radius),
paste("-searchrz", -1*search_radius, search_radius),
paste("-inweight", template_brain_weight),
opts)
flirt_opts = paste(flirt_opts, collapse = " ")
omat = tempfile(fileext = ".mat")
trans = tempfile(fileext = ".nii.gz")
if (verbose) {
message("Registering template brain to brain image")
}
res = flirt(
infile = template_brain,
dof = 12,
reffile = brain_image,
outfile = trans,
retimg = FALSE,
omat = omat, opts = flirt_opts,
verbose = verbose > 1)
if (verbose) {
message("Applying transformation to biometric mask")
}
outfile = tempfile(fileext = ".nii.gz")
outfile = flirt_apply(
template_biometric_mask,
reffile = brain_image,
outfile = outfile,
retimg = FALSE,
opts = "-interp nearestneighbour",
initmat = omat,
verbose = verbose > 1)
if (verbose) {
message("Reversing the reorientation from first step")
}
outfile = reverse_rpi_orient_file(
outfile,
convention = rpi_img$convention,
orientation = rpi_img$orientation, verbose = verbose > 1)
attr(outfile, "transformation_matrix") = omat
return(outfile)
}
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