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#' @title SPM12 Realign (Estimate and Reslice)
#'
#' @description Performs SPM12 realignment estimation
#' and reslicing on an Image
#' @param filename Files to be realigned and resliced
#' @param fwhm Full-Width Half Max to smooth
#' @param register_to Should the files be registered to the first or the mean
#' @param reslice Options for reslicing all - all images in filename,
#' 2:n - all images in filename 2:length(filename),
#' all+mean - all images and the mean, mean - mean only
#' @param prefix Prefix to append to front of image filename
#' @param add_spm_dir Add SPM12 directory from this package
#' @param spmdir SPM dir to add, will use package default directory
#' @param clean Remove scripts from temporary directory after running
#' @param verbose Print diagnostic messages
#' @param outdir Directory to copy results.
#' If full filename given, then results will
#' be in \code{dirname(filename)}
#' @param install_dir directory to download SPM12
#'
#' @param ... Arguments passed to \code{\link{run_spm12_script}}
#' @export
#' @return Result from run_matlab_script
spm12_realign.deprecated <- function(
filename,
fwhm = 5,
register_to = c("first", "mean"),
reslice = c("all","2:n", "all+mean", "mean"),
prefix = "r",
add_spm_dir = TRUE,
spmdir = spm_dir(verbose = verbose,
install_dir = install_dir),
clean = TRUE,
verbose = TRUE,
outdir = NULL,
install_dir = NULL,
...
){
# .Deprecated(new = "spm12_realign"s)
install_spm12(verbose = verbose,
install_dir = install_dir)
########################
# Getting Number of Time points
########################
if (verbose) {
message("# Getting Number of Time Points\n")
}
time_points = ntime_points(filename)
reslice = match.arg(
reslice,
c("all","2:n", "all+mean", "mean"))
# check filenames
filename = filename_check(filename)
###################
# If reslice is just mean, then the file is simply returned
###################
if (verbose) {
message(paste0("# Reslice is ", reslice, "\n"))
}
if ( (reslice %in% "mean") ) {
outfile = filename
} else {
outfile = file.path(dirname(filename),
paste0(prefix, basename(filename)))
}
reslice = switch(reslice,
"all" = "[2 0]",
"2:n" = "[1 0]",
"all+mean" = "[2 1]",
"mean" = "[0 1]")
stub = nii.stub(filename, bn = TRUE)[1]
rpfile = file.path(dirname(filename),
paste0("rp_", stub, ".txt"))
meanfile = file.path(dirname(filename),
paste0("mean", stub, ".nii"))
matfile = file.path(dirname(filename),
paste0(stub, ".mat"))
##########################################################
# Pasting together for a 4D file
##########################################################
filename = paste0(filename, ",", time_points)
filename = rvec_to_matlabcell(filename)
register_to = match.arg(register_to, c("first", "mean"))
register_to = switch(register_to,
first = 0,
mean = 1)
jobvec = c(filename, prefix, fwhm, reslice,
register_to, spmdir)
names(jobvec) = c("%filename%", "%prefix%", "%fwhm%", "%reslice%",
"%registerto%", "%spmdir%")
res = run_spm12_script(
script_name = "Realign",
jobvec = jobvec,
mvec = NULL,
add_spm_dir = add_spm_dir,
spmdir = spmdir,
clean = clean,
verbose = verbose,
...)
stopifnot(res == 0)
####################
# Copy outfiles
####################
if (!is.null(outdir)) {
file.copy(outfile, to = outdir, overwrite = TRUE)
file.copy(rpfile, to = outdir, overwrite = TRUE)
if (!is.null(meanfile)) {
file.copy(meanfile, to = outdir, overwrite = TRUE)
}
file.copy(matfile, to = outdir, overwrite = TRUE)
}
l = list(outfiles = outfile,
rp = rpfile,
mean = meanfile,
mat = matfile)
return(l)
}
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