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#' SPM12 fMRI Contrasts
#'
#' @param spm Path to SPM.mat file
#' @param ... Arguments passed to
#' \code{\link{matlabbatch_to_script}}
#' @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 delete_existing Delete existing contrasts
#' @param contrast_list List of contrasts to pass to
#' \code{\link{spm12_contrast_list}} for conversion
#' @param install_dir directory to download SPM12
#'
#' @return A list of output and results
#' @export
spm12_contrast_manager = function(
...,
add_spm_dir = TRUE,
spmdir = spm_dir(verbose = verbose),
clean = TRUE,
verbose = TRUE,
install_dir = NULL
) {
install_spm12(verbose = verbose,
install_dir = install_dir)
L = build_spm12_contrast_manager(...)
spm = L$spm
if (verbose) {
message("# Running matlabbatch job")
}
res = run_matlabbatch(
spm,
add_spm_dir = add_spm_dir,
clean = clean,
verbose = verbose,
spmdir = spmdir)
if (res != 0) {
warning("Result was not zero!")
}
L$result = res
return(L)
}
#' @rdname spm12_contrast_manager
#' @export
build_spm12_contrast_manager = function(
spm,
delete_existing = TRUE,
contrast_list = NULL,
...
) {
# if (length(contrast_list) == 1) {
# contrast_list = list(contrast_list)
# }
contrast_list = spm12_contrast_list(contrast_list)
delete_existing = as.integer(delete_existing)
spmmat = normalizePath(spm)
xspmmat = spmmat
class(spmmat) = "cell"
spmmat = convert_to_matlab(spmmat)
names(contrast_list) = paste0("consess", names(contrast_list))
spm = list(
stats = list(
con = list(
spmmat = spmmat,
contrast_list,
delete = delete_existing
)
)
)
spm = list(spm = spm)
class(spm) = "matlabbatch"
script = matlabbatch_to_script(spm, ...)
L = list(
spm = spm,
script = script)
L$spmmat = xspmmat
return(L)
}
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