#' @title Neurovault Query Atlas Region
#'
#' @description Searches atlas for specified region and related synonyms.
#' If no matches are found, it will search the NIF ontology
#' recursively for children of the specified region that are
#' found in the atlas. If no matches are found,
#' it will search recursively for parents that are found in the atlas.
#' Returns the corresponding to the X, Y and Z coordinates,
#' respectively, of the matching voxels. Coordinates are in mm in MNI space.
#'
#' @param region Region to search or query on
#' @param collection_name Collection name of the atlas
#' @param atlas_name Name of the atlas
#' @param secure passed to \code{\link{nv_base_url}} for https
#' @param verbose print diagnostic messages
#' @param ... additional options to pass to \code{\link{GET}}
#'
#'
#' @return List of the result of the \code{\link{GET}} call and
#' the content
#' @export
#'
#' @examples
#' res = nv_atlas_region(
#' region = "middle frontal gyrus",
#' collection_name = "Harvard-Oxford cortical and subcortical structural atlases",
#' atlas_name = "HarvardOxford cort maxprob thr25 1mm")
#' head(res$content$voxels)
nv_atlas_region = function(
region,
collection_name,
atlas_name,
verbose = TRUE,
secure = TRUE,
...) {
url = nv_base_url(secure = secure)
path = "/atlases/atlas_query_region/"
url = paste0(url, path)
query = list()
query$region = region
query$collection = collection_name
query$atlas = atlas_name
query = lapply(query, as.character)
L = get_results(
url, query = query,
verbose = verbose, ...)
L$content = append_results(
content = L$content,
verbose = verbose,
query = query,
...)
vox = L$content$voxels
vox = cbind(x = vox[[1]], y = vox[[2]], z = vox[[3]])
L$content$voxels = vox
return(L)
}
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