Creates a hierarchical anatomical tree

Makes a hierarchical tree using ontogeny from Allen Brain Institute

Usage

makeMICeDefsHierachical(defs, abijson)

Arguments

defs

CSV file describing anatomical labels. See details about format

abijson

The JSON file from the Allen Brain Institute

Value

a data.tree object containing the full anatomical hierarchy

Details

Takes the label definitions from a CSV file (same as the rest of the anat family of functions) and places it into a tree (using data.tree). The CSV file must thus have an extra column giving the corresponding name of each structure in the Allen Institute's nomenclature.

Currently the left and right structures are leaves at the end of the tree, and so are the first to be combined into the bilateral volumes. It is possible that in the future keeping hemispheres separate will be an option.

Examples

if (FALSE) { # \dontrun{
abijson <- "allen.json"
defs <- "Dorr_2008_Steadman_2013_Ullmann_2013_mapping_of_labels.csv"
hdefs <- makeMICeDefsHierachical(defs, abijson)
} # }