makeMICeDefsHierachical: Creates a hierarchical anatomical tree

In Mouse-Imaging-Centre/RMINC: Statistical Tools for Medical Imaging NetCDF (MINC) Files

Creates a hierarchical anatomical tree

Description

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

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.

Value

a data.tree object containing the full anatomical hierarchy

Examples

## Not run: 
abijson <- "allen.json"
defs <- "Dorr_2008_Steadman_2013_Ullmann_2013_mapping_of_labels.csv"
hdefs <- makeMICeDefsHierachical(defs, abijson) 

## End(Not run)

Mouse-Imaging-Centre/RMINC documentation built on Nov. 12, 2022, 1:50 p.m.