QSM2Phylo: Convert QSM format to a phylo3D object

In treeDbalance: Computation of 3D Tree Imbalance

Convert QSM format to a phylo3D object

Description

qsm2phylo3D - Wrapper function that converts the output .mat-file of the software treeQSM (version 2.0 or 2.4.x) to a rooted tree in phylo3D format.

qsmList2phylo3D - Converts a list containing QSM data to a rooted tree in phylo3D format.

Usage

qsm2phylo3D(file, version = "2.4.x", setConnection2zero = TRUE)

qsmList2phylo3D(qsm_list, setConnection2zero = TRUE)

Arguments

file	File name (with path if not located in working directory), e.g.: "C:/...path.../myMatlabQSMfile.mat"
version	Specifies the version of the treeQSM .mat-file. Available are - "2.0" for version 2.0 and - "2.4.x" for version 2.4.1 and 2.4.2.
setConnection2zero	Logical value (default TRUE) indicating if the width of the edges, which connect two consecutive cylinders, should be set to zero. If FALSE, then the radius is set to the radius of the "child" cylinder.
qsm_list	List containing the QSM-data, with the attributes "radius", "length", "start", "axis", "parent" and "extension".

Value

qsm2phylo3D(file) A rooted tree in phylo3D format.

qsmList2phylo3D(qsmList) A rooted tree in phylo3D format.

Author(s)

Sophie Kersting

Examples

mat_file <- system.file("extdata", "exampleQSM.mat",
  package = "treeDbalance"
)
new_phylo <- qsm2phylo3D(file = mat_file)
new_phylo <- qsmList2phylo3D(NULL)

treeDbalance documentation built on Feb. 25, 2026, 1:06 a.m.