rcylinders: Sample cylinder compartments

In midi: Microstructure Information from Diffusion Imaging

Sample cylinder compartments

Description

This function samples n cylinder compartments with given axis, radius and diffusivity distributions.

Usage

rcylinders(
  n,
  axis_mean,
  radius_mean,
  diffusivity_mean,
  axis_concentration = Inf,
  radius_sd = 0,
  diffusivity_sd = 0,
  restricted_model = c("Callaghan", "Neuman", "Soderman", "Stanisz", "Van Gelderen")
)

Arguments

n	An integer value specifying the number of compartments to sample.
axis_mean	A numeric value specifying the mean of the axis distribution.
radius_mean	A numeric value specifying the mean of the radius distribution.
diffusivity_mean	A numeric value specifying the mean of the diffusivity distribution.
axis_concentration	A numeric value specifying the concentration of the axis distribution. Defaults to Inf in which case the axis is fixed to the mean value.
radius_sd	A numeric value specifying the standard deviation of the radius distribution. Defaults to 0 in which case the radius is fixed to the mean value.
diffusivity_sd	A numeric value specifying the standard deviation of the diffusivity distribution. Defaults to 0 in which case the diffusivity is fixed to the mean value.
restricted_model	A character vector specifying the restricted diffusion model to use. Defaults to callaghan. Possible values are callaghan, neuman, soderman, stanisz, and vangelderen.

Details

The axis distribution is given by a mean and a concentration parameter and the Dimroth-Watson distribution is used to sample values. The radius and diffusivity distributions are given by a mean and a standard deviation and the Gamma distribution is used to sample values. If the concentration parameter is set to Inf the axis is fixed to the mean value. If the standard deviation of the radius and diffusivity distributions are set to 0 the radius and diffusivity are fixed to the mean values. If all parameters are fixed, only one compartment is sampled.

Value

A list of n cylinder compartments of class CylinderCompartment.

Examples

# Sample 10 cylinder compartments with fixed axis, radius and diffusivity
# set.seed(42)
cyl_distr <- rcylinders(
  n = 10L,
  axis_mean = c(0, 0, 1),
  radius_mean = 5,
  diffusivity_mean = 3
)

midi documentation built on July 6, 2026, 1:08 a.m.