voxel_point_intersect: Finds material properties of bone at any point

In BoneDensityMapping: Maps Bone Densities from CT Scans to Surface Models

Finds material properties of bone at any point

Description

Finds material properties of bone at any point

Usage

voxel_point_intersect(
  vertex_coords,
  nifti,
  ct_eqn = NULL,
  ct_params = NULL,
  rev_x = FALSE,
  rev_y = FALSE,
  rev_z = FALSE,
  check_in_vol = FALSE
)

Arguments

vertex_coords	Matrix
nifti	nifti object
ct_eqn	String. Equation to use for density calibration. Currently only "linear" is supported.
ct_params	Numeric vector. Calibration parameters for density calculation. For linear, first value is beta coefficient (y intercept), second value is sigma coefficient (gradient)
rev_x	Logical. Reverses x voxel coordinates
rev_y	Logical. Reverses y voxel coordinates
rev_z	Logical. Reverses z voxel coordinates
check_in_vol	Logical. Include check that model is in scans volume and print dimensions

Value

Vector. Vector with value for each point on surface

Author(s)

Scott Telfer [e-mail]

Examples

  # Download CT scan
  url <- "https://github.com/Telfer/BoneDensityMapping/releases/download/v1.0.2/test_CT_hip.nii.gz"
  scan_filepath <- tempfile(fileext = ".nii.gz")
  download.file(url, scan_filepath, mode = "wb")
  nifti <- import_scan(scan_filepath)
  url2 <- "https://github.com/Telfer/BoneDensityMapping/releases/download/v1.0.2/test_CT_femur.stl"
  bone_filepath <- tempfile(fileext = ".stl")
  download.file(url2, bone_filepath, mode = "wb")
  surface_mesh <- import_mesh(bone_filepath)

  # get density of surface bone directly
  mat_peak <- voxel_point_intersect(surface_mesh, nifti,
                                    ct_eqn = "linear",
                                    ct_params = c(68.4, 1.106),
                                    check_in_vol = FALSE)

  # remap and get density (for group level comparisons)
  landmark_path <- system.file("extdata", "test_femur.mrk.json",
                               package = "BoneDensityMapping")
  landmarks <- import_lmks(landmark_path)
  mapped_coords <- surface_points_template(surface_mesh, landmarks,
                                           no_surface_sliders = 1000)
  mat_peak <- voxel_point_intersect(mapped_coords, nifti,
                                    ct_eqn = "linear",
                                    ct_params = c(68.4, 1.106),
                                    check_in_vol = FALSE)

BoneDensityMapping documentation built on Aug. 8, 2025, 6:46 p.m.