surface_normal_intersect: Find material properties of bone at surface point using...

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

Find material properties of bone at surface point using surface normal

Description

Find material properties of bone at surface point using surface normal

Usage

surface_normal_intersect(
  surface_mesh,
  mapped_coords = NULL,
  normal_dist = 3,
  nifti,
  ct_eqn = NULL,
  ct_params = NULL,
  rev_x = FALSE,
  rev_y = FALSE,
  rev_z = FALSE,
  check_in_vol = FALSE
)

Arguments

surface_mesh	Mesh object
mapped_coords	Data frame. 3D coords of remapped surface points. If NULL, surface_mesh vertices will be used
normal_dist	Numeric. Distance surface normal should penetrate surface
nifti	Nifti CT scan image
ct_eqn	String. Equation to use for density calibration. Currently "linear" 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)
  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 <- surface_normal_intersect(surface_mesh, normal_dist = 3.0,
                                       nifti = nifti, ct_eqn = "linear",
                                       ct_params = c(68.4, 1.106))

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