morphomapAlignment {morphomap}

morphomapAlignment

Description

Align a femur bone following the protocol proposed by Ruff (2002)

Usage

morphomapAlignment(
  mesh,
  set,
  side = c("left", "right"),
  param1 = 4,
  iter1 = 2000,
  iter2 = 2000,
  iter3 = 2000,
  from1 = 180,
  to1 = 360,
  from2 = -5,
  to2 = 5,
  from3 = -5,
  to3 = 5,
  tol = 0.5
)

Arguments

mesh

3D mesh: femur long bone mesh

set

matrix: 7 landmarks acquired on the mesh (see details)

side

character: specify if the femur bone is "left" or "right" side

param1

numeric: parameter for spherical flipping (usually ranged between 3 and 4)

iter1

numeric: number of iterations first alignment

iter2

numeric: number of iterations second alignment

iter3

numeric: number of iterations third alignment

from1

numeric: inferior range of the allowed rotation in the first alignment

to1

numeric: superior range of the allowed rotation in the first alignment

from2

numeric: inferior range of the allowed rotation in the second alignment

to2

numeric: superior range of the allowed rotation in the second alignment

from3

numeric: inferior range of the allowed rotation in the third alignment

to3

numeric: superior range of the allowed rotation in the third alignment

tol

numeric: maximum allowed error in the alignment expressed in mm

Details

The function 'morphomapAlignment' is designed to align a femur bone. I did not tested on other long bones. The function requires 7 anatomical landmarks samples as follow: 1-the point at the center of the diaphysis in posterior view after the less trochanter, 2- the most posterior point on the lateral epicondyle, 3-the most posterior point on the medial epicondyle, 4- the most inferior point on the intercondilar fossa, 5- neck of the femur, 6- the most inferior point on the medial epicondyle and 7-the most inferior point on the lateral epicondyle. If the function in a short time does not complete the alignement, please stop the R session, check your landmark configuration or try to increase the value of the argument 'tol'.

Value

sur: mesh of the aligned femur bone

coo: coordinates of the landmark used in the alignment (plus two added automatically)

mech_length: mechanical length of the aligned femur bone

Author(s)

Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi