Overview of the methods

For my dissertation, I created endocasts for 28 individuals (14 males and 14 females).


For All Specimens:

Creating the Endocasts (original and mirrored), Fixed Landmarks, Curve Semillandmarks:

For the Original Endocast:

- Create an endocast for the original scan using Avizo
- Save the project and export the endocast
- Place the 29 fixed landmarks
- Place landmarks for each of the 7 curves
- export the fixed landmarks and curves
- use resample.exe to resample the curves
- add the resampled curve landmarks to the fixed landmarks file using excel
- simplify the surface mesh using Meshlab

Files:
Morton####endocast_orignal_simplified.ply
Morton####_fixed_curve_landmarks.txt

Mirrored Endocast:

- mirror the simplified mesh using Meshlab
- mirror the landmarks and change the order


Files:
Morton####endocast_mirrored_simplified.ply
Morton####_fixed_curve_landmarks_mirrored.txt


Creating the Surface Semi-landmarks:

First create a template of the surface semi-landmarks:
- choose one specimen to be a template:
- use the geomorph package in R to create a template file

Files:
template.txt
Morton1306ply.nts (or specimen name used to create template)
surfslide.csv

Place surface semi-landmarks on the rest of the original and mirrored endocasts:
- use geomorph to place the landmarks on the rest of the specimens
- create a file indicating which landmarks are curves and the direction they can slide

Files:
an .nts file for each specimen's original and mirrored endocasts
curveslide.csv

Geometric Morphometric Analysis

Align all of the specimens' original and mirrored endocasts and slide the semi-landmarks:

- perform a generalized procrustes superimposition of all the specimens and slide the semilandmarks

Files:
gpaspecimens_slid_coords


Align each specimen's original and mirrored endocasts and calculate the Overall Asymmetry Value:

- perform a generalized procrustes superimposition on each specimen's data and calculate Procrustes distance

Files:
morton####alignedproc
ProcDistAll
ProcDistMales
ProcDistFemales

Calculate the Procrustes distance between each corresponding landmark of each specimen's original and mirrored endocasts:

- calculate Procrustes Distance


Files:
morton####ProcDist
ProcDistLandmarks_all_matrix
ProcDistLandmarks_all_mean
ProcDistLandmarks_males
ProcDistLandmarks_females
ProcDistLandmarks_males_mean
ProcDistLandmarks_females_mean


Visualizing the Procrustes distances:

-Add color to the Proc. distances

Files:
All landmarks:
scaledmeandist
meanprocdistcolorscale
surface semi-landmarks:
scaledmean_surfdist
mean_surfdist_colorscale

-Create an average coordinate shape:

Files:
mean_original_shape
mean_flipped_shape

-Export a point cloud (.ply) with the colored Proc. distances

Files:
mean_original_shape.ply

After data is read out:

- create a mesh from the point cloud and transfer the landmark color


Visualizing the direction of asymmetry:

-Plot the direction of asymmetry using R
-Plot the direction of asymmetry using MATLAB