Table of contents

• Overview
• Brief summary of the publication
• Video summary of the publication
• Requirements and setup
• Resources included in this repository
• Available MATLAB scripts
• Limitations and notes about reproducibility

Overview

This repository contains the data, models and the MATLAB scripts to inspect and reproduce the results of the following publication:

@article{Modenese2021bonedef,
  title={Dependency of Lower Limb Joint Reaction Forces on Femoral Version},
  author={Luca Modenese, Martina Barzan and Christopher P. Carty},
  journal={Gait & Posture},
  volume = {88},
  pages = {318-321},
  doi = {https://doi.org/10.1016/j.gaitpost.2021.06.014},
  year={2021},
  keywords = {Femoral version, Femoral anteversion, Musculoskeletal modeling, Tibiofemoral contact force, Knee Loading, Femur, Walking}
}

The paper is available open access at this link.

Brief summary of the publication

In our manuscript:

• We presented a MATLAB tool for applying torsional profiles to the bones of generic musculoskeletal models in OpenSim format. This tool is openly developed at this link.
• We investigated how the joint reaction forces in a musculoskeletal model of the lower limb change when the femoral version of that model is modified.
• We assessed the results of our simulations against the in vivo measurements of knee loads available at https://simtk.org/projects/kneeloads for patient 5, to identify the most accurate models.
• We found that the most accurate models were those with anteversion angle closer to that of the actual femur of the considered subject.
  

Video summary of the publication

Luca gave a talk at the 26th Congress of the European Society of Biomechanics presenting this work. The recorded presentation is available at the following link

Requirements and setup

In order to take full advantage of the content of this repository you will need to:

1. download OpenSim 3.3. Go to the Download page of the provided link and click on Previous releases, as shown in this screenshot.
2. have MATLAB installed in your machine. The analyses of the paper were performed using version R2020a.
3. set up the OpenSim 3.3 API. Required to run the provided scripts. Please refer to the OpenSim documentation.
4. (optional) NMSBuilder. NMSBuilder can be used to visualize how the femoral anteversion was estimated in the femoral geometries of the baseline model and in the segmented femur of the GC5 patient.
5. clone this repository together with the bone-deformation submodule using the following command on git:

git clone --recursive https://github.com/modenaxe/femoral_anteversion_paper.git

or if you have cloned it without the recursive option please refer to this post and use:

git submodule init
git submodule update

Resources included in this repository

This repository includes:

1. 1_scale_model folder:aA full-body OpenSim model that was reduced removing the arms and scaled to the anthropometrics of the fifth patient of the Grand Challenge Competition to Predict In Vivo Knee Loads.

2. 2_make_knee_weaker folder: scripts to make the knee crossing the knee joint weaker by 40%. GC5.osim is the model resulting from this operation, which is referred to as the baseline model in the manuscript.

3. 3_deform_femur_l folder: script that generates models applying a femoral anteversion ranging from 2 degrees retroversion to 40 degrees anteversion. These are referred to as modified models in the manuscript. The scripts depends on the bone-deformation tool that we have released with this publication. The bone geometries produced by the tool are available in the Geometry folder for model visualization.

4. 4_run_simulations folder: contains all the results from the simulations run for this publication. Please note that some input files are common to simulations with all models, so they were stored in the Common inputs folder. These common inputs are:

   • raw motion capture files (c3d folder, copied from the Grand Challenge website,
   • marker files (trc folder) ,
   • joint kinematics (IK folder),
   • ground reaction forces (External Loads folder). The Dataset folder then contains a folder for each model, e.g. GC5_FemAntev19Deg, and each folder includes:
   • muscle forces and activations estimated by static optimization (SO subfolder),
   • joint reactions (JR subfolder)
   • matlab files collecting all the simulation results (Mat_summary subfolder)

5. 5_analyze_results folder: includes scripts to analyze and plot the results of the simulations. Details of the scripts are presented in the next section. Other items are:

   • 2021-02-17_table_results.xls: the table of results then reported in the paper. A version of this table is generated automatically by analyze_JRFs.m.
   • Figure2_wt_text: the Figure 2 included in the manuscript. A version of this figure is automatically generated by plot_JRFs.m and stored in the folder 5_analyze_results/Figure_2.
   • eTibia_data.mat: a MATLAB file that stores in vivo medial and lateral forces for all patients of the Grand Challenge Competition to Predict In Vivo Knee Loads. It includes self-explicative column headers.

6. 6_muscle_length_variations folder: contains the scripts, mostly duplicated from the 5_analyze_results folder, to quantify the change in length of the muscles after the femur was deformed using the deformation tool. A table of results is included, together with a plot of the change in joint reaction forces after scaling the musculotendon parameters to the new length.

Available MATLAB scripts

The provided MATLAB scripts allow the reader to reproduce the results and figures included in the manuscript. The most relevant scripts are described in the following table:

Script name	Script action	Related item in the manuscript
make_knee_muscle_weaker.m	reduces the strenght of knee-spanning muscles in the specified model by 40%. Depends on getJointsSpannedByMuscle.m	N/A
create_femAnt_models.m	creates OpenSim model with the specified range of femoral anteversion angles. The baseline model has a femoral anteversion angle of 12 degrees. Depends on the bone-deformation toolbox in the msk_bone_deformation folder	N/A
step1_create_dataset.m	arranges contents of folders for running the simulations (only results are provided).	N/A
save_mat_summaries.m	converts the simulation results in a format usable for further analyses.	N/A
plot_JRFs.m	plots the joint reaction forces obtained from simulations with models having different femoral anteversion.	Figure 2.
analyze_JRFs.m	runs basic analyses on the joint reaction forces resulting from the simulations.	Table 1
a_muscle_lengths_vars.m	computes the length of the musculotendon paths and their percentage differences with respect to the baseline model.	Appendix B

Other MATLAB scripts included in the repository are dependent functions.

Limitations and notes about reproducibility

• All input, output and setup files required to run the simulations are provided, with the exception of the workflow employed for running the simulations in batch.
• Using the provided OpenSim setup files might require adjusting the input/output folders to your local setup.