tag v1.0

.gitignore

@@ -1,2 +1,6 @@
 *.asv
 *.log
+*.fig
+*.png
+*.mat
+*.m

NOTICE.txt

@@ -31,4 +31,4 @@ by citing the following paper:
 
 Modenese L and Kohout J (2020). Automated Generation of Three-Dimensional 
 Complex Muscle Geometries for Use in Personalised Musculoskeletal Models. 
-Annals of Biomedical Engineering (under review).
+Annals of Biomedical Engineering, https://doi.org/10.1007/s10439-020-02490-4.

README.md

@@ -1,9 +1,20 @@
-# Overview
+# Table of Contents  <!-- omit in toc -->
+- [Overview](#overview)
+	- [Brief summary of the publication](#brief-summary-of-the-publication)
+	- [Video summary of the publication](#video-summary-of-the-publication)
+- [Requirements](#requirements)
+- [Contents](#contents)
+	- [Visualizing the anatomical dataset](#visualizing-the-anatomical-dataset)
+	- [Visualizing the OpenSim models](#visualizing-the-opensim-models)
+	- [Running the MATLAB scripts](#running-the-matlab-scripts)
+- [Limitations and notes about reproducibility](#limitations-and-notes-about-reproducibility)
+- [Future work](#future-work)
 
+# Overview
 This repository contains the data, models and the Matlab scripts to inspect and reproduce the results of the following publication:
 
 ```bibtex
-@article{Modenese2019three,
+@article{Modenese2020three,
   title={Automated Generation of Three-Dimensional Complex Muscle Geometries for Use in Personalised Musculoskeletal Models},
   author={Modenese, Luca and Kohout, Josef},
   journal={Annals of biomedical engineering},
@@ -27,6 +38,13 @@ ranges of motion consistent with normal gait. If you need some background readin
 
 ![muscle_deformations](https://github.com/modenaxe/3d-muscles/blob/master/images/muscle_deformations.png)
 
+## Video summary of the publication
+
+The paper associated with this repository was awarded the [:trophy: Athanasiou postdoctoral award :trophy: of the Biomedical Engineering Society (BMES)](https://www.bmes.org/athanasiou) and the talk Luca gave for the occasion, presenting the work and its future developments, has been recorded and shared on YouTube. Click on the image below to see the recorded:
+
+[![Alt text](images/youtube_thumbnail.png)](https://youtu.be/4YHMiScyYtg)
+
+
 # Requirements
 In order to take full advantage of the content of this repository you will need to:
 1. download [OpenSim 3.3](https://simtk.org/projects/opensim). Go to the `Download` page of the provided link and click on `Previous releases`, as shown in [this screenshot](https://github.com/modenaxe/3d-muscles/blob/master/images/get_osim3.3.PNG).
@@ -40,7 +58,7 @@ This repository includes:
 1. LHDL Anatomical dataset (see [reference publication](https://www.jstage.jst.go.jp/article/physiolsci/58/7/58_7_441/_article)) including:
 
 		a. bone geometries (pelvis, right femur)
-		b. muscle geometries for _iliacus_, _psoas_, _gluteus maximus_ and _gluteus medius_
+		b. muscle geometries for iliacus, psoas, gluteus maximus and gluteus medius
 		c. muscle attachments (as point clouds)
 2. OpenSim model with `straight-lines muscles` built from the LHDL dataset using NMSBuilder
 3. Motion data in OpenSim format (`.mot` files) to simulate the following hip motions:
@@ -78,7 +96,7 @@ So the order is:
 # Limitations and notes about reproducibility
 * The highly discretized muscle models are meant to be used for simulating the provided hip joint tasks and nothing else.
 * Please note that the results for the highly discretized muscles presented in the manuscript were generated from kinematic simulations 
-performed in LHPBuilder, a multimodal viewer for biomechanical application that is not developed or supported anymore. 
+performed in LHPBuilder, a multimodal viewer for biomechanical applications that is not developed or supported anymore. 
 A version of LHPBuilder compatible with the use done in this paper can be downloaded from 
 [this website](https://mi.kiv.zcu.cz/en/research/musculoskeletal.html). LHPBuilder is a complex
  tool requiring preliminary training to be used, so we decided instead to implement the muscle fibre kinematics in the OpenSim models directly. 

_support_functions/Storage2MatStruct.m → _support_functions/sto2MatStruct.m

@@ -5,7 +5,7 @@
 % DO NOT REDISTRIBUTE WITHOUT PERMISSION
 %__________________________________________________________________________
 %
-function StorageMatStruc = Storage2MatStruct(Storage_file)
+function StorageMatStruc = sto2MatStruct(Storage_file)
 % OpenSim suggested settings
 import org.opensim.modeling.*
 OpenSimObject.setDebugLevel(3);

c_generate_Fig4_Fig5.m

@@ -21,7 +21,7 @@
 % ----------------------------------------------------------------------- %
 % last modified 16 Oct 2017
 
-function c_generate_Fig3_Fig4()
+function c_generate_Fig4_Fig5()
 
 clc; close all;
 

d1_Table1_mom_arms_compare.m

@@ -60,7 +60,7 @@
     cur_task = task_set{n_t};
     % load mom arms from OpenSim model (saved from OpenSim GUI)
     MSK_results_file = [MSK_results_folder, filesep ,model,'_',cur_task,'.mot'];
-    osim_MA_task = Storage2MatStruct(MSK_results_file);
+    osim_MA_task = sto2MatStruct(MSK_results_file);
     % load results from highly discretized muscles
     load(fullfile(biomech_res_folder, ['Results_',model,'_',cur_task]));
 

d3_Table2_mom_arms_straight_lines.m

@@ -55,7 +55,7 @@
     in_deg = 'yes';
 
     % load mom arms from OpenSim model (saved from OpenSim GUI)
-    osim_MA = Storage2MatStruct(MSK_results_file);
+    osim_MA = sto2MatStruct(MSK_results_file);
     if strcmp(cur_task, 'hip_flexion')
         osim_MA.data = osim_MA.data(1:71, :);
     end