Qualisys PAF – OpenSim Example

Getting Started

To download this example project to your computer, you can either:

• Click here to download it as a zip file.
  — or —
• Clone this repository to your computer.

Video Tutorial

A video tutorial is available in the repository, providing an overview of how to use the PAF – OpenSim example.

Preparing Qualisys Data for OpenSim Processing

Note: QTM 2025.1 Update 1 introduces new export features for TRC (marker data) and STO (force data) files. Exports can now be performed directly within QTM and through any PAF modules. OpenSim models with Sport, CAST, and IOR marker sets are available in this repository at: paf-opensim-example-main\Templates\OpenSim

Prerequisites

• Install QTM 2025.1 Update 1 or later from Qualisys website

Export Options

Option 1: Export via PAF OpenSim Example

The PAF OpenSim example uses native QTM export functionality:

1. Start QTM and open the project 'PAF OpenSim Example'
2. Create or navigate to data:
   • Use the Project view (Ctrl+R) to create a person and session , or
   • Navigate to existing example files
3. Capture or import .qtm files, or use demo files
4. Filter marker data (recommended before export):
   • Open each measurement
   • Select all trajectories in the Labelled Trajectories list
   • Right-click and select Smooth trajectory (Butterworth)
   • To change filter frequency: Open Trajectory Editor → Modify Cutoff Frequency → Apply filter
5. Generate export files:
   • At session level: Start Processing → Generate .trc and .sto
   • This generates TRC and STO files for all QTM files in the session
6. Locate exported files:
   • Right-click session folder in QTM Project view
   • Select "Open folder in explorer"
   • Find .trc and .sto files

Option 2: Single Export from QTM Trial

• Open a qtm trial then go to File → Export → To TRC… or To STO…

Option 3: Batch Process Export

1. In QTM: File → Batch Process…
2. Navigate to folder with QTM files
3. Select multiple files using Ctrl + click → Open
4. Configure settings:
   • ✓ Enable: Export to TRC file and Export to STO file
   • ✗ Disable: Auto-backup files before processing, Pre-process 2D data, Gap-fill the gaps, Track the measurements
5. Press OK
6. Files are exported to same folder as QTM trials

Using Exported Files in OpenSim

Note: For detailed instructions or to use a different model, please refer to the OpenSim documentation.

Step 1: Setup

1. Start OpenSim 4.5
2. Load OpenSim model:
   • Model location for different marker sets: paf-opensim-example-main\Templates\OpenSim
   • File → Open Model → Navigate to gait2392_simbody_....osim

Step 2: Scale the Model

1. Tools → Scale Model
2. Click folder icon next to "Adjust Model Markers"
3. Navigate to your Static TRC file → Open
4. Click Run
5. Verify: Navigator tab shows new model with ...-scaled suffix

Tip: Check OpenSim documentation for additional scaling settings and marker fixation options to improve results.

Step 3: Run Inverse Kinematics

1. Tools → Inverse Kinematics
2. Click folder icon next to highlighted field
3. Navigate to your motion .trc file → Open
4. Click Run
5. Verify:
   • Skeleton moves in 3D viewer during processing
   • Navigator tab shows IKResults

Step 4: Run Inverse Dynamics

4.1 Configure External Loads

1. Tools → Inverse Dynamics → External Loads tab
2. Enable External Loads checkbox
3. Click note icon with pen
4. Select your STO trial file

4.2 Setup Right Leg Forces

1. Click Add
2. Configure force parameters:
   • Force Name: Right
   • Applied to: calcn_r
3. Set Force Columns (assuming right leg on force plate 1, check in QTM for that trial):
   • Column 1: 1_ground_force_vx
   • Column 2: 1_ground_force_vy
   • Column 3: 1_ground_force_vz
4. Set Point Columns:
   • Column 1: 1_ground_force_px
   • Column 2: 1_ground_force_py
   • Column 3: 1_ground_force_pz
5. Enable Applied Torque and set:
   • Column 1: 1_ground_torque_x
   • Column 2: 1_ground_torque_y
   • Column 3: 1_ground_torque_z

4.3 Setup Left Leg Forces

• Repeat steps above using 2_ground... prefixes
• Applied to: calcn_l

Important: Force plate numbers vary based on which plate each foot strikes. Verify in your QTM trial.

4.4 Complete Analysis

1. Click Save to save force configuration for the future use
2. Note the Output directory in Main Settings tab where you inverse dynamics results will be save as inverse_dynamics.sto
3. Click Run

4.5 Plot Results

1. Tools → Plot
2. Y-Quantity → Load File → Select inverse_dynamics.sto
3. Select desired signals (for example ankle_angle_r_moment) → OK
4. X-Quantity → Select Time
5. In Curves List: Select figure → Add

EMG in OpenSim

EMG analysis can be integrated with OpenSim. Reference example: EMG-informed Computed Muscle Control for Dynamic Simulations of Movement.

Additional Resources

• OpenSim documentation
• Tutorial 3 - Scaling, Inverse Kinematics, and Inverse Dynamics

Resources for Qualisys Project Automation Framework (PAF)

The Project Automation Framework (PAF) streamlines the motion capture process from data collection to final report. This repository demonstrates how PAF implements custom automated data collection in Qualisys Track Manager (QTM) and connects QTM to processing engines.

PAF Documentation

Full documentation for PAF development: PAF Documentation

PAF Examples

Official examples for various processing engines:

• AnyBody
• Cleanse
• Excel
• Matlab
• OpenSim
• Python
• Theia Markerless
• Theia Markerless Comparison
• Theia Markerless True Hybrid
• Visual3D

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License Note: As of QTM version 2.17, official Qualisys PAF examples can be used without additional license. Advanced analysis types require "PAF Framework Developer kit" license (Article number 150300).