Practical 2 – manual

1. Introduction
1.1. Preparation
• Read the information below;
• Download the necessary MATLAB functions from Canvas;
• Bring a USB stick to transfer the data to your computer/laptop;
• Bring tight shorts and a sleeveless shirt.

1.2. Organisation of the practical

In this practical, you work in a group to collect data according to the instructions below. In the
subsequent data analysis part of the practical, you will analyse the data and answer the questions
in this assignment to critically evaluate and interpret the data. You will write a short report
(individually) about the last exercise (jump-landing experiment); for more information, see the
template of the report on Canvas.

1.3. Equipment
For this practical, we will use a digital video camera (Nikon COOLPIX W300) and a 3D infrared
motion capture system (Optotrak Certus). Below you can find brief operating instructions.

1.3.1. Video camera

General use
• To capture the movement in the 2D video image correctly, align the video camera as good
as possible with the plane of movement of the task chosen.
• We will use pieces of sports tape as contrast markers taped to the skin to facilitate motion
tracking. Palpate the landmarks that you use for marker placement in a posture which is in
the middle of the movement range to reduce the effects of skin movements on your data.
Mark these anatomical landmarks with a pencil to replicate them later. Make a small
opening in the middle of the sports tape makers, through which you stick the Optotrak
LEDs. Attach the tape markers to the skin and fixate the LED in the middle of the tape
marker using double-sided tape.
• Next to the markers on the participant, we’ll also use four markers on a known vertical and
horizontal distance from each other on a board which we’ll put in the plane of movement,
perpendicular to the camera. These markers will be used as calibration markers to convert
video image coordinates to real-world coordinates later.

Perform a recording with the video camera

• Start the camera using the on/off button.
• You can check the camera setting using the menu button. Not many camera aspects can be
set in this simple camera. The focus, exposure and white balance are adjusted automatically
throughout the recording. The focus mode can be selected using the MOVIE AF MODE
in the shooting menu. Select the centre to avoid changes of focus during recording. Go
back in select MOVIE MODE and click OK to check the resolution and frame rate. Set
this to 1920x1080 (pixels per image) and 30 fps (frames per second) and Press OK.

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 • During recording, the camera only captures the part of the image screen between the two
horizontal green lines. The camera only has a digital zoom option. We do not use that as it
only reduces resolution. Make sure that you position your camera at such a distance from
your participant that all markers will be visible (between the green lines) throughout the
entire motion you want to record.
• Press the recording button to start recording a video.
• Press the recording button to stop recording a video.
• Turn off the camera.
• Video files will be stored on the SD card in the camera. You can transfer these files to your
computer using the USB cable. Open the side panel of the camera to connect the camera
to your computer. Turn on the camera again. Save your files in your folder.

Track markers of video data using Kinovea

• Open Kinovea.
• If the program settings are in Dutch go to the menu bar <opties>, <taal> and select
<English>.
• Open video file in the menu bar using <file>, <open video file..>.
• Mark the time frame of interest in the video file using the slider and green [ and ] symbols
below the video screen.
• Define a reference frame in your video by selecting <Image> from the menu bar. Then
select <coordinate system origin>. Click with your cursor in the video frame in the pop-up
window, to set the origin of your coordinate system, and click <apply>.
• Select the markers you want to track by clicking on this marker with the right mouse button,
and select <track path>. You can select multiple markers to track. Remember the order in
which you select these markers, as that will be the order in which they are stored in the
output file. Also, track the calibration markers.
• Press the play button to track the markers.
• Select <file> on the menu bar and then <export to spreadsheet>, select the format
<trajectories to simple text>.

1.3.2. Optotrak
General use
One Optotrak unit will be used in this practical together with one camera array (containing 3
cameras), that uses active infrared LED markers. The Optotrak camera will have to be connected
to the Optotrak control unit, which also takes a wired input from the ‘strober’. The strober is
connected to the LED lights (see Figure 1).

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Figure 1: Basic Optotrak (Certus) system.

FBWM-program
Optotrak data will be collected on a measurement computer. The program for collecting the data
is called ‘FBWM’.
• On the measurement computer, start the FBWM-program.
• Create a folder on the D-disk as a subfolder d:\data, where you wish to store your data.
Select this folder for further data acquisition.
• Note, when you get a message indicating that the parameter file is missing just continue
(you will set the ‘parameters’ (settings) of the measurement system later).
• Choose Experiment/Set Parameters.
• In General:
o Application name: "FBW (Default)".
o Set the collection time
o ‘EMG Sync pulse’ and ‘Timer’ off
• In Optotrak (kinematics):
o Enable Optotrak
o Set the number of markers you will use with each strober unit
o Set the sample rate
o Use interpolation off
o The Strober Voltage is the voltage applied to the markers, the default value of 7V
is OK

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 o The duty cycle is the fraction of time that a marker is actually turned on during the
o marker period, the default value of 0.5 is OK
o The marker frequency specifies the frequency at which individual markers are
strobed, the default value of 2800 Hz is OK
• Click OK to close this window.
• Choose Optotrak/Determine Optotrak Configuration, to check whether the system is
connected in the right way.
• Choose Optotrak/Calibrate to calibrate the system, i.e. to convert data from the local
reference frame of the Optotrak camera to the desired global reference frame in the
laboratory.
• Connect the calibration cube to the system.
• Enable Optotrak real time display.
• Check visibility of the markers of the cube in the field of view of the camera. Is this field
of view sufficient to record the position of the markers during your selected movement?
• Load the cube file corresponding to the calibration cube (under rigid body file).
• Select register and click collect data to start the calibration
• Place the cube in the right orientation to indicate the desired global reference frame.
• Select align and collect data to align the system.
• Check the result and close the window by pressing Quit.
o Click ‘OK’

Perform a measurement with Optotrak

• Choose Experiment/Measurement:
o The Optotrak data will be stored in TNxxxxxx.ndf. These data can be loaded in
MATLAB using the function readndf which you can find on Canvas. The output
of the Optotrak system is in millimetres.

2. Rigid stick experiment

Data collection
Use the calibration cube to calibrate the Optotrak system. As this calibration is automatically
performed by the software, we want to perform a small test to check whether this calibration went
successful. To do so, get the stick which has two markers attached at both end sites. Measure the
intermarker distance using a measurement tape and then move the stick around in the field where
we expect to measure.

Data analysis
a. Calculate the distance between the two makers of your measurements using Pythagoras
theorem. Was the calibration of the Optotrak system successful?

3. Jump-landing experiment
Data collection
The central question in this assignment is whether there are (kinematic) differences in forward and
backward jump-landing. In this assignment, you will measure the planar, unilateral joint positions
during ‘normal’ forward jump-landing from a box and backward jump-landing from the same box.

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Place markers on the following locations: malleolus lateralis (‘axis of rotation’ of the ankle joint),
epicondylus lateralis femoris (‘axis of rotation’ of the knee joint), pars superior of the trochanter
major (‘axis of rotation’ of the hip joint) and the tuberculum majus (‘axis of rotation’ of the
shoulder). Think about:
• The protocol for each measurement;
• The instructions that you will give to your participant;
• The number of measurements that you need to perform to draw a proper conclusion.

Data analysis – part 1

a. Make plots for each measurement (one for each mode of execution) for both video and
Optotrak data. Do you note any specific issues regarding the quality of your data for each
of both systems? If your data contains missing markers, interpolate your data and use the
interpolate data from this point onwards.
b. Calibrate the video data. To do so, calculate the distance between the calibration markers
in the video data and use this distance to convert the x- and y-coordinates of the video data
to real-world coordinates. Again, make plots for each measurement of the video data. Was
the calibration of the video data successful?
c. Make plots for each mode of execution, for this use only the Optotrak data. Interpret the
data and try to identify the different phases of the jump-landing. To what extent was the
experiment reproducible within the same type of jump-landing? Think of outcome
measures to indicate this.
d. Calculate the thigh length both in 2D as well as in 3D, for this use only the Optotrak data.
Plot the 2D and 3D-calculated thigh length as a function of time. 1) What could be the
reason for a non-constant thigh length? 2) What is the variance in thigh length? 3) Do you
think that this non-constant thigh length is an issue to answer your research question, why
(not)?
e. Calculate the knee angle using the function calcjointangle, do this for both Optotrak
and video data. Plot the knee angle as a function of time, interpret this plot to check whether
your calculations went successful. 1) Interpret the plot by describing the (change) in knee
angle over time. 2) Is there a difference between the knee angle of the Optrotrak and video
data? If so, what could be the reason?
From now onwards, only use the Optotrak data.
f. Calculate the centre of mass of each segment using Table 1. Plot the vertical positions of
the markers together with the vertical position of the centre of mass of each segment as a
function of time. Check whether your calculations were successful.
g. Calculate the centre of mass of the whole body, for this purpose use the function calccom.
Read the function description to check which inputs you need. For the (relative) masses of
the segments, you can use Table 2. Plot the vertical position of the centre of mass of the
whole body as a function of time in the previous plot (i.e., the plot with vertical positions
of the markers and the vertical position of the centre of mass of each segment as a function
of time). Check whether your calculations were successful.
h. Calculate the velocity and subsequently the acceleration of the centre of mass of the whole
body by using the MATLAB function gradient. Plot the vertical position, velocity and
acceleration of the centre of mass of the whole body in three (sub)plots. 1) Relate these
(sub)plots to each other, do they make sense? 2) Can you understand why there is
substantially more ‘noise’ in the acceleration signal than in the position signal?

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 i. Filter the acceleration of the centre of mass of the whole body (acom). Think of what type
of filter you should use and which cut-off frequency/frequencies. Use the function
filterfunc and test your filter by plotting the unfiltered and filtered acom as a function
of time in one plot.
j. Apply Newton’s second law of motion and calculate the ground reaction force based on
the mass of the participant, the gravitational acceleration and acom. Plot acom and the ground
reaction force in two (sub)plots. Relate these (sub)plots to each other, do they make sense?

Data analysis – part 2

The second part of the data analysis should be documented in a short report (see canvas). For some
items, you can use the (results of the) analysis done in part 1. There are a few items which could
be included in your report:
• The validity and reliability of your measurements; can the difference between both types
of jump-landing fully describe the execution of both tasks or are there possible
confounders?
• Compare the kinematic data of both types of jump-landings. Think about which kinematic
data (differences) you want to include/discuss and think about proper plots and/or tables to
stress out this data/these differences.
• Discuss the implication of the differences between both types of jump-landings. For
example, what might be the consequences of differences in ground reaction force (between
both types of jump-landings) for the reaction force in the knee and subsequently on the risk
of injury?

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Table 1: Relative centre of mass of each segment with respect to the proximal marker
Segment Proximal marker Distal marker Men Women This practical
Foot Ankle MTP5 0.500 0.500
0.500
Lower leg Knee Ankle 0.434 0.419
Upper leg Trochanter major Knee 0.433 0.428
Pelvis L5S1 Trochanter major 0.634 0.634
Trunk+head Shoulder L5S1 0.306 0.337
0.500
Upper arm Lateral epicondyle Shoulder 0.564 0.542
Lower arm Caput ulna Lateral epicondyle 0.570 0.566

Table 2: Segment masses as a proportion of body mass

Segment Men Women
2 x Foot 0.0286 0.0266
2 x Lower leg 0.0950 0.1070
2 x Upper leg 0.2100 0.2350
Pelvis 0.0792 0.1022
2 x Upper arm 0.0650 0.0580
2 x Lower arm 0.0374 0.0314
2 x Hand 0.0130 0.0100
Trunk 0.3892 0.3478
Head+neck 0.0826 0.0820