c3d2OS – Tutorial

1. Preliminary information

This tutorial aims to give the step-by-step procedure of c3d2OS.m MatLab© routine. Its main
propose is easily converting c3d experimental biomechanical data into OpenSim input files. No
additional software other than MatLab© is required. Users with little or no knowledge of
computer programing are encouraged to use it. The routine was developed by Felipe Costa
Alvim, PhD student from the Biomedical Engineering Program of the Federal University of Rio
de Janeiro, Brazil (PEB/COPPE/UFRJ). Some subroutines were developed by Gustavo Leporace
and Jasper Menger, which the author would like to thanks. The project is advised by L. L.
Menegaldo and the funds were provided by CNPq, CAPES, FAPERJ and FINEP, Brazilian
Government research agencies.

The .c3d file data will provide a .trc file with the reflexive markers trajectories and a .mot file
with joint angles, calculated by your motion capture system. To record a .mot file containing
also the external loads applied to your subject you will need a .csv file with forces, moments and
center of pressure of all force sensors used during data capture. Most of commercial motion
capture system allows selecting the desired data and recording it in a .csv file. Therefore, two
input files are required: a .c3d and a .csv.

A complete set of data for a three step single leg hop test is provided to help the user testing
the routine. The data was collected with a MOCAP system with eight infra-red cameras and two
AMTI XXX force plates.

2. Getting started

Download the c3d2OSpackage.rar, save it in a folder of your choice and decompress it. Open
your Matlab and select the folder witch you unzipped the c3d2OSpackage.rar file as “current
folder”. Then type “c3d2OS” in your command window. The routine will start to run and the
following sections explains how to proceed after that. The routine was implemented in version
XX of Matlab©. These routines were developed and tested with Matlab© 2014.

3. Choice what types of files to record

In the first window, choose the types of files you will want to write to use in OpenSim. You can
select one, two or all the options available.
After selecting (you can use Ctrl key to select more than one option) press “OK” button to
proceed. Sections 4, 5 and 6 describes how to proceed if you select “.trc (marker trajectories)”,
“.mot (generalized coordinates)” and “.mot (ground reaction forces)”, respectively.

We suggest starting from the static trial, selecting the 1st option (.trc maker trajectory). In the
c3d demo file, you can select the markers’ from T10 to RTOE2. This trial will be used to scale the
model.

4. Generating .trc (marker trajectories) file

If you have selected the option “.trc (marker trajectories)” in first window, the next window to
appear is as follows:
This window allow selecting the .c3d file with the markers trajectories history. Once you have
find your files choose only one and click in “Open” (“Abrir” on the figure below, in Microsoft
Windows 8 Portuguese version).

Write the output filename and press “OK”. You do not need to put “.trc” extension:

Select which markers will be uploaded in your .trc file (you can use Ctrl key to select multiple
markers). Markers will appear in this window with the same names you gave in the motion
capture system. The window below shows an example:
Once you have finished, click on “OK” button.

In the next window, select the motion capture system you used to collect your data. This step is
needed because each system defines its own (X,Y,Z) reference frames, which should be
converted to OpenSim standard. Two motion capture systems are predefined in the present
version of the routine: Vicon© and BTS©. Otherwise, edit the “convert_traj_axes.m” function to
match your needs.

For running the demo data, choose “VICON”.

After select you system, press “OK” button.

Luckily, your .trc (marker trajectories) file was written.

You can take a look on how your markers’ data look like using the OpenSim “Preview motion
data” option in the “File” menu.

5. Generating .mot (generalized coordinates) file

If you have only select .mot (generalized coordinates) in the first window (see section 3) you
must choose a .c3d file with the joint angles calculated by you motion capture system (see first
step of section 4). Otherwise, if you selected both .trc (marker trajectories) and .mot
(generalized coordinates), the routine will proceed without asking you to select any different
.c3d file than the one used in the previous step.

First, you should write an output filename and press “OK” button. You do not need to insert the
“.mot” extension:
Scroll down the window to select the joint angles calculated externally that will be taken into
account in the .mot file of generalized coordinates. Observe the example below:

Now, again, you must select the system used during data capture (See section 4). If your system
uses an alternative to Vicon© or BTS© lab configuration, please change the
“convert_traj_axes.m” routine.

Sometimes, you need to invert some generalized coordinates amplitudes depending upon you
model configuration in OpenSim. A window will ask you if you want to invert one or more
generalized coordinates.

The next window allow you selecting which coordinates should be inverted:
If you select joint angles that are not considered as generalized coordinates (or degrees of
freedom) in your OpenSim model, the message “DOF_not_allowed” will appear. Otherwise, you
can edit the “adapta_nomes_coordgen.m” function to add degrees of freedom to your model
and write new generalized coordinates data to your .mot file.

If you are using the demo data, you should invert hip_flexion, hip_rotation and ankle angle, for
both r and l sides.

In the end, your .mot (generalized coordinates) file will be recorded.

6. Writing .mot (ground reaction forces) file

First, you will be asked if kinetic data is available for both lower limbs. This step is necessary to
define the labels in first row of data. After pressing “OK”, you should select you .csv file
containing the ground reaction forces data.

Define the force plates sample rate (in Hertz):

Now a window will ask you to type the number of first line that ground reaction forces data
appears on the .csv file:

For example, in the figure below, ground reaction data starts at line 43:

In you ground reaction forces .csv file, by default, data must follow the order: Force (x,y,z),
Moments (x,y,z) and Center of Pressure (x,y,z). If you have two force plates, you should have:
Force1, Force2, Moment1, Moment2, CoP1 and CoP2. Otherwise, edit “lercsv1.m” function to
define a different order of data.

Type the output filename (without .mot extension) and press “OK”.
Now, select the ground reaction force device you use to collect data. Again, redefine the axes, if
necessary, by editing “convert_traj_axes.m” routine. The demo data uses “AMTI”.

Done! Your files were recorded!