Version 3.

BodyBuilder for
Biomechanics

Oxford Metrics Ltd

 1997 Oxford Metrics Ltd

All rights reserved

Revision history
Created July 1995
Development version of VICON Editor and Modeller software (16 bit)
First update August 1995
Version 1.0 of VICON Editor and Modeller (16 bit) - limited release
Second update February 1996
Production version 2.0 (32 bit), renamed BodyBuilder
Third update April 1996
Production version 2.0 (32 bit), BodyLanguage manual separately bound
Fourth update February 1997
Production version 3.0, BodyLanguage manual re-integrated
Fifth update November 1997
Production version 3.5
Biomechanics edition

Intended Audience
This manual is intended for operators of VICON 370 systems who are familiar with Windows 95 or
Windows NT operating software, and with VICON 370 application software. Manuals for these
products are supplied separately
The following are registered trademarks or trademarks with registration pending:
Windows 95
Windows NT
i486, Pentium
IBM
Acclaim
Power Animator
Kinemation
SoftImage 3D
N-World
Lightwave 3D
Prisms
VICON, VICON 370, VICON 370E, VICON 140
BodyBuilder
BodyLanguage
DynaCal

Microsoft Corp.
Microsoft Corp.
Intel Corp.
International Business Machines Inc.
Acclaim Technologies Inc.
Alias Inc
Wavefront Inc
SoftImage Inc
Nichimen Graphics
NewTek
Side Effects Inc.
Oxford Metrics Ltd
Oxford Metrics Ltd
Oxford Metrics Ltd
Oxford Metrics Ltd

This manual was produced using Doc-To-Help, by WexTech Systems, Inc.

Oxford Metrics Ltd.

14, Minns Estate
West Way
Oxford OX2 0JB
tel.
+44 1865 261800
fax
+44 1865 240527
http://www.vicon.com, http://www.metrics.co.uk
Manual author: [email protected]

Contents
Introduction

Overview .................................................................................................................................. 1
Licensing .................................................................................................................................. 2
Computer Requirements ........................................................................................................... 2
Related Documentation and Technical Support........................................................................ 3
How to Use this Manual ........................................................................................................... 3
Software Installation................................................................................................................. 4

Using BodyBuilder

The Working Environment ....................................................................................................... 5

Manipulating Data .................................................................................................................... 5
Writing and Running Models ................................................................................................... 6
Work Flow................................................................................................................................ 7
Static Trials ................................................................................................................ 8

Workspace Window

Opening the Workspace Window ............................................................................................. 9

Selecting Trajectories ............................................................................................................. 10
Display of Trajectories and Sticks .......................................................................................... 10
Workspace Definition............................................................................................................. 12
Rotating the Viewpoint........................................................................................................... 12
Zooming the Viewpoint.......................................................................................................... 14
Moving the centre of rotation and zoom in the viewplane...................................................... 14
Changing the centre of rotation and zoom to a selected point on a trajectory ........................ 15
Alternative Display Modes ..................................................................................................... 16
Labels List .............................................................................................................................. 16
Label Mode .............................................................................................................. 17
Replay Control Bar................................................................................................................. 19

Graph Editor Window

21

Graph Editor ........................................................................................................................... 21

Controlling the Display........................................................................................................... 22
Changing the Time Scale.......................................................................................... 24
Changing the Vertical Scale ..................................................................................... 24
Moving the display laterally without changing scale................................................ 24
Moving the display vertically without changing scale.............................................. 25
Version 3.5 BodyBuilder for Biomechanics

Contents i

Selecting a Field Range........................................................................................................... 25

Point Dragging ........................................................................................................................ 27

Text Editor Window

29

Text Editing ............................................................................................................................ 29

Opening a Text Editing Window ............................................................................................ 29
Editing Text Files and Testing Changes.................................................................................. 30

File Menu Commands

33

File Menu................................................................................................................................ 33
Open........................................................................................................................................ 33
Merge ...................................................................................................................................... 34
Close ....................................................................................................................................... 34
Save......................................................................................................................................... 34
Range to Save ......................................................................................................................... 35
Save As ................................................................................................................................... 36
Write C3D............................................................................................................................... 37
Axis Changing .......................................................................................................... 39
Write ASCII ............................................................................................................................ 39
Options ..................................................................................................................... 41
Previous Files.......................................................................................................................... 42
Preferences.............................................................................................................................. 42

Edit Menu Commands

43

Edit Menu ............................................................................................................................... 43

Undo and Redo ....................................................................................................................... 43
Snip ......................................................................................................................................... 43
Delete ...................................................................................................................................... 45
Add Point ................................................................................................................................ 46
Create New Trajectory ............................................................................................................ 49
Delete Trajectory .................................................................................................................... 50
Delete Model Outputs ............................................................................................................. 50
Defragment Trajectories ......................................................................................................... 50
Delete and Fill......................................................................................................................... 51
Fill Gaps In ......................................................................................................................... 51
Fill All Gaps............................................................................................................................ 52
Maximum Fill Gap.................................................................................................................. 52
Copy Pattern ........................................................................................................................... 53
Move Point Mode ................................................................................................................... 55
Simple....................................................................................................................... 56
Weighted A mode ..................................................................................................... 57
Weighted B mode ..................................................................................................... 58
Expand/Reduce mode ............................................................................................... 59
Filter........................................................................................................................................ 60
Filter Characteristics................................................................................................. 60
Spike Removal.......................................................................................................... 61
ii Contents

Version 3.5 BodyBuilder for Biomechanics

Re-Sampling ........................................................................................................................... 62

View Menu Commands

65

View Menu ............................................................................................................................. 65

Toolbar ................................................................................................................................... 65
Status Bar ............................................................................................................................... 65
Rotation Centre....................................................................................................................... 66
Markers................................................................................................................................... 66
Stick Figure ............................................................................................................................ 66
Floor ....................................................................................................................................... 67
Flicker Free............................................................................................................................. 67
Always Refresh....................................................................................................................... 67
Set Frame Rate ....................................................................................................................... 67

Model Menu Commands

69

Model Menu ........................................................................................................................... 69

Run Model.............................................................................................................................. 69
Run Model for Subject ........................................................................................................... 70
Create ASF ............................................................................................................................. 70
Create AMC............................................................................................................................ 71
Create AMC Files............................................................................................................... 71
Axis Permutation .................................................................................................................... 72
View Model ............................................................................................................................ 73
View Parameters..................................................................................................................... 73
View Last Error ...................................................................................................................... 74
Adjust Parameters................................................................................................................... 74
Subject Settings ...................................................................................................................... 74

Interactive Parameter Adjustment

77

Parameters .............................................................................................................................. 77
Starting Interactive Adjustment .............................................................................................. 77
Parameter List......................................................................................................................... 78
Adjusting Values .................................................................................................................... 79
Finishing IPA.......................................................................................................................... 80

Workspace Menu Commands

81

Workspace Menu.................................................................................................................... 81
Select Centre........................................................................................................................... 81
Hide Trajectories .................................................................................................................... 81
Show Trajectories ................................................................................................................... 81
Hide Other Trajectories .......................................................................................................... 82
Hide All Trajectories .............................................................................................................. 82
Show All Trajectories............................................................................................................. 82
Toggle All Trajectories........................................................................................................... 82
Toggle Before Display............................................................................................................ 82
Version 3.5 BodyBuilder for Biomechanics

Contents iii

Toggle After Display .............................................................................................................. 83

Designing Biomechanical Models

85

Defining the Problem .............................................................................................................. 85

Dividing the Body into Segments ........................................................................................... 86
Approximations and Errors....................................................................................... 88
Modelling the Joints ................................................................................................. 89
Points, Lines, Planes and Segments ........................................................................................ 90
Single Point............................................................................................................... 90
Two Points................................................................................................................ 91
Three Points.............................................................................................................. 91
Four Points................................................................................................................ 92
Choice of Origin and Axes...................................................................................................... 93
Rotations ................................................................................................................................. 94

BodyLanguage

95

Overview................................................................................................................................. 95
Kinematic Modelling with BodyLanguage ............................................................................. 95
Before Starting ........................................................................................................................ 96
Writing the Model Script ........................................................................................................ 96
Verifying Model Scripts ........................................................................................... 96
Using Kinetic Data: Terms and Definitions ............................................................................ 97
Force ......................................................................................................................... 97
Moment..................................................................................................................... 98
Reaction.................................................................................................................... 98
Work and Energy...................................................................................................... 98
Power........................................................................................................................ 99
Moment of Inertia ..................................................................................................... 99
Applying the Model ................................................................................................................ 99
Displaying the Results ............................................................................................ 100

Objects

101

Types of Object..................................................................................................................... 101

Numbers.................................................................................................................. 101
Points ...................................................................................................................... 101
Segments................................................................................................................. 102
Rotations................................................................................................................. 102
Reactions ................................................................................................................ 103
Object Names........................................................................................................................ 103
Limitations of Object Names .................................................................................. 104
Reserved Names ..................................................................................................... 104
Object Assignment and Type Definition............................................................................... 105
Inputs .................................................................................................................................... 106
Optional Points ....................................................................................................... 106
Outputs.................................................................................................................................. 107
Parameters............................................................................................................................. 108
iv Contents

Version 3.5 BodyBuilder for Biomechanics

Samples ................................................................................................................................ 108

Expressions

109

Types of Expression ............................................................................................................. 109

Numbers ................................................................................................................. 109
Points...................................................................................................................... 109
Segments ................................................................................................................ 110
Segment Definition................................................................................................. 111
Segment Definition across Hinge Joints................................................................. 113
Singularities and Dead Band .................................................................................. 114
Anti-Flip................................................................................................................. 115
Hierarchical Skeletons............................................................................................ 119
Rotations of Segments .......................................................................................................... 121
Rotation Definition................................................................................................. 122
Helical Vectors....................................................................................................... 122
Global Rotations..................................................................................................... 123
Rotations about Fixed or Floating Axes ................................................................. 123
Gimbal Lock........................................................................................................... 124

Kinetic Modelling

125

Mass and Inertia Properties of Segments.............................................................................. 125

Direct Definition of Mass Properties...................................................................... 125
Definition using a Table ......................................................................................... 125
Correcting for the Mass of a Prosthesis.................................................................. 127
Reactions, Forces and Moments ........................................................................................... 128
Force ...................................................................................................................... 128
Moment .................................................................................................................. 128
Reaction ................................................................................................................. 129
Force Plate Data ................................................................................................................... 130
Segment (free body ) Equations of Motion ............................................................ 131
Connection of other reactions................................................................................. 131
Gravity.................................................................................................................... 132
Linear Acceleration and Angular Velocity and Acceleration................................. 132
Intersegmental Power Flow.................................................................................... 132
Units ....................................................................................................................... 133

Operators

135

Types of Operator................................................................................................................. 135

Number Operations ................................................................................................ 136
Point Operations..................................................................................................... 136
Segment Operations ............................................................................................... 138
Rotation Operations (none permitted) .................................................................... 138
Selection Operator.................................................................................................. 139

Functions
Version 3.5 BodyBuilder for Biomechanics

141
Contents v

Types of Function ................................................................................................................. 141

Number Functions................................................................................................................. 141
Point Functions ..................................................................................................................... 142
Segment Functions................................................................................................................ 144
Rotation Functions ................................................................................................................ 144
Special Functions .................................................................................................................. 144
Spine ..................................................................................................................................... 146
Length and Stiffness ............................................................................................... 147
Multiple Segments/Vertebrae Mode ....................................................................... 147
Shorthands and Tokens ......................................................................................................... 148
Non-Assigning Statements.................................................................................................... 149
Conditionality Tests .............................................................................................................. 149
Dealing with Marker Occlusions ............................................................................ 149

Macros

151

Uses of Macros ..................................................................................................................... 151

Text Concatenation Operator ................................................................................................ 152

Other Expressions

153

Comments ............................................................................................................................. 153

Error Codes ........................................................................................................................... 153

Example Model - FOOT

155

Anatomical Structure ............................................................................................................ 155

Axis Definitions...................................................................................................... 155
Handedness............................................................................................................. 156
Model Script ......................................................................................................................... 156
Comment Section.................................................................................................... 156
Macro Substitute4 ............................................................................................... 157
Optional Points ....................................................................................................... 159
Segment Definitions................................................................................................ 159
Angle Output Section.............................................................................................. 168
Left Foot Script ..................................................................................................................... 168

Example Model - Kinetic Leg Model

169

Kinematic Principles and Limitations ................................................................................... 169

Force Vectors ........................................................................................................................ 170
Segment Definitions.............................................................................................................. 171
Definition and Output of Rotations....................................................................................... 175

Glossary of Terms

191

Index

195

vi Contents

Version 3.5 BodyBuilder for Biomechanics

Introduction

Overview
BodyBuilder for Biomechanics is a software package which enables the
user to:

Manipulate data produced by VICON 370

Edit and modify trajectories

Interpolate broken trajectories

Create kinematic and kinetic models

Choose any marker set

Model body segments and joints

Calculate angles and moments

View results on screen

Output results to file

Display results in a flexible format

Create text file output

Define and save output formats

BodyBuilder for Biomechanics is a powerful set of tools for investigating

human movement. Models and outputs can be as simple or complex as
required.
The BodyBuilder for Biomechanics package contains two program
applications: BodyBuilder and Reporter. BodyBuilder is the data
manipulation and modelling element, and Reporter is the flexible graphic
output element.

Version 3.5 BodyBuilder for Biomechanics

Introduction 1

Licensing
It is intended that BodyBuilder for Biomechanics should be installed on
the PC Workstation which forms part of each VICON 370 motion
capture system. BodyBuilder for Biomechanics is hardware-protected,
meaning that you require a dongle (hardware key), issued by Oxford
Metrics, plugged into your computers parallel port, in order to run the
program.
Licensed users may wish to run additional copies of BodyBuilder for
Biomechanics on other computers. This will require additional dongles,
even if those computers are part of the same local area network. For
additional dongles, refer to Oxford Metrics Ltd or local agent.

Computer Requirements
To run BodyBuilder for Biomechanics, you need a PC with a 486
(minimum) or Pentium (recommended) processor. The better your
processor and the faster your clock speed, the faster the program will
run. A substantial video memory is advisable, with PCI bus 800600
accelerated graphics, and at least 16MB RAM. A large hard disk
(recommended minimum 200MB, ideally 1GB)is essential; and a backup
device such as a ZIP or DAT drive is strongly recommended. A 32-bit
operating system, either Windows NT (recommended) or Windows 95 or
98, is required.
When large .C3D files are opened or generated, the computer may
require a very large swap file. This will cause slow running if your hard
disk does not have a significant amount of free space (as much as 60MB
may be needed). If you are using Windows 95, this may give the
appearance of hanging up; Windows NT behaves better in this respect,
and is the recommended operating system. Windows NT comes in two
versions, Server and Workstation. The Server version, as the name
implies, is intended for computers which are the hub of a network,
controlling shared resources, while the Workstation version is for
computers used for running applications such as BodyBuilder for
Biomechanics. Standalone computers should use the Workstation
version.

2 Introduction

Version 3.5 BodyBuilder for Biomechanics

Related Documentation and Technical Support

BodyBuilder for Biomechanics is designed to process data created by the
VICON 370, VICON 370E, and VICON 140 three-dimensional motion
capture systems from Oxford Metrics Ltd. Manuals for these products
are supplied separately. Further copies of these manuals, technical
advice, software and documentation updates, service and support are
available from Oxford Metrics, both directly and through their agents
and representatives, for a period of one year from the date of the original
purchase. After this period, an extended service contract is available in
most areas - please refer to Oxford Metrics or your local agent.
BodyBuilder for Biomechanics is supplied with online help, the text of
which is similar to the manual. Example model script files and data are
also supplied with the program.

How to Use this Manual

This manual contains all the information which you need to use,
or learn to use, BodyBuilder for Biomechanics.

Some chapters are largely explanatory and are recommended

for new users.

Some chapters are largely reference material, describing

features, functions and commands in detail.

If you are a new user, you should read this chapter, which contains
general information about the software, and then install the software if
that has not already been done. You should also read the next chapter,
Using BodyBuilder, which is a brief introduction to the BodyBuilder
program. The following ten chapters contain detailed reference material
relating to BodyBuilder. Keep this section to hand when you start using
the program and need to look up information on specific points. The
following two chapters, about designing biomechanical models using
BodyLanguage, provide a general discussion of the principles of
modelling, and should be read by all users. The following seven chapters
contain detailed reference material about BodyLanguage.
It is possible to use BodyBuilder for Biomechanics without learning the
details of BodyLanguage, or writing models, because example models
are supplied. However, the flexibility of being able to write or modify
models is the most important feature for many users. Users who do not
Version 3.5 BodyBuilder for Biomechanics

Introduction 3

want to develop their own models may benefit from an understanding of

the models they use, so a look at the section on BodyLanguage is
recommended. Commented example models are included, and if you are
using one of these models, it is a good idea to read through the comments
and to gain an idea of what the model does.
If you are upgrading from another version and are already familiar with
BodyBuilder and Reporter, you should look at the sections describing the
new features (kinetic extensions to BodyLanguage, interactive parameter
adjustment, and multiple subject trials).

Software Installation
For all VICON-related software, the top level directory should be
C:\VICON
where C: is the local hard disk drive. Each application program should
have a subdirectory in the above top level directory, so BodyBuilder and
Reporter will be installed in the directories
C:\VICON\BODYBLD

and

C:\VICON\REPORTER

respectively. These directories will be created by the installation utility,

unless the user chooses otherwise. Certain additional subdirectories will
be created for the associated files and example data shipped with the
application programs.
The installation utility provides its own instructions, but if any problem
should arise with this process, please contact Oxford Metrics or your
local agent.

4 Introduction

Version 3.5 BodyBuilder for Biomechanics

Using BodyBuilder

The Working Environment

The term BodyBuilder refers to the application program which carries
out the functions of editing and modifying the original data; applying
models; providing facilities for model editing; and displaying 3dimensional data through the Workspace display window. This manual is
concerned with BodyBuilder; Reporter is documented separately.
In common with most Windows applications, when BodyBuilder is
launched, a blank window opens with a limited number of menus and
commands available. Once a data file is opened, however, more menus
and commands become available. A certain number of other files are
required in addition to the 3-dimensional data, including model scripts
and their parameters, and marker labels with stick-figure links.

Manipulating Data
BodyBuilder can be used for data editing without modelling. The editing
functions include filtering, interpolation, trajectory snipping and
deleting, trajectory copying and moving, re-sampling of trajectories to a
different sample frequency, and relabelling. These functions alone
provide a significant range of tools which may be used to improve data
which is imperfect (for example, interpolating short gaps, filtering of
high-frequency noise, and rectifying errors in the reconstruction and
initial labelling). These functions may be regarded as tools for cleaning
up previously unsatisfactory data. Often, these functions are used before
going on to modelling and data presentation.
The editing functions also allow the user to modify the data by moving
points, creating new trajectories, and otherwise making substantial
changes to the original data so that the output no longer represents what
Version 3.5 BodyBuilder for Biomechanics

Using BodyBuilder 5

was measured in certain respects. These functions allow for experiments

and for testing of different cases based on a limited initial amount of
data. However, the user should be aware of the degree to which the data
has departed from the reality of what was actually measured, particularly
if the results are to be interpreted as an accurate and objective study of
human movement. Even excessive filtering or interpolation can lead to
important departures from objectivity in certain cases, and the user must
develop a clear sense of the boundary between making minor
improvements to the data, and significantly changing the original
measurements.
The commands used to open files, control the display of data, and to use
the editing functions, are listed in the File, View, Workspace and Edit
menus.

Writing and Running Models

The model script is a separate file with the extension .MOD, and it is
normally stored in the directory
C:\VICON\MODELS
The script to be used must first be selected (loaded). When BodyBuilder
is first launched, no script is loaded; a selection must be made before the
modelling-related commands become active. Only one script may be
open at any time.
A text editing window is opened when a model script is loaded, allowing
changes to be made. Changes take immediate effect, and do not have to
be saved before they can be run. A parameter file is used in all but the
simplest models, which contains values that may change frequently (eg.
the physical measurements of the subject) and are stored this way so that
they can be modified without editing the model script itself.
As with the model script, it is necessary to select and open a data file on
which to operate; no data file will be opened automatically.
If a data file is open, and a model script loaded, and assuming that they
are compatible, the command Run Model may be used to apply the
model to the data. BodyBuilder then goes through the data frame by
frame, calculating all the new points and other variables defined in the
6 Using BodyBuilder

Version 3.5 BodyBuilder for Biomechanics

model script. The results are then displayed in the Workspace window,
and may be saved (until saved, the newly calculated points are held only
in volatile system memory; the original data file on disk is not modified
unless the user chooses to overwrite it).
It is possible to make changes to a model script and immediately apply
the changed script to some data to see the effect. This allows rapid model
development and testing. It is also possible to make changes to the values
of parameters and to see the effects of these changes immediately in the
workspace, using interactive parameter adjustment.
When a model script has been fully developed, the text editor window
need not be displayed; the model can simply be loaded and run without
change.

Work Flow
The flexibility of BodyBuilder for Biomechanics allows the following
order to be changed according to needs, however this is the normal flow
of work when processing data using an existing model:

Decide the purpose of the measurements, select model and

marker set

Measure physical parameters (if appropriate) of subject, and

attach markers

Collect data using VICON 370

Reconstruct and identify the trajectories, using labels

corresponding to those specified in the model script

Produce C3D file

Start BodyBuilder and open C3D file

Use editing tools to clean up the data if necessary

Load model and check parameters

Run model and examine results

Select suitable output format and save

Start Reporter, load output data and print results

Version 3.5 BodyBuilder for Biomechanics

Using BodyBuilder 7

Static Trials
A common variation on the above procedure is the inclusion of a static
trial. This is a short data capture during which the subject remains still
(or nearly so) and is for the purpose of measuring certain parameters.
Users who need to produce Acclaim Skeleton Files use static captures for
this purpose. Static trials can also be used together with conditional parts
of a model script, to measure certain quantities and write them to the
parameter file, so that they are available when the dynamic data is
processed. In some cases, variations on the marker set are used for the
static trial. An example is the extra heel markers used during the static
trial required by VICON Clinical Manager (VCM) gait analysis software.
In that case, the purpose of the static trial is to allow the dynamic gait
analysis to take place using the minimum possible marker set.
In version 2.5 of VICON 370 software, it is possible to label data semiautomatically, having first manually labelled a static trial. The C3D (trial
data) files produced in this way retain information about the subject
name and the marker set used during auto-labelling, and whether the trial
was a static trial for auto-labelling purposes.

8 Using BodyBuilder

Version 3.5 BodyBuilder for Biomechanics

Workspace Window

Opening the Workspace Window

BodyBuilder uses a VICON 370 Workspace window to display the
contents of a .C3D file, to facilitate data editing, and to display the
results of kinematic modelling. To open a Workspace window, select
File | Open, then select the desired .C3D file. More than one Workspace
window may be open simultaneously, but only one may be active at any
time. The active window has a highlighted title bar. To make a different
window active, place the pointer within it and click the left mouse
button. Trajectories in the active window may be selected and edited.

VICON Workspace windows use true perspective projection, rather than

isometric or planar projection. This enhances the realism and usability of
the display.
Version 3.5 BodyBuilder for Biomechanics

Workspace Window 9

The Workspace window in BodyBuilder does not display objects defined

in .WKS or .OBJ files. For clarity, the floor tiling is automatically sized
to show the area covered by the motion data.

Selecting Trajectories
Up to 24 trajectories may be
selected at a time. Current
selections are lost when the
current trial is closed.

Most editing features operate on selected trajectories. To select a

trajectory, move the pointer close to the chosen trajectory and click the
left mouse button. The selected trajectory changes from blue to yellow.
Subsequent selections change to red, purple, and dark blue, with this
colour cycle repeating for further selections. You cannot select a
trajectory until the mouse helper appears - this may take a few moments.
To de-select a trajectory, click the right mouse button (with the pointer
anywhere in the window). If several trajectories have been selected, they
are de-selected in reverse order.

By default, the Mouse Helper

is active. To disable it, use
the View | Mouse Helper
command.

There is an aid, called the Mouse Helper, to assist selection. When the
tip of the pointer arrow is close enough to a trajectory to allow that
trajectory to be selected, a box appears on the pointer containing the
label and the field number of the point closest to the mouse pointer. If
the trajectory is unlabelled, the box contains a dash.

Display of Trajectories and Sticks

3D data can be displayed as

markers at 3D points in the current field

sticks connecting 3D points in the current field

trajectories connecting points before and/or after the current

field

Use the View|Markers command to turn the marker display on and off.
If the user needs to label (or re-label) a trajectory or segment of a
trajectory, a .MKR file containing the desired label set must be made
available. Use the Model | Subject Settings... command to select a .MKR
10 Workspace Window

Version 3.5 BodyBuilder for Biomechanics

file with the required label names and stick connections between labelled
points. The initial .MKR file available when BodyBuilder is started, is
the one selected in the application preferences. This may not be
appropriate to the file you wish to edit. When editing a .MKR file, take
care to enter the correct number of labels and stick connections.
Some marker set files may contain several different display sets (that is,
different sets of sticks). These may be selected from the drop down list
above the list of markers at any time.
Stick connections may be defined which connect the points which result
from the reconstruction of real marker positions by VICON 370, and also
the virtual points created by a kinematic model. Sticks are displayed as
green lines.
Unlabelled trajectories and points are displayed in white. Labelled
trajectories and points are displayed in cyan. Selected trajectories are
displayed in a colour which depends on the order of selection. By
default, the length of trajectory displayed is one field either side of the
current field. The length displayed may be controlled by the user.
Initially, the trajectory
length displayed is one field
either side of the current
field.

Use the Before and After scroll bars in the lower right corner of the main
window to control the length of the trajectory display before and after
the current field.
If the Before and After slide bars are moved all the way to the left, no
trajectories are displayed in any Workspace window. The markers on the
current field may still be displayed, according to the setting of the View |
Markers command. In this state, trajectory selection is not possible in the
Workspace window.

Workspace Definition
Workspaces are built on an outlined and tiled floor that represents the
area or workspace where the kinematic data was collected. The size
and shape of the outline and tiles are automatically set and are not userselectable, as they are in VICON 370. This simplification has been made
in order to avoid a cluttered appearance in the window, and because
BodyBuilder is not concerned with kinetic (force) data.
Version 3.5 BodyBuilder for Biomechanics

Workspace Window 11

Rotating the Viewpoint

The Workspace is a 3-dimensional, perspective view of the experimental
volume. The viewpoint may be changed by rotating the workspace and
by moving towards or away from the rotation centre of the workspace to
widen or narrow (zoom) the field of view.

It is easiest to select the best point of view after stopping the replay of
moving points and sticks.
If the replay is running, you can stop it by pressing the spacebar.
Rotate about a vertical axis through the current centre of the image by
positioning the pointer anywhere within the dark area of the Workspace
window, holding down the left mouse button, and moving the mouse left
or right. The workspace rotates in the direction of mouse movement until
the pointer runs off the edge of the screen.

12 Workspace Window

Version 3.5 BodyBuilder for Biomechanics

Rotate about a horizontal axis by holding down the left mouse button and
moving the mouse up and down. The workspace rotates in the direction
of mouse movement. The viewpoint can move through a range which
takes it from directly underneath (yellow floor grid) to directly overhead
(white grid). In VICON 370 software, the viewpoint cannot be moved
below floor level or over the top of the workspace, since this would turn
the view upside down. In BodyBuilder, this potentially confusing point
of view is permitted, but should be used with caution.
Horizontal and vertical rotations can be combined in a single mouse
movement.

Zooming the Viewpoint

Version 3.5 BodyBuilder for Biomechanics

Workspace Window 13

Zoom by positioning the pointer anywhere within the dark area of the
Workspace window, hold down the right mouse button, and move the
pointer up to zoom-in or down to zoom-out. If the mouse pointer runs off
the edge of the screen, release the button, move the pointer back into the
screen, and repeat the zoom action. There is no theoretical limit to the
range of zoom that can be applied.
Rotations and zooms cannot be made simultaneously.

Moving the centre of rotation and zoom in the viewplane

The current centre of
rotation is displayed by
default as a small purple
diamond. To remove it, use
the View | Rotation Centre
command.

The Workspace rotates around a position called the centre of rotation.

Zoom operates toward or away from it. When a Workspace window is
first opened, this is located at the origin of the kinematic coordinate
system.
The centre can be moved in the current plane of view. With the pointer
anywhere within the dark area of the Workspace window, hold down the
Control key and the left mouse button, and move the pointer horizontally
and/or vertically. The Workspace view moves in the same direction,
creating a new centre of rotation and zoom. Alternatively, you can press
both mouse buttons together and move the mouse, to move the Rotation
Centre.
A combination of rotation and viewplane movements allows the centre of
rotation and zoom to be placed anywhere within the Workspace.

Changing the centre of rotation and zoom to a selected point

on a trajectory
The centre of rotation and zoom can be changed to any point on a
selected trajectory.

14 Workspace Window

Version 3.5 BodyBuilder for Biomechanics

The selected trajectory remains selected after centring. The chosen point
on a selected trajectory may not correspond to the current field. In the
above example, the selected trajectory is shown yellow; the chosen point
for centring is marked by a white cross. You cannot select a trajectory
until the mouse helper appears - this may take a few moments depending
on your PC.
Shortcut: C key

Hold the pointer steadily at the chosen point and click with the left
mouse button to select this point. If the trajectory segment is the
only one selected, it changes colour to yellow. If other trajectories
are already selected, another colour is used. Use the Workspace |
Select Centre command to make the selected point the new
rotation centre.

Alternative Display Modes

BodyBuilder can run on a wide range of computers. Some computers
have fast processors, some have fast graphics hardware, and others use
fast data transfer buses. The optimal display mode setting for Workspace
windows depends on the relative performance of these variable
resources.
Change the plotting mode by using the View | Flicker Free and View |
Always Refresh commands.

Version 3.5 BodyBuilder for Biomechanics

Workspace Window 15

Labels List
The .MKR file can be edited
using any text editing utility,
and is normally found in
the \MODELS directory.
If the Windows NOTEPAD
editor is used, remember to
Save any changes, and then
update the displayed list by
using the Edit | Attach
Marker Set... command.
It is not necessary to close
the NOTEPAD editor
between modifications as it
does not "lock the file.

On the right hand side of the main program window, there is space for a
list of labels. When a .C3D file is opened, if it was autolabelled, the
marker set used for labelling will be loaded. For a manually labelled
C3D file, if it is located in a session directory, BodyBuilder reads the
SES file and locates the corresponding MKR file.
If there is no such .MKR file, BodyBuilder displays the last label list
used in previous work. If this list is unavailable, the label list is blank.
If multiple .C3D files are open simultaneously, the list corresponding to
the currently active Workspace window is displayed.
If all Workspace and Graph Editor windows are closed, the list box is
blank. If a Text Editor window is active, the list box turns blank
temporarily.
If the list of labels is too long to be displayed in the box, a scroll bar is
displayed at the right allowing you to scroll up or down to see further
labels.
If you select a different (or edited) .MKR file, the new list appears and is
available for use immediately. Different .MKR files may be selected
using the Model | Subject Settings command.
The label box has three modes: Label, Select and Graph, chosen by
clicking on the relevant button at the bottom of the list.
When in Label mode, you can select a trajectory and click on the
appropriate label name to apply that label to the selected trajectory.
When in Select mode, you can click on a label name to select the
corresponding trajectory. When in Graph mode, you can click on a label
name to open a Graph Editor window for that trajectory (or change the
current Graph Editor window to the new trajectory).

16 Workspace Window

Version 3.5 BodyBuilder for Biomechanics

Label Mode

In BodyBuilder, it is unlikely
that you will find it
convenient to unlabel and
relabel more than one
trajectory at a time.

If you want to change the label of a segment, select and unlabel that
segment. It will then be displayed in white, and can be given a new label.
To label trajectories, ensure you are in Label mode, then select between
one and twenty-four unlabelled trajectories by clicking on each in turn,
using the left mouse button. Selected trajectories are highlighted
cyclically in yellow, red, purple, and blue. Next, click on the required
label for each trajectory, in the same order as the selection. Each
trajectory changes to cyan as it is labelled.
If a trajectory is broken, the same label should be applied to each
segment.

Version 3.5 BodyBuilder for Biomechanics

Workspace Window 17

Relabelling
The label of a trajectory or segment can be changed directly by selecting
it and clicking on the revised label in the Labels List.

Select Mode
In Select mode, click on a label in the list to select and highlight the
trajectory or segments with that label. Up to 24 trajectories can be
selected in this manner.

De-Selection
De-select trajectories by clicking the right mouse button while pointing
anywhere within the Workspace window.

Unlabelling
Use the Unlabel button to remove a label from a selected trajectory. Up
to 24 trajectories may be selected and unlabelled in sequence.

Replay Control Bar

Use the Replay Control Bar at the bottom of the screen to control the
replay of data.
Keyboard shortcuts:
Left Control-left arrow
Right Control-right arrow

Use the large Left

and Right
Play buttons on the left of
the bar to play (change the current field) Forward and Backward,
respectively. Use the View | Real-Time Playback command to control
the speed of replay.

Shortcut: Space bar

Use the large

replay.

Stop button (between Play buttons), to stop the

The numbers under the

replay slide bar indicate the
first, current, and last fields.

18 Workspace Window

Version 3.5 BodyBuilder for Biomechanics

When dragging, try to avoid

moving the mouse pointer
off the slide bar as the slider
returns to its starting
position.

Drag the slider on the central field number bar to move to an individual
video field. Single-step by clicking on the small arrow buttons at either
end of the slide bar.

Version 3.5 BodyBuilder for Biomechanics

Workspace Window 19

20 Workspace Window

Version 3.5 BodyBuilder for Biomechanics

Graph Editor Window

Graph Editor
The Graph Editor window provides a range of tools allowing the user to
alter trajectories, move points, and to create new points and trajectories.
The Graph Editor window contains three graphs, which display the X, Y
and Z components of the selected trajectory, against time, and makes a
variety of tools available for manipulating the data.
In order to use these tools, you must have a .C3D file open. Although it
is possible to close the Workspace window and still use the Graph Editor
window to operate on the .C3D file, the two windows are designed to be
viewed together, vertically tiled within the main program window. There
are three methods of opening a Graph Editor window:

Select the trajectory you want to alter in the active Workspace

window. Use the Window | New Graph Editor command.

Select Graph mode at the bottom of the labels list, and then
click on the label corresponding to the trajectory you want to
alter. A new Graph Editor window opens, displaying the
components of the selected trajectory.

Use the Edit | Create New Trajectory command. A new Graph

Editor window opens, with no trajectory or label displayed.

The second method can also be used to change the trajectory displayed in
an existing Graph Editor window. If a Graph Editor window is active
(with a highlighted title bar), you can use the second method to select an
alternative trajectory, which will replace the one currently displayed in
the active Graph Editor window. Alternatively, it is also possible to open
additional Graph Editor windows, using the Window | New Graph Editor
command, but multiple Graph Editor windows which are tiled will be too
small to be useful. It is recommended that only one Graph Editor window
is used at one time. Any operation which deletes the trajectory displayed
in a Graph Editor window will close that window.
Version 3.5 BodyBuilder for Biomechanics

Graph Editor Window 23

Controlling the Display

When a Graph Editor window is opened, the vertical (X, Y or Z
component) and horizontal (time) scales are automatically set, with the
current field in the centre of the horizontal scale. The current field is
indicated by a vertical red cursor, and the value of the component shown
by a line, which is interrupted if there is a gap between segments of the
same trajectory.

24 Graph Editor Window

Version 3.5 BodyBuilder for Biomechanics

The vertical red cursor indicates the current field, and in each graph the
current point is highlighted by a black square.
The top left corner of each graph shows the label of the trajectory (unless
it is a newly-created and unlabelled trajectory), the name of the
component (X, Y or Z), the units of the vertical scale marks and the
current field number.
If the current field number is changed, either by using the replay buttons,
the replay slider bar, or by clicking the left mouse button at a different
left-right position within the Graph Editor window, the red cursor will
move to the appropriate position. Any change in the current field, by any
means, will cause the replay slider bar, the Workspace window, and the
Graph Editor window, to be updated together.

Changing the Time Scale

Keyboard alternative: G

To change the time scale, position the pointer within the Graph Editor
window and press the right mouse button. Slide the pointer to the right to
expand the time scale. There is a limit on this expansion to prevent the
horizontal space between markers becoming too large. Slide the pointer
to the left to contract the time scale. A limit is reached when the display
scale is one pixel per field.
The horizontal time scale is the same on all three graphs within a single
Graph Editor window whichever component the pointer is positioned
over when the change is made. The red cursor remains static while the
time scale is changed.

Changing the Vertical Scale

To change the vertical scale, position the pointer within the area
displaying the component whose scale you want to change, and press the
right mouse button. Slide the pointer up to expand the distance scale, and
down to contract it. The change will only affect the component displayed
in the section where the pointer was located when the right mouse button
was pressed.
When the right mouse button is held down, the up-down and left-right
pointer movements may be combined, changing the time scale of all

Version 3.5 BodyBuilder for Biomechanics

Graph Editor Window 25

three components and the distance scale of one simultaneously. New

users may find it simpler to make one adjustment at a time.

Moving the display laterally without changing scale

If the replay slide bar is used to change the current field outside the range
displayed in the Graph Editor window, the graph display will move
laterally so that the current field is kept in view.
The keyboard alternative to
holding down both mouse
buttons is F.
The scroll bar is the easiest
method to move the display
laterally.

It is also possible to move the graph display laterally, either using the
scroll bar at the bottom of the window, or by positioning the pointer
within the Graph Editor window, holding down both mouse buttons, and
moving the pointer left or right. This has the effect of dragging the
display. It is possible to continue dragging over the border of the Graph
Editor window, thus taking the current field out of view. All three
components move together during this adjustment.

Moving the display vertically without changing

scale
You can move the display of a single component in the vertical direction
by positioning the pointer within the appropriate section of the display,
holding down both mouse buttons, and moving the pointer up or down to
drag the display.
When both mouse buttons are held down, up-down and left-right mouse
movements can be made simultaneously, moving all three displays
laterally and one display vertically. New users will find it simpler to
make one adjustment at a time.

Selecting a Field Range

For those operations which act on a range of fields (rather than the
current field), you need to select the start and end points of the range
before carrying out the operation.

26 Graph Editor Window

Version 3.5 BodyBuilder for Biomechanics

Select the start of the range by making it the current field by any method
(eg. point and click within the Graph Editor window, or drag the replay
slider bar). The red cursor will indicate this point. Then position the
pointer within the Graph Editor window at the end of the desired range
and left-click while holding down the Control key. A green cursor will
appear over the selected end field.

In this example, the current field number (311) is shown above the field
numbers and the red cursor. The start and end points of the range (292
and 339) are shown below and with the two green cursors, and points
within the range are highlighted by black squares.

Version 3.5 BodyBuilder for Biomechanics

Graph Editor Window 27

You can change the selected end field by repositioning the pointer and
repeating the Control-click. The second green cursor will move to the
new end field.
Each field within the range is highlighted by a black point, unless the
time scale is such that there is no space to show each point. In this case, a
reduced number of points within the range is shown. Use the scale
change and lateral drag features to fit the selected range to the size of the
window.
Once the start and end fields of the range have been selected, you can
change the current field without changing the start and end fields of the
range, by dragging the slider bar or by clicking on a highlighted point
within the range (on any of the three graphs). If you change the current
field, the red cursor will move from the start field of the range, to the
new current field. The start of the range will then be indicated by a green
cursor. However, if you change the current field by pointing and clicking
within the Graph Editor window (other than on a highlighted point), the
selected range will be dropped, and the new current field can be used as
the start of a different range.
The operations which can be carried out on the points within a range are
described in the chapter on Edit Menu commands.

Point Dragging
If the pointer is placed on a highlighted square, that co-ordinate can be
dragged by the mouse and dropped at a new value. This has the effect of
changing the chosen co-ordinate to a new value. The effect of point
dragging is displayed in the associated Workspace window, if one is
open.

28 Graph Editor Window

Version 3.5 BodyBuilder for Biomechanics

In this example, the Z component of the point LFWT has been dragged
down. The effect this has on the data is displayed in the associated
Workspace window, in which the point is shown displaced downwards.
This form of point dragging is the simplest form of data manipulation
using the Graph Editor window. More sophisticated tools are available in
the Edit Menu.
For more details on point moving operations, see Move Point Mode.

Version 3.5 BodyBuilder for Biomechanics

Graph Editor Window 29

Text Editor Window

Text Editing
Two types of file - .MOD and .MP - control the action of BodyBuilders
most important function, kinematic modelling. When developing
BodyLanguage models and adjusting parameters, it is often convenient to
work by a process of repeated trials, with small changes to the model or
parameter file tested immediately by application to typical data.
It would be possible to do this by using any standard text editor, such as
Notepad, saving the text file after each change, switching to BodyBuilder
by Alt-Tab, reloading the modified file, and then testing it. This would
be a laborious procedure if it involved more than a few repetitions.
A text editing window has been provided within BodyBuilder so that this
procedure can be carried out more efficiently.

Opening a Text Editing Window

In order to open a text editing window, select View Model from the
Model menu. If a .MOD file can be found according to the settings for
the current subject, it will appear in the text editing window.

Version 3.5 BodyBuilder for Biomechanics

Text Editor Window 31

The same procedure is used to open a parameter file editing window:

select Model | View Parameters and a similar text editing window will
open.
MOD, MP and MKR files, as well as AST files, may also be opened in a
text window directly by using File Open, and selecting the appropriate
file type. In this case, the file is not necessarilly associated with a
particular trial or subject. In particular, any changes to MKR files can
only be made to take effect by saving the file, and opening the Subject
Settings dialogue, checking that the correct file MKR file is selected, and
clicking the Okay button.

Editing Text Files and Testing Changes

The text editing window works in a similar way to other Windows text
editors (eg. Notepad), with Cut, Copy, Paste, Find and Replace
commands available in the Edit menu, and Save or Save As commands
in the File menu. Changes can be undone using the Edit | Undo
command, but only the most recent change is available with the Undo
function. Note that Replace operations are not reversible using the Undo
command.
However, it is not necessary to save changes to MOD or MP files before
testing them. Simply selecting the Model | Run Model command applies
the changed model directly, since BodyBuilder detects that the files have
already been loaded.

32 Text Editor Window

Version 3.5 BodyBuilder for Biomechanics

When the text file is in a satisfactory form, it should be saved before

closing the editor window. Failure to save changes will result in their
being lost when the BodyBuilder main window is closed, however, a
warning message will appear if the main window is closed with unsaved
changes outstanding. If a long editing and testing session is undertaken,
the usual precautions should be taken to save work periodically in case
of power failure.

Version 3.5 BodyBuilder for Biomechanics

Text Editor Window 33

34 Text Editor Window

Version 3.5 BodyBuilder for Biomechanics

File Menu Commands

File Menu
The File menu is always available while BodyBuilder is running,
although the options within it depend on whether a .C3D file is open.
The File menu can be accessed by pointing and clicking on the word
File, or by the keyboard alternative Alt-F.

Open
The File | Open command (keyboard alternative: Control-O) opens the
File Open browse box:

This default type allows the

user to save modified data
under the same filename,
updating the extension to
.C3E, .C3F and so on.

The default file type is .C3* and the desired file can be selected either by
clicking on its name and then on the OK button, or double-clicking on
the file name.

Version 3.5 BodyBuilder for Biomechanics

File Menu Commands 35

The File Open toolbar symbol is at the left end of the toolbar. The last
four files used are listed in the file menu for quick re-selection.

Merge
If a very long data capture has been carried out, creating a large .TVD
file, it may speed processing if it is cut into subsections before
reconstruction and labelling. This is because very long 3D files make
excessive demands of system memory. A utility is available with VICON
370 for this purpose. The result of reconstructing a divided .TVD file is
multiple .C3D files, and before kinematic modelling is carried out, it may
be necessary to merge these back into a single file. In order to carry out
this merging, begin by opening the first .C3D file in the normal way.
Then, use the Merge command. This opens a browse box similar to the
Open File browse box. The second .C3D file can be selected from this
browser. The contents of this file will be merged with the first.
Subsequent files are added in the same way.
Only files which belong together as part of the same data capture should
be merged, or there may be unpredictable results.

Close
The Close command (or its toolbar shortcut) has the effect of closing the
active window, whether it is a Workspace, Graph Editor, or Text Editor.
If the active window is a Workspace or Graph Editor, and there are other
windows displaying the same .C3D file, all will be closed.

Save
The Save command saves the the data in the currect trial, overwriting the
C3D file containing the original data. The data is saved in the same
format as the original file.
If a limited range of fields has been selected for saving, only the select
number of fields will be saved.
36 File Menu Commands

Version 3.5 BodyBuilder for Biomechanics

A new feature in version 2.0,

this is not available in
VICON 370 version 1.x

BodyBuilder saves unlabelled trajectories in the .C3D file. Unlabelled

trajectories may result from the use of the Unlabel command, or the
Create New Trajectory command.

Multiple segments with the

same label will be stored as
a single trajectory. This is
equivalent to defragmenting
the trajectories.

All data resulting from editing and modelling is written to file. Virtual
points created by modelling are flagged as such within the working
session in which they are created, and can be identified as such and
removed using the Delete Model Output command. However, once they
are written to file, the flag is lost and modelled points become
indistinguishable from any others.
Kinematic angles calculated by modelling are stored as angles, and will
be recognised as such when the file is read back in BodyBuilder or
Reporter. A new parameter POINT:ANGLES is used to identify them.
As with modelled points, they are flagged as model output when first
created. (Previous versions of BodyBuilder saved angles in a form
indistinguishable from points.)

The units these data are

saved in depend on the data
type.For more information,
see the Save As section.

Kinetic variables are also saved as trajectories in the file, and marked
according to their type. They are recognised when re-loaded in
BodyBuilder, and can be deleted by the Delete Model Outputs function.

Range to Save
The Range to Save command opens the Trial Save Range box:

Version 3.5 BodyBuilder for Biomechanics

File Menu Commands 37

By default, the save range is set to the whole length of the file. If, though,
only part of the data is of interest, it is possible to select a range of fields
which will be written to file when one of the commands Save As, Write
C3D or Write ASCII is used.
When a save range is specified, analog data outside that range will not be
saved.

Save As
The Save As dialog box appears. By default the name of the original file
is prompted. If this is accepted, the original data will be over-written.
Any other name will cause a new file to be created with the edited data.

It is possible to save edited data under the same name if the extension is
changed (eg. to .C3E or .C3F). Note that Windows 95 may not show all
file extensions in applications such as Explorer unless requested. If you
save your work under a new name, this will appear in the title bar of the
current Workspace and Graph Editor windows.
The Range To Save frame range will be used.
The data can be stored in the file in different formats, according to the
C3D file specifications. The data can be saved as Integer data or Real
38 File Menu Commands

Version 3.5 BodyBuilder for Biomechanics

(floating point) data, in formats native to PC (Intel compatible), MIPS

(SGI or Sun) or DEC (Vax) formats. Loading and saving files in the PC
format will be slightly quicker on PC compatibles computers. The
default setting matches that of the original file.
The Real data type takes up twice as much space as the Integer format,
but can represent values, especially values calculated as a result of
kinetic modelling, with much better precision than the Integer format. In
the integer format, some variables can lose precision when the file is
saved, and when it is re-opened, graphs of such values will have steps in
them.
The units for the kinetic data are also dependent on the data type. For
Real types, the kinetic data are always saved in the same unts as are used
internally, that is N, Nmm, and mW. If the Integer data type is selected,
the largest range of values for each kinetic quantity is found, and hence a
unit chosen, and the trajectories appropriately scaled, such that the data
just fit in the range permitted by the integer type. This gives the best
resolution for integer storage, without requiring any further scaling or
offsets to each data type. It does mean that the units for each quantity
may vary from trial to trial.
Note that some older programs (such as VCM for example) only support
one data type. Normally, for historical reasons, this will be Integer DEC
format.

Write C3D
Write C3D is similar to the Save As command, in that it allows you to
save the data displayed in the Workspace window to disk as a .C3D file.
However, Write C3D provides the facility to choose what data is saved.
If a limited range of fields has been selected for saving, this command
appears in the menu as Write C3D Range

Version 3.5 BodyBuilder for Biomechanics

File Menu Commands 39

The user must select data to write to the output file using the Add (or
Add All) and Remove (or Remove All) buttons. Two other buttons are
provided: the first, Add Model Inputs, enters the labels of all trajectories
in the input file in the Data to Write field; the second, Add Model
Outputs, enters the labels of all the trajectories and angles generated by
kinematic modelling in the current working session. If the Remember
List box is checked, the same write list will be presented the next time
the operation is invoked, subject to that data being available. Otherwise
the Write list will initially be blank.
At least one label must be entered in the Data to Write list for a .C3D file
to be created, and a valid path and file name must be provided.
All analog data and parameters are maintained when saving a .C3D file.
(Previous versions of BodyBuilder could write only kinematic data
output.)

Axis Changing
Write C3D provides the facility to change the order in which the coordinates are written to file. Normally (but not necessarily), VICON 370
measurements are expressed in a Cartesian frame of reference in which
the vertical axis is called Z. Thus, in the .C3D files created under this
convention, the first two co-ordinates of a point represent the two
horizontal components, and the third, the vertical.

40 File Menu Commands

Version 3.5 BodyBuilder for Biomechanics

Some applications - such as computer animation packages which follow

the convention by which the vertical axis is called Y - may require a
different co-ordinate order. The user must select to map the XYZ coordinate order to one of three options.
The default option, XYZ, leaves the order unchanged.
The second option, YZX, writes the original second (Y) co-ordinate first;
the original third (Z) co-ordinate second; and the original first (X) coordinate third. The result is that the vertical direction in the new file is
labelled Y.
The third option, ZXY, writes the original third co-ordinate (Z) first; the
original first (X) co-ordinate second; and the original second (Y) coordinate third. The result is that the vertical direction in the new file is
labelled X.
The three possibilities described are not the only possibilities; an
exhaustive choice of axis permutations is offered by the Model | Axis
Permutation command. However, that command affects model output to
.ASF and .AMC files; only Write C3D allows the creation of .C3D files
with changed axes. The choice of command depends on the output
format needed.

Write ASCII
The Write ASCII command provides a highly flexible means of writing
motion data to a text file suitable for display in a spreadsheet or for input
to other applications.
If a limited range of fields has been selected for saving, this command
appears in the menu as Write ASCII Range
The Write ASCII command opens a box:

Version 3.5 BodyBuilder for Biomechanics

File Menu Commands 41

The user must select data to write to the output file using the Add (or
Add All) and Remove (or Remove All) buttons. Two other buttons are
provided: the first, Add Model Inputs, enters the labels of all trajectories
in the input file in the Data to Write field; the second, Add Model
Outputs, enters the labels of all the trajectories and angles generated by
kinematic modelling in the current working session. If the Remember
List box is checked, the same write list will be presented the next time
the operation is invoked, subject to that data being available. Otherwise
the Write list will initially be blank.
At least one label must be entered in the Data to Write list for a .C3D file
to be created, and a valid path and file name must be provided.
The Delimiter is the character which separates values which are entered
on a single line. By default, values are separated by tabs. In this format,
the file created will be easily readable by spreadsheet applications.
If another delimiter is required, click on Other, and enter the delimiter in
the Other field. Any character may be used apart from combination
keystrokes (eg Control-character).

42 File Menu Commands

Version 3.5 BodyBuilder for Biomechanics

The Invalid Co-ordinate Value field is blank by default. This means that
if a co-ordinate does not exist in a given data field (perhaps because the
marker was not visible in that field), a space will be left in the output file.
Some applications require a value to be entered on every line whether or
not a particular marker was in view; this is called the Invalid Co-ordinate
value. For example, the value -9999 might be used instead of a blank
space, but the value does not have to be a numeral.
The Map XYZ function behaves similarly to the corresponding function
in Write C3D described above in the section on Axis Changing.

Options
The Options allow the user to control details of the file format.
Header Information, if checked, causes file header lines to be written
containing information required by the 3D Studio computer animation
package, and other application software. To maintain 3D Studio
compatibility, select Header Information, Column Headings, Sample
Number Columns, Time Column, and Force Start to Sample 1, Time 0.
Column Headings causes each column to be headed with the label and
component (X, Y or Z). By default the label appears on one line, and the
component name on the next line; but if Headings on One Line is
selected, the labels and component names are placed on the same line,
separated by a colon.
Sample Number Column causes the first entry on each line to be the field
(sample) number of the data on that line.
Time Column causes the second entry on each line to be the time of the
field in seconds (unless Sample Number is deselected, in which case
Time is the first entry on the line).
Force Start to Sample 1, Time 0 writes the sample number and time
information such that the first line of data is always sample number 1, at
time zero, whether or not the first field in the trajectory save range is
actually field number 1 of the .C3D file.
Separate Files per Data Item causes each trajectory to be written to a
different file. If this option is selected, a sub-directory is created with the
Version 3.5 BodyBuilder for Biomechanics

File Menu Commands 43

name shown in the Filename box. Each ASCII file is placed in it, with
the same name as the trajectory it describes and the extension as chosen
in the Filename box.

Previous Files
A list of the four .C3D files most recently opened is available in the File
Menu for rapid access.

Preferences
The Preferences command allows the user to control certain aspects of
the Undo operation of BodyBuilder.
Certain operations cannot be Undone: these are listed in the Preferences
under the General tab. If you check these operations, a warning message
will appear when these operations are invoked to remind the user that the
Undo command will not be available after the operation. Such warnings
allow the user to save their work prior to invoking irreversible
operations. However, if the user prefers not to have warning messages,
they can be disabled.
The number of operations which can be Undone is user-controllable.
However, it is recommended that this number should not be increased
much beyond the default value of 10 because it makes substantial
demands on system memory.
If the Maximise CPU usage box is checked, the application will remain
active when it has no tasks running, rather than lying idle. Depending on
system resources, this may allow certain functions to perform a little
better, such as data replay and workspace rotation. In most situations,
though, this will make no noticeable difference.
The marker size as displayed in the workspace can be changed. The
value is in millimetres. This has no effect on any modelling, where the
marker size should be accounted for in the modelling script.
The default modelling files listed under the Model tab indicate the file
names that are searched for when an Anonymous trial (one that has
44 File Menu Commands

Version 3.5 BodyBuilder for Biomechanics

been manually labelled) is loaded, and the folder to be searched for

models indicated by all trials.
Acclaim output files (ASF and AMC files) can either be output to the
same directory as the trial used to generate them, or a single directory
can be specified, where all of the output files are placed. Note that the
old files will be overwritten if a new file is generated with the same
name. Care may be needed in using this option, for example with
manually labelled files which automatically generate the file name
ANONYMOUS.ASF for static trials.
Options for the naming of AMC files, and for the ASF files used for the
generation of the AMCs can be selected under the AMC files tab. For
trials with just a single subject, the AMC file is normally called
<Filename>.AMC, unless the Use for both single and multiple subject
trials checkbox is checked. In this case the subject name is included too.

Version 3.5 BodyBuilder for Biomechanics

File Menu Commands 45

Edit Menu Commands

Edit Menu
The Edit Menu provides a range of powerful tools for manipulating the
data in a .C3D file as displayed in Workspace and Graph Editor
windows.
The exact range of options available depends on the types of window
open. The full range of options is available when a .C3D file is open in a
Workspace Window and a Graph Editor window has also been opened.

Undo and Redo

Keyboard alternatives:
Undo
Control-Z
Redo
Control-A

Most operations in BodyBuilder can be undone, ie. the data can be

restored to the condition prior to carrying out the operation. Certain
operations are not reversible in this way, and unless they have been
disabled in File | Preferences, warning messages will appear before these
operations take effect.
If an operation is Undone, it can be redone either by invoking the
original command, or by using the Redo command.

Snip
A trajectory consists of a time-series of points which are linked together
by having a common label. If you want to separate a trajectory into more
than one segment, possibly so that one or other segment can be given a
different label, the snipping function allows you to introduce breaks
without deleting any points.
Version 3.5 BodyBuilder for Biomechanics

Edit Menu Commands 47

To snip a trajectory, select the point at which you want to snip, and
choose Snip from the Edit menu. A break is introduced after the selected
point (ie. the selected point becomes the last point of the earlier segment,
and the next point becomes the first point in the later segment). At this
stage, the two segments still share the same label, but they can be
selected separately, and can be re-labelled individually.
This function may be useful if two nearby trajectories show a crossover error. Both trajectories can be snipped at the cross-over and relabelled without losing any data.
Selecting a range of two
consecutive points is the
same as only selecting the
first.

It is also possible to snip out a range of points. Select the first point as
above, and the second using Control-click. The Snip command deletes
the points between the selected end points. The selected points
themselves remain undeleted.

In the above example, two points (highlighted by white crosses) define

the end points of a range. After the Snip command is invoked:

48 Edit Menu Commands

Version 3.5 BodyBuilder for Biomechanics

The end points of the range remain; the points in between are deleted.
The earlier of the two trajectory segments remains selected (shown
yellow); the later segment is unselected (cyan).

Delete
To delete a single point, position the pointer on it and click the left
mouse button. A white cross will appear on the selected point. The
trajectory will also change colour, indicating selection. If the wrong point
is selected, move to the correct point and left click again.
Keyboard Alternative: (minus sign)

Select Edit | Delete. A break will appear in the selected trajectory,

indicating that the selected point has been removed.
To delete a range of points from a trajectory, select one end of the range
as described above. Select the other end by pointing to it, holding down
the Control key, and clicking the left mouse button. A second white cross
will appear over the selected point. If the second point is incorrectly
selected, move to the desired point and Control-click again.
Select Delete from the Edit menu. The two selected points, together with
all the points between them, will be removed from the trajectory.

Version 3.5 BodyBuilder for Biomechanics

Edit Menu Commands 49

Add Point
This command is available if a Graph Editor window is open and
showing a trajectory which has a gap, and if the current field is set within
that gap.
The action of the Add Point command is to create a new point with the
label of the selected trajectory, which is placed in the current field by
linear interpolation from the rest of the data.

50 Edit Menu Commands

Version 3.5 BodyBuilder for Biomechanics

In this example, a Graph Editor window is open, displaying a trajectory

LELB in which there is a gap. The red cursor indicates that the current
field is set within the gap. The Add Point command has placed a new
point within the gap, as shown by the square.
This use of the Add Point feature, depending as it does on linear
interpolation, is less useful for filling gaps in trajectories than the Fill
Gaps command, which uses more sophisticated interpolation methods.
The Add Point feature may be more useful in extending trajectories
which start later or finish earlier than desired. Trajectories cannot be
extended beyond their end points by interpolation, so there are two other
methods available. One is to write a model script which creates new
points by defining the position of the missing marker relative to others
which are present in the field range concerned (see BodyLanguage
documentation for instructions). The other is to use Add Point to create a
new point outside the existing range of data, drag the new point to a good
position, and interpolate over the gap. Extra points may be added in the
gap to guide the interpolator. This use of Add Point is shown below:

Version 3.5 BodyBuilder for Biomechanics

Edit Menu Commands 51

In the above example, the trajectory LELB begins at field 61. It is

necessary to create data before that time. The user has placed the red
cursor at field 11, making it the current field. The Add Point command
has created a new point with the label LELB in field 11. As there is no
prior data for linear interpolation, Add Point set the co-ordinates of the
new point equal to the values at the nearest end of the trajectory. The
user can now drag the new point to a suitable position. Other points have
been added and dragged in the gap to guide the interpolator.
The Fill Gap command then invokes the interpolator, and finally the new
data can be manipulated with other editing tools until the desired result is
obtained.
52 Edit Menu Commands

Version 3.5 BodyBuilder for Biomechanics

In the above example, after raising the maximum fill gap limit from the
default 10 fields, the Fill Gap command is invoked. The interpolator fills
in the missing points. The new data can be filtered and adjusted as
necessary.

Create New Trajectory

This command opens a new Graph Editor window showing no data and
with no label. It is possible to create data within such a window, and to
Version 3.5 BodyBuilder for Biomechanics

Edit Menu Commands 53

attach a label to the new data, so as to have the effect of producing a new
trajectory. This is an alternative method to using kinematic modelling to
create trajectories, but may have advantages in certain situations.
If the Add Point command is invoked in a blank Graph Editor, a new
point will be created at the origin (0,0,0). It is possible, for example, to
create such a point, move it to a desired place, create another point in a
different field, move it somewhere else, and interpolate between the two.
This has the effect of creating a new, straight-line trajectory.

Delete Trajectory
The Delete Trajectory command deletes all selected trajectories. The
command can be Undone.

Delete Model Outputs

When a model is run, the points created (including points representing
kinematic angles) are flagged as modelled points. The Delete Model
Output command will delete all such flagged points.
If a file containing modelled points is saved, then re-opened, these flags
are lost, and the modelled points are indistinguishable from other points.
In this case the Delete Model Output command will have no effect on
them.
This operation is not reversible using the Undo command.

Defragment Trajectories
If a trajectory is broken, or has been snipped, into several segments, it
will have a fragmented appearance. Selecting one segment will not
necessarily select the others with the same label. This can be repaired
using the Defragment Trajectories command. All segments with the same
label will be stored as a single trajectory. After defragmenting, selecting
any segment will select the whole trajectory. Defragment does not invoke
any interpolation.
54 Edit Menu Commands

Version 3.5 BodyBuilder for Biomechanics

If two segments with the same name overlap, when the defragment
command is invoked, some points may be lost from the earlier trajectory.
When a .C3D file is saved (written to disk), defragmentation takes place
automatically. This operation is not reversible by the Undo command.

Delete and Fill

Often, the purpose of deleting a point or range of points, is to smooth the
trajectory by interpolating over the selected range. BodyBuilder can fill
gaps by interpolating from the data either side of the gap. The
interpolated data will have no high-frequency components, ie. it will
have a smooth appearance. Thus, the delete and fill command amounts to
low-pass filtering by a different method.
A range of points within a trajectory can be selected as described above.
If the Delete and Fill option is selected from the Edit menu, the selected
range of points is cut from the trajectory, and the gap is filled by the
interpolator. The keyboard shortcut for this function is the Delete key.

Fill Gaps In
If a trajectory has been selected, this command appears as, for example,
Fill Gaps In LELB. If several trajectories have been selected, the last
selected is nominated.
This command invokes an interpolation routine which creates new points
in any gap in the selected trajectory which are shorter than the maximum
number of fields for interpolation (default 10).
The interpolation routine produces a series of points in the gap(s) which
should be a reasonable estimate of the position of the marker during the
period it was obscured from view. If the maximum fill gap is set to a
much larger value than 10, the interpolated points will not be an accurate
estimate of the position of the marker. In this case it may be better to use
kinematic modelling to recreate the missing points, if possible.

Version 3.5 BodyBuilder for Biomechanics

Edit Menu Commands 55

If a range of points within a trajectory has been selected, only gaps in

that range will be filled. In this case, the maximum fill gaps limit does
not apply.
The interpolated segment(s) of trajectory will be smooth. This means that
no frequencies above half the sampling rate will be represented.
Interpolation is therefore, to some extent, an alternative to filtering; this
option is provided by the delete-and-fill command. For more details on
filtering, see the section on Filter Characteristics.

Fill All Gaps

This command invokes the interpolation routine for all trajectories,
whether selected or not. It operates on any gap shorter than the maximum
fill gap.

Maximum Fill Gap

This command opens a box allowing the user to select the maximum
number of fields over which the interpolation commands will operate. It
is also possible to remove this limit entirely, although this may result in
some very long gaps being unrealistically filled.

By default, the maximum is set to 10 fields, because this should result in

realistic interpolations. In the example above, the No Restriction option
is selected, removing the maximum gap limit.

56 Edit Menu Commands

Version 3.5 BodyBuilder for Biomechanics

The Set button applies the selected limit and closes the box without
invoking the interpolation routine. The Fill All Now button applies the
new limit, closes the box, and invokes the Fill All Gaps command.

Copy Pattern
The Copy Pattern command is available only once a Graph Editor
window is open, displaying one trajectory, and a Workspace window
displaying the same .C3D file data is also open, with a different
trajectory selected.
The purpose of Copy Pattern is to fill a gap in one trajectory over a
certain range, using another trajectory as a pattern. The trajectory with
the gap to be filled should be displayed in the Graph Editor window,
with the start and end points of the range to be filled selected. There must
be data points at the start and end of the range to be filled: if necessary,
one or both of these can be created using Add Point and dragged to
suitable places. The selected range is indicated by green cursors, with the
red cursor, as usual, indicating the current field.
The Copy Pattern command takes another trajectory as the template for
filling the gap highlighted in the Graph Editor window. You can use
point-and-click within the Workspace window to select the pattern
trajectory. The pattern trajectory should be complete throughout the
selected range.

Version 3.5 BodyBuilder for Biomechanics

Edit Menu Commands 57

In this example, the Graph Editor window shows the trajectory RFHD,
which is missing from the range 20 to 85. The first appearance of this
point is in field 85; a point has been added in field 20, and dragged to a
realistic position. The two points, highlighted in the Graph Editor
window, have been selected as the beginning and end of the range.
Next, the pattern trajectory (RBHD) should be selected in the Workspace
window.
When these steps have been completed, click on the Graph Editor
window title bar to make it the active window. The Copy Pattern
command will then be available in the Edit menu. In the example above,
the command would appear as Copy Pattern from RBHD.

Continuing the example above, the trajectory RBHD has been selected in
the Workspace, and the Graph Editor window made active once again.
At this point, the Copy Pattern command has been used. A trajectory
similar to that of RBHD in the range 20 to 85, has been added to RFHD,
and forced to fit the end points of the gap in RFHD.
If necessary, the new points can be further manipulated until satisfactory.
The Copy Pattern function works as follows. For each component (X, Y
and Z), the pattern trajectory is analysed and the deviations of the
trajectory from a straight line between the end-points of the range are
stored. (The function makes no changes to the pattern trajectory).

58 Edit Menu Commands

Version 3.5 BodyBuilder for Biomechanics

The target trajectory must have two end points, so that a straight line can
be drawn between them. The Copy Pattern function then applies the
stored deviations to that straight line, creating the new data. In this way,
the shape of the new trajectory resembles that of the pattern, but
stretched to fit the required end points.

Move Point Mode

Move Point is a useful tool for modifying data in the Graph Editor
window. There are four modes, which are selected from a submenu under
the Move Point Mode command. Move Point is a mouse dragging
operation by which a component of a trajectory can be changed by
dragging its highlighted square up or down the graph. If a single field
value is selected (ie. a range of one field), the operation is so simple that
it is not affected by the selection of any Move Point mode. However, if a
range of several points is selected, four choices of mode are available.

Simple
In Simple mode, a range of one component of a trajectory may be
dragged using the mouse. The whole of the selected range is dragged up
or down the graph together, by an equal amount, with a sharp
discontinuity resulting at the end of the range.

Version 3.5 BodyBuilder for Biomechanics

Edit Menu Commands 59

In this example, the Y component has been dragged down in simple

mode. In simple mode, it makes no difference which point is dragged.
There is a discontinuity at field 85 between the dragged points and those
which remain where they were. This would show as a sudden jump in the
trajectory.

Weighted A mode
To make a smoother trajectory, you can use Weighted A mode, in which
the point that is dragged is moved according to the distance dragged, and
the rest of the points in the range are moved by a lesser amount.

60 Edit Menu Commands

Version 3.5 BodyBuilder for Biomechanics

In this example, the selected range of the Y component has been moved
in Weighted A mode. The actual point dragged - shown by the red cursor
- moves according to the extent of mouse movement. The other points in
the range move by a lesser amount, forming a sigmoid curve. The
steepness of the sigmoid curve is determined by side-to-side mouse
movement. This example shows mid-range steepness.
The function used to create the new values of the modified component is
called a sigmoid. Three rules govern this curve:

The end points remain fixed

The dragged point moves to the extent determined by dragging

The mid-points of each wing of the curve move by half that

amount

The steepness of the sigmoid curve is determined by lateral mouse

movement. At one extreme the shape resulting is a straight-sided triangle
fitted through the points determined by the three rules:

Version 3.5 BodyBuilder for Biomechanics

Edit Menu Commands 61

This is reached by moving

the mouse to the left while
dragging the apex point
down.

At the other extreme, the shape is something like a top-hat function,

fitted through the points determined by the three rules:
This is reached by moving
the mouse to the right while
dragging the apex point
down.

Weighted B mode
This is similar to Weighted A mode, but follows different rules. The midpoint of each wing of the curve is no longer fixed; instead, it is moved by
lateral mouse shift to create either a convex or concave curve:
This effect results from
moving the mouse to the left
while dragging the apex
point down.

The midpoint of the lateral mouse shift range produces a straight sided
triangle. The opposite extreme is a convex curve with a spike
appearance:

62 Edit Menu Commands

Version 3.5 BodyBuilder for Biomechanics

This effect results from

moving the mouse to the
right while dragging the
apex point down.

Expand/Reduce mode
The fourth Move Point mode allows you to exaggerate the curvature (ie.
departure from a straight line) of the selected range of points. Once
again, the dragged point (indicated by the red cursor) is moved by the
amount of up/down drag. All other points are moved by an amount which
depends on their deviation from a straight line drawn between the start
and end points, and proportional to the amount of mouse drag.
This effect was produced by
selecting expand/reduce
mode and dragging the apex
point (red cursor) upwards.

Opposite mouse movement causes deviation in the opposite direction:

This effect was produced by
selecting expand/reduce
mode and dragging the apex
point (red cursor)
downwards.

Filter

Version 3.5 BodyBuilder for Biomechanics

Edit Menu Commands 63

Filtering operates either on selected trajectories, or if none are selected,

on all trajectories. The effect is to pass only low frequencies, ie. to
smooth the trajectories by ironing out sharp features.
The frequency characteristics of the filter function are user-selectable. If
you select Filter from the Edit menu, a box appears offering the choice of
filtering options.

The first option determines which trajectory or trajectories are filtered. It

is possible to limit the filter to a selected range of a particular trajectory
by selecting the trajectory and defining the range using a Graph Editor
window.

Filter Characteristics
The second option determines the filter characteristics. The filter with the
highest passband is called 3-point. This filter modifies each coordinate according to the function
New Value = (previous sample + 2 old value + subsequent sample)/4
where previous sample and subsequent sample are the neighbouring
points in the trajectory. This is called a 1-2-1 filter function, and will
smooth out trajectories with a sawtooth appearance.

64 Edit Menu Commands

Version 3.5 BodyBuilder for Biomechanics

Stronger filters are also available, with 5-point (1-3-4-3-1) and 7-point
(1-4-7-8-7-4-1) functions. These substantially reduce the frequency
content of the data and should therefore be used with caution. For
example, the motion of body parts which naturally have high-frequency
components, such as feet or fists, may become blurred by excessive
filtering. Repeated use of the 1-2-1 filter will have a similar effect to the
use of a stronger filter.
Because filters remove high frequency components, they also have the
effect of reducing the excursion of a point from the overall direction of
its movement. With repeated heavy filtering, the trajectory of a marker
which was moving in a roughly linear path, would ultimately become a
straight line. Similarly, if a marker is moving in a circular path, without
overall displacement, the effect of filtering will be to reduce the radius of
curvature of the path. If repeated, this would ultimately bring the point to
a standstill.
If a segment of a trajectory is snipped at both ends and selected, the filter
will act only on the selected segment. Repeated filtering will tend to
reduce it to a straight line. This is unlike the delete and fill function,
which produces a smooth path between the end points, but maintains
curvature. Repeated delete and fill operations on the same segment
would not produce further changes.

Spike Removal
If Remove Spikes is selected from the Filter box, you may choose to
remove spikes from the selected trajectory. Spikes occur when the
reconstruction process has located a single point which is to one side of
the position which would be expected from the surrounding points. Spike
removal is a special case of the Delete and Fill function, in which the
program automatically identifies such points and carries out a delete and
fill on each one.
The threshold setting determines how far a point has to be from those on
either side, to be identified as a spike. A higher value leads to fewer
points being identified as spikes. Once again, this function should be
used with care.
When spike removal is used, the selected trajectory is analysed, and a
spike value representing the degree to which each point deviates from a
smooth path is calculated. A point which lies directly between its
neighbours has the minimum spike value of 1; a point which deviates
Version 3.5 BodyBuilder for Biomechanics

Edit Menu Commands 65

from this path has a higher spike value. Any point with a spike value
higher than the threshold is then deleted and filled. A threshold value
close to 1 will, therefore, result in a high proportion of points being
deleted and filled. A value of 2 may result in only a few points being
removed. The most appropriate value of the threshold can only be
determined by trial, beginning with a higher value and reducing it until
the desired result is obtained.
Refer to VICON 370 Users
Manual for advice on
improving your data.

If there are many spikes, it may be better to filter the whole trajectory
rather than spike-remove a high proportion of points. If spikes are a
frequent problem, it would be a good idea to re-calibrate and see if a
better result can be obtained. It may be necessary to re-linearise the
cameras. However, if the problem is not excessive, spike removal and
filtering will enable you to produce satisfactory results without repeating
data capture.
If both filtering and spike removal are selected, spike removal is carried
out first.

Re-Sampling
If the desired output is a time-series of point data at time intervals
different to that of the input file, the re-sample function allows the user to
fit a curve to the data and calculate new points at a user-specified time
interval. This function may be used to produce new points at either a
higher or lower sample rate than the original sample rate.
If the output field rate is a precise sub-multiple of the original (eg. 10Hz
from an original 60Hz), the user may choose to use the original data by
discarding the appropriate intermediate points. However, in most cases
the re-sampling function works by fitting a curve which is a close
approximation to the original data, and then using this to calculate new
points. There is, in this case, a minor low-pass filtering effect.

66 Edit Menu Commands

Version 3.5 BodyBuilder for Biomechanics

If gaps are present in the data, re-sampling will have the effect of
invoking the Fill All Gaps command with no maximum gap size limit.
Re-sampling is not reversible using the Undo command - if you are in
any doubt about re-sampling, save the data to your hard disk before using
this command.
Because of the problems involved in resampling analog data, especially
when it is captured at a multiple of the video rate, the resample feature is
disabled when analog data is present.

Version 3.5 BodyBuilder for Biomechanics

Edit Menu Commands 67

68 Edit Menu Commands

Version 3.5 BodyBuilder for Biomechanics

View Menu Commands

View Menu
The View Menu controls the appearance of certain items in the main and
Workspace windows. Most of the commands in the View menu are only
available if a Workspace window is active.

Toolbar
The toolbar appears by default (ie. unless you select otherwise). The
toolbar is a row of buttons which provide rapid alternatives to menu
commands. Each button corresponds to a frequently used command. Not
all commands are represented by tools; the View menu commands are
not represented.
The tools cannot be changed by the user, only selected for display or
otherwise. They are grouped according to the menu to which the related
command belongs, and given symbols suggesting function. The File
Open tool is commonly used by Windows programs and will be familiar;
others are specific to BodyBuilder. The user should gain familiarity with
the tools by pointing at them; a device called Tool Tips causes the name
of the related command to appear when you point at a tool for longer
than one second. If the user prefers not to have the toolbar displayed, the
Toolbar command in the View menu toggles the display on or off.

Status Bar
The Status Bar appears at the bottom of the main program window,
occasionally displaying helpful messages indicating program function
and status.
Version 3.5 BodyBuilder for Biomechanics

View Menu Commands 69

If the user finds this unhelpful, it can be removed, which allows the
working windows to be displayed slightly larger. If the user prefers not to
have the status bar displayed, the Status Bar command in the View menu
toggles the display on or off.

Rotation Centre
In a Workspace window, the centre of rotation (if selected) is shown by a
purple diamond. The axes of Workspace viewpoint rotation pass through
this point, and the zoom function acts towards or away from this point.
Like all the View menu commands, this one works as a toggle, meaning
that it has two states, and each point-and-click on the command changes
the state. If the user prefers not to have the rotation centre displayed, this
command can be used to turn off the display. The keyboard alternative is
R.

Markers
In the Workspace window, the positions of the markers in the current
field are shown by small circles (or, to be precise, octagons).
If Markers are deselected, these will be hidden, leaving the trajectory and
stick displays to indicate the motion of points. The keyboard alternative
is M.

Stick Figure
The display of sticks joining points is usually helpful, but if the user
prefers not to display sticks, they can be deselected. The keyboard
alternative is S.

Floor
70 View Menu Commands

Version 3.5 BodyBuilder for Biomechanics

The 500mm square tile floor appears by default in the plane defined by
Z=0. If this is not helpful, it can be deselected by this toggle. The
keyboard alternative is W.

Flicker Free
Depending on the hardware (in particular the use of graphics
acceleration) it may reduce flickering if the processor takes control of the
Workspace window, at the expense of replay speed. Use this toggle to
select the display mode which gives the best result on your PC. The
keyboard alternative is Control-F.

Always Refresh
Depending on personal preference, the user may choose to refresh the
Workspace window after each field is drawn, during a replay, at the
expense of replay speed. Use this toggle to select the preferred mode.
The keyboard alternative is Control-R.

Set Frame Rate

The Workspace window may replay every frame of data at the speed
determined by the processor and graphics hardware, or can replay the
data as if it were captured at different rates. Pressing the Reset button
returns the replay rate to the true capture rate.

Version 3.5 BodyBuilder for Biomechanics

View Menu Commands 71

72 View Menu Commands

Version 3.5 BodyBuilder for Biomechanics

Model Menu Commands

Model Menu
The model menu commands allow the user to apply kinematic models
written in BodyLanguage, and to view the results in the Workspace
window. The model menu is also the key to animation-format output
functions.

Run Model
The Run Model command runs the BodyLanguage model for the current
trial (.C3D file). The sequence of operations is as follows:

Read .MP and .MOD script files

Carry out kinematic modelling as defined in the script

Calculate required outputs

Update Workspace window to show outputs

Update parameters (.MP file) if required

The Run Model command causes a model to be run for each subject in
the trial, using the model and parameters as specified in the Subject
Settings dialogue box.
Although the Workspace window will appear different after the Run
Model command is invoked, no new file is created. The model outputs
are held in system memory, until the user saves the data by writing to
disk. Until the data is saved, the operation can be Undone by selecting
the Delete Model Outputs command from the Edit menu.

Version 3.5 BodyBuilder for Biomechanics

Model Menu Commands 73

Note that if required, a new model can be selected, and run, using the
outputs from the previous model as inputs to the new model.
If there are any errors in the model script, an error message will appear
describing the error, and if appropriate, a text editor window will be
opened with the offending line in the script highlighted. See the View
Last Error command for more details.

Run Model for Subject

If the trial data currently displayed in an active Workspace window has a
single subject (performer), or has been labelled manually in VICON 370,
and there are no label prefixes, the Run Model for Subject command has
exactly the same effect as the Run Model command. The subject is
identified as Anonymous in such cases.
If the trial data currently displayed has been automatically labelled in
VICON 370 (version 2.5 or above) and so has subject-identifier label
prefixes, then it is possible to run the model in such a way as only to take
effect for one named subject. This is useful if more than one subject
appears in the data. The currently named subject is shown at the top of
the marker list bar on the right of the Workspace.
Using the Run Model for Subject command allows the use of different
models for subjects with different names, appearing in the same trial.

Create ASF
Acclaim Skeleton Files are
used by certain computer
animation systems. Refer to
the documentation provided
for those systems.

The Create ASF command is intended for those users who want to
produce an Acclaim Skeleton File using a BodyLanguage model and a
.C3D file of static data. The specific requirements for this are explained
in the section on Acclaim format modelling.

The .ASF file produced is based on a template file with the extension
.AST which must match the input data and the model script.
The Create ASF command carries out the same procedure as the Run
Model command, with the difference that the line
74 Model Menu Commands

Version 3.5 BodyBuilder for Biomechanics

$Static = 1

is added to the beginning of the .MP file before the combined script is
executed. This signifies that the data is a static trial, to be used for
creating the skeleton data file. The result of running such a model is a
text file with the extension ASF.
The .ASF file created by this command will have the same name as the
input .C3D file.

Create AMC
The Create AMC command is used to create an Acclaim motion file
using a BodyLanguage model and a .C3D file of motion data. The
specific requirements for this are explained in the section on Acclaim
format modelling.
The Create AMC command carries out the same procedure as the Run
Model command, with the difference that the line
$Static = 0

is added to the beginning of the .MP file before the combined script is
executed. The result of running this kind of model is a text output file
with the same name as the input .C3D file, and the extension .AMC.
An .ASF file is required before this command can be used.

Create AMC Files

This command allows the user to process multiple .C3D files and create
.AMC files in batch mode. The input files are selected in the Create
AMC dialogue.
The .C3* input data files must all be in the same folder. This may be
selected by clicking the adjoining Browse button, and selecting one of
Version 3.5 BodyBuilder for Biomechanics

Model Menu Commands 75

the required AMC files from the folder. By default, all trials are selected
except for those which already have .AMC files.
In the case of auto-labelled trials, the ASF file, and model and parameter
files used for processing are determined from the subject name, and the
marker set file name used during auto-labelling. Where these files cannot
be found, or a manually labelled trial is selected, the default files as
shown at the bottom of the dialogue will be used. The model and
parameter files are the same as those set in the Preferences dialogue, and
the ASF file is initially set to be most recently generated one. A different
ASF can be selected by clicking the browse button.
When the OK button is pressed, the trials will be processed automatically
without any need for further intervention by the operator. One AMC file
will be generated for each subject, in each of the selected trials.

Axis Permutation
The Axis Permutation command is used before the Run Model or Create
ASF/AMC commands to change the axis convention used from the usual
VICON convention (vertical component = Z) to another convention.
The Axis Permutation box appears:

Any global point co-ordinates in the output will be permuted in the way
selected. In .AMC files, in which most movements are described relative
to other body segments rather than in global co-ordinates, there is a root

76 Model Menu Commands

Version 3.5 BodyBuilder for Biomechanics

segment which is specified in global co-ordinates permuted in the way

selected.
So, if the data as captured uses the normal VICON convention, it may be
(for example) that the subject is facing the X-direction, with the Ydirection on their left, and the Z-direction upward. Then, their root
segment in a .AMC file would have a rotation of approximately 0,0,0.
If it is preferred to change to the convention that the subject is facing the
Z-direction (out of the screen), with the Y-direction upward, the
permutation required is ZXY. The rotation values of the root segment
will now be calculated in the order appropriate to the chosen format. For
this reason, the Axis Permutation does more than simply re-order global
position co-ordinates, like the Map XYZ As function in the Write C3D
command dialog box.
The data will be unchanged if the XYZ permutation is selected. The
default selection is the last option used.

View Model
The View Model command will open a text editor window displaying the
model script file for the current subject of the active trial. Subsequent
invoking of the View Model command brings the model window to the
top and opens it if it is minimised.
The window can be closed directly.

View Parameters
The View Parameters command displays the current subjects parameter
file in a text editor window, in the same manner as the View Model
command.

View Last Error

If the Run Model, Create ASF or Create AMC command generates an
error, the View Last Error command opens a text editor window. The
Version 3.5 BodyBuilder for Biomechanics

Model Menu Commands 77

line at which the error occurred will be highlighted, and the error
message will appear at the bottom of the main application window. If the
error was due to a macro call, subsequent selections of View Last Error
will toggle the highlighted line between the call to the macro, and the
offending line within the macro.

Adjust Parameters
The Adjust Parameters command starts Interactive Parameter
Adjustment (IPA) mode. The use of this mode is described in the next
section.

Subject Settings
The first field in the Subject Settings box is a drop-down list of subjects
for the current trial. Below this are the marker, model and parameter files
currently selected for the given subject. These files may be changed
using the Browse button beside each field.
When an automatically labelled C3D file is first opened in BodyBuilder,
the model and parameter files are assumed to have the same name as the
marker set used to perform the auto-labelling. Thus, a subject labelled
using the file LEGS.MKR is assumed to be compatible with the model
LEGS.MOD. For a dynamic trial, the parameter file is assumed to have
the same name as the subject. For a static trial, if the parameters file is
not explicitly named, the basic parameter file for the model is loaded
initially (e.g. LEGS.MP) to act as a template for a new parameters file
with the subjects name.

78 Model Menu Commands

Version 3.5 BodyBuilder for Biomechanics

Version 3.5 BodyBuilder for Biomechanics

Model Menu Commands 79

Interactive Parameter Adjustment

Parameters
Parameters are numerical values which are part of a model, but which are
stored in a parameter file separate from the model script itself, because
the numbers are subject to frequent change. For example, they may
include values of segment sizes which depend on the individual subject
and the exact placement of markers, and so can vary from day to day.
The parameter file is added to the model script when the model is run,
but stored separately.
Often it is useful to edit the values in the parameter file during a
modelling session, in order to change the results in some way. You may
want to tilt a segment, or change the location of an internal point (such as
a joint centre) in relation to the actual markers. These adjustments can be
made interactively, with the effects of the change displayed immediately
in the Workspace window. When interactive adjustment is completed,
the final values of the selected parameters are entered in the parameter
file just as if they had been entered using the keyboard.

Starting Interactive Adjustment

When a C3D file has been selected and the Workspace window is open,
interactive parameter adjustment (IPA) mode can be entered by selecting
Adjust Parameters from the Model menu. The IPA dialog bar will
appear on the left of the Workspace.
If either the parameter file or the model file is currently open (ie. a text
editor window has been opened, displaying the contents of these files),
they will become locked while IPA is active. The files cannot be edited
and the text editor windows cannot be closed. This prevents any
mismatch arising between the files and the parameter and model text
Version 3.5 BodyBuilder for Biomechanics

Interactive Parameter Adjustment 81

being used by the IPA function. The Static check box is also locked for
the same reason.

Parameter List
The upper part of the IPA dialog bar contains a list of all the parameters
found in the parameter file for the current subject in the C3D file (if a
multiple subject file is open, only the currently selected subject is
affected by changes). Parameter names must begin with the $ symbol to
be recognised. The name of the parameter is shown on the left, and the
value on the right. The relative width of the name and value columns
may be changed by moving the split at the top of the pane.
Each parameter name has a symbol to its left, indicating the type - scalar,
point or angle. A scalar has a small circle beside the name. A point (three
dimensional quantity) has an arrow. An angle has a mathematical angle
symbol. In some cases, a parameter is defined by an expression, rather
than a simple definition. These values cannot be adjusted directly, but
they are listed anyway with their values, and have no symbol beside the
name.

82 Interactive Parameter Adjustment

Version 3.5 BodyBuilder for Biomechanics

The lower pane contains a display of PARAM outputs that would be

appended to the parameter file if the model were run.

Adjusting Values
To adjust a parameter, left-click the parameter name. If that parameter is
adjustable, a small thumbwheel window will appear.
A single thumbwheel will appear for scalar values, and a window with
three thumbwheels will appear for Point and Angle types. Up to three
such windows can exist at once. Further parameters can be adjusted by
Control-Left-Clicking other names. The three thumbwheel windows are
distinguishable by a coloured lozenge in their top bar. An identical
lozenge also appears to the left of the corresponding parameter name.
Values can then be adjusted in two ways. First, the thumbwheels can be
grabbed by left clicking the mouse, and dragged up, to increase the
value and down to decrease it. For Point and Angle thumbwheels, the
leftmost wheel controls the X value, the middle wheel the Y value, and
the right wheel Z. Pressing the Shift key while dragging in increases the
amount the value is changed, and pressing Control reduces it.
Second, the value can be changed by typing in the edit box in the centre
of the IPA bar. The parameter that appears here is the one most recently
adjusted. When typing, invalid formats (e.g. missing commas for Point
definitions) are ignored.
Each time the value is changed, the model is run for the single frame that
is displayed in the workspace, and the outputs updated. Changes to the
parameter values can be undone or redone by selecting Undo or Redo
from the edit menu.
The thumbwheel windows can be closed by clicking the button at the
bottom of the window. They also disappear automatically when new
parameters are selected for adjustment.
The current frame may be changed during IPA. Model outputs for each
frame selected during IPA will remain intact. The trial may also be
played (using the forward and back arrow buttons) but play will stop if a
parameter value is changed, and the model therefore re-run.

Version 3.5 BodyBuilder for Biomechanics

Interactive Parameter Adjustment 83

Different C3D Workspace windows may be selected, by clicking them if

already displayed, or opening them from the file menu. IPA will load the
corresponding models and parameter files. Parameter settings for the
previous trial will be remembered and recalled when that trial is reselected, although the thumbwheel windows will disappear.
In multiple subject trials, the subject may be changed, and the new
subjects parameters will be adjustable. The display set may also be
changed for the given subject.

Finishing IPA
Once the parameters have been adjusted to the required values, IPA
mode may be switched off by pressing the Finish button at the bottom
of the IPA dialog bar. The bar will disappear, and the final values for the
parameters adjusted will be inserted in their appropriate places in the
parameter file text. At this stage, the model can be run for the complete
static trial, generating the required additional parameters.
Any changes to the parameters file or the trial made during IPA must be
saved before closing the trial as the Finish button does not write the new
values to disk. If a text editor window is not open for the parameters, the
option to save them is offered when the Workspace window is closed.
The Cancel button also exits IPA mode without making any changes to
the parameters text, and any trajectories generated by the model during
the IPA mode are removed.
The Reset button causes the IPA mode to restart. The thumbwheel
windows disappear, the parameter name and output panes are cleared and
re-filled by re-reading the parameter file and re-running the model.

84 Interactive Parameter Adjustment

Version 3.5 BodyBuilder for Biomechanics

Workspace Menu Commands

Workspace Menu
The commands in the Workspace menu are all concerned with the
display of data in the Workspace window.

Select Centre
The centre of rotation and zoom can be changed to any point on a
selected trajectory. Hold the pointer steadily at the chosen point and
click with the left mouse button to select this point. If the trajectory
segment is the only one selected, it changes colour to yellow. If other
trajectories are already selected, another colour is used. Use the Select
Centre command to make the selected point the new rotation centre.

Hide Trajectories
If you want to turn off the display of certain trajectories, such as phantom
points (false reconstructions), select them and use the Hide Trajectories
command. When a trajectory is hidden, it cannot be selected, and the
mouse helper will not appear, even if the marker outline is still visible.

Show Trajectories
To turn the display of selected trajectories back on, use the Show
Trajectories command.

Version 3.5 BodyBuilder for Biomechanics

Workspace Menu Commands 85

If the hidden trajectory(s) is no longer selected, you can either use the
label list to re-select them, or use the Show All Trajectories command.

Hide Other Trajectories

This command hides the display of all trajectories other than those
selected. This is useful if you want to concentrate on one or two
trajectories with extended Before and After settings, as the other
trajectories will clutter the window.

Hide All Trajectories

If you prefer to see only marker outlines, without trajectory lines, the
Hide All Trajectories command turns off the display of all trajectory
lines.

Show All Trajectories

This command restores the display of all trajectory lines.

Toggle All Trajectories

This command allows you to turn the display of trajectories on and off
rapidly. The keyboard alternative T is the most useful way to invoke this
command.

Toggle Before Display

This command works the same way as Toggle All Trajectories, but
affects only that part of each trajectory prior to the current field. The
keyboard alternative B is the most useful way to invoke this command.

86 Workspace Menu Commands

Version 3.5 BodyBuilder for Biomechanics

Toggle After Display

This command works the same way as Toggle All Trajectories, but
affects only that part of each trajectory after the current field. The
keyboard alternative A is the most useful way to invoke this command.

Version 3.5 BodyBuilder for Biomechanics

Workspace Menu Commands 87

88 Workspace Menu Commands

Version 3.5 BodyBuilder for Biomechanics

Designing Biomechanical Models

Defining the Problem

BodyBuilder for Biomechanics is not an application you simply load and
run, like a word processor or a game. It is designed as a tool to enable
users to design and carry out complex experiments in biomechanics, and
because it allows total flexibility, there is no single, standard way to use
it. The user must design their own experiment and way of working.
To derive useful results from your measurements, first it is necessary to
have a clear idea of the purpose of the experiment. BodyBuilder for
Biomechanics enables the user to model the body as a group of
segments, each of which is treated as if it were a rigid body. These
segments are linked to each other by joints. The purpose of a
measurement, or series of measurements, might be:

to develop a new model, based on new segment and joint

definitions, or a new marker set

to verify that a particular model is valid for its purpose

to apply a verified model to a particular subject, to learn

something about that subject

In the first case, the user will make extensive use of the BodyLanguage
model-writing facility, editing the model and testing the changes to see
the effect they have. In the second case, the user will process data using a
particular model, and assess the results to see if they are anatomically
useful. In the third case, the user aims to learn something about the
individual subject or patient, rather than about the model.
The flexibility of BodyBuilder for Biomechanics therefore allows the
user to study individual subjects; to study a modelling method; or to
develop new methods and test them against real life. The purpose of the
work being carried out will affect every aspect of data processing and
Version 3.5 BodyBuilder for Biomechanics

Designing Biomechanical Models 89

presentation, and for this reason it is only possible to use the tools
available once the purpose has been thoroughly defined.
The process of designing and writing a model is fundamental to the use
of BodyBuilder for Biomechanics. Even if the purpose of a particular
study is to apply an existing model to a particular subject, it is useful to
understand the way in which a model is developed.

Dividing the Body into Segments

Kinematic modelling is not
limited to human bodies,
and has been applied to
animals and machinery;
however, the following
discussion refers only to
human studies

The design of a model begins with a need to describe the human body
and its motion for a certain purpose. The purpose may be the study of an
abnormality by comparison with normal individuals; the study of physical
stresses and the avoidance of injury; the study of mechanical efficiency
and its improvement; or the study of a sporting skill and the effects of
various kinds of training and coaching. There are limitless possibilities,
and each case requires an appropriate model.
The purpose will determine the way in which the body is modelled. The
body must be divided into segments, which are assumed to behave as
rigid elements, joined in certain ways. The number of segments and the
overall complexity of the model will be determined by the purpose of the
study. For example, if the purpose is to analyse power transmission at the
knee joint in Olympic weightlifters, it is not necessary (and may be
impossible) to measure and model the movement of each finger.
However, if the purpose is to analyse repetitive movements in typing,
each finger may need to be modelled as two or even three segments.

90 Designing Biomechanical Models

Version 3.5 BodyBuilder for Biomechanics

When designing a kinematic

model, it may help to begin
by making an outline
drawing to show the
segments and joints.
In the case of this simple 10segment model, each limb is
modelled in two segments,
plus the body and head.
Thie may be adequate for a
gross description of large
movements.
This diagram does not show
exactly how each joint is
modelled

In most biomechanical studies, the division of the body into segments

will begin with a study of anatomy. The concept of modelling the body
as a number of linked, rigid segments is based on the anatomical fact that
the skeleton is made up of rigid bones which are linked by various kinds
of joint, whose characteristics are well known. The user must judge to
degree to which this approach gives realistic results.
For example, a large bone, such as the femur, will lend itself easily to
modelling as a single segment, but there may be some difficulty in
finding marker locations which are not prone to substantial amounts of
skin movement relative to the underlying bone. A complex body part
such as the foot, although presenting fewer skin movement problems,
contains many individual bones and compound joints, and will have to be
modelled using approximations and simplifications. A body part such as
the forearm may be simple to model as a single rigid segment, but it is
more difficult to model the relative motion of the radius and ulna. The
degree to which a model is realistic will depend on the validity of the
approximations and simplifications used, judged within the context of the
purpose for which the model is written.

Version 3.5 BodyBuilder for Biomechanics

Designing Biomechanical Models 91

In a more anatomically
sophisticated model, it will
be necessary to consider the
relationship of actual bones
to modelled segments; the
degree of complexity
required; the level of
realism needed; what it is
possible to measure using
markers attached to the
skin; and the significance of
any kinetic quantities to be
derived from the model.
The foot is an example of a
body part which may be
modelled with various levels
of complexity. The degree of
anatomical realism required
depends on the purpose for
which the results are to be
used.

Approximations and Errors

Modelling the body as an assembly of rigid bodies linked by joints, and
then measuring the motion of those segments using skin markers, is
subject to inherent errors and approximations.
Firstly, if it is the aim of the measurement to establish the motion of the
skeletal components concerned, there is an error associated with the
movement of skin relative to bone. This can be reduced, but not
eliminated, by careful choice of marker location. Some experiments may
be required to find out the best places to locate markers in order to
minimise the effects of skin movement.
Secondly, even if there were no skin movement, there would be some
uncertainty involved in the relationship of the marker positions to the
underlying skeletal structure and joints. This source of error may be
reduced by choosing easily located anatomical points at which the bony
structure can be found close to the skin, or by correcting for the
uncertainty after the measurement by using adjustable parameters; but it
is not possible to eliminate it completely.

92 Designing Biomechanical Models

Version 3.5 BodyBuilder for Biomechanics

Thirdly, the rigid-body concept is an approximation. Even the bones

themselves are not perfectly rigid, and the joints contain elastic
components such as ligament and cartilege, which can deform slightly
under load. These are likely to be insignificant sources of error, though,
compared to the movement of soft tissue. Given sensible choices of
marker location, soft tissue movement should not be a source of large
errors in kinematic studies (concerned with motion), but may be
important in kinetic studies (concerned with forces).
Finally, the measurements of marker trajectories are themselves subject
to error, and users should be aware of the extent to which these errors
may be significant. For example, when calculating the moment about a
joint such as the hip, the result is usually the product of a large force and
a small distance. Position-measurement errors, although small in absolute
terms, may be amplified when such quantities are calculated. Also, the
measurement of the rotation of a long, thin segment about its long axis
may be more sensitive to small positional errors because of the nearcolinearity of the markers on the segment. Techniques to address this
error include the use of markers on sticks.

Modelling the Joints

The joints between the segments can be modelled with various degrees
of freedom. A joint such as the hip or shoulder, for example, being a
ball-and-socket type of joint, can rotate about three axes, and in most
kinematic models, it is necessary to measure all these degrees of freedom
if the results are to be realistic and useful. The knee and elbow, however,
may in some cases be modelled as simple hinge joints with only one
degree of freedom. Although this is a simplification, it may be
adequately realistic for many purposes. It is necessary to decide how
many degrees of freedom to allow each joint, because this determines the
number of markers needed to measure the movements concerned.
In most cases, modelling a joint involves estimating the position of an
internal location, such as the centre of a ball-and-socket joint, or the axis
of a hinge joint, using the measurements of external markers, combined
with knowledge of anatomy. This may be as simple as placing a marker
on an anatomical landmark and assuming that the internal point can be
derived from that markers position by adding a certain distance in a
specified direction. Alternatively, it may be a more complicated
procedure involving several markers and detailed anatomical parameters
measured by radiography. Any level of complexity is permitted, and the
user must decide how sophisticated the model needs to be, if it is to be
suitable for its purpose.
Version 3.5 BodyBuilder for Biomechanics

Designing Biomechanical Models 93

Points, Lines, Planes and Segments

Having decided on the division of the body into segments, and the kind
of joints between those segments, the user can begin to write the model
and design the marker set which goes with it. At this stage, it is essential
to have a clear idea of the number of markers required per segment.

Single Point

It is clear that the measurement of the position of a single marker

(expressed as three co-ordinates, relative to a particular frame of
reference), is not sufficient information to fix the location and orientation
of a body segment. Even if we assume that we already know the size and
shape of the segment, knowing the location of just one point belonging to
it is not enough to determine its location and attitude completely.

94 Designing Biomechanical Models

Version 3.5 BodyBuilder for Biomechanics

Two Points

It is also obvious that the positions of two markers (six co-ordinates in

total) defines a line. In fact, knowing the positions ot two markers gives
us more than just a line; it gives us the length of the line (the distance
between the two markers), the sense of direction (think of an arrow rather
than a line), and the location of each end of the line, or any other point of
interest along it. This, though, is still not enough to fix the location and
attitude of a body segment.

Three Points

If we know the positions of three markers which all move together as

part of a single body segment (a total of nine co-ordinates), we have
enough information to define a plane. Any three points define a plane
(unless they are co-linear). However, three points can define more than
just a plane; they can define a segment in both position and orientation.
If one of the markers is nominated as the origin; the direction from that
origin to another marker is used to define a first axis; a second axis is
defined at right angles to the first (in the plane defined by all three
markers together); and a third axis is defined at right angles to the plane;
Version 3.5 BodyBuilder for Biomechanics

Designing Biomechanical Models 95

then we have defined a complete origin-and-axes system, with its

location and attitude fully determined, but only on condition that the
three markers are not co-linear.

Four Points
If we have the positions of four markers belonging to one segment, again
on the condition that they are not co-linear, we have redundant
information, which we can use for other purposes. For example, if one of
the markers is temporarily obscured from view, we can use our
knowledge of its relationship to the other three, to fill in the gap. This
technique is very useful in kinematic modelling, especially in the case of
complex motions where markers are often obscured from view.
Alternatively, we could use the redundant information to average out
errors due to measurement noise, skin movement and so on.
To summarise:

one marker defines the location of one point, but not of a whole
segment

two markers define a line, with length and direction (ie. an

arrow or vector)

three non-colinear markers define a plane, and also a complete

segment (with location and attitude)

four markers provide extra information which can be useful for

interpolating obscured markers or averaging out measurement
noise

It is worth remembering that one or more of the points used to determine

the location and attitude of a model segment may be derived from a
neighbouring segment. In fact, if the positions and attitudes of the
neighbouring segments are fully determined, and the degrees of freedom
of the joints are defined, it may be possible to determine the location and
attitude of a segment without any markers being attached to it. This
technique is demonstrated in the model FOOT, supplied with
BodyBuilder for Biomechanics.
BodyLanguage allows the user to define a segment using whatever
marker locations are suitable in the circumstances. It also allows for the
fact that if several markers are attached to one body segment, although in
theory they should move together, in fact they will each individually be
subject to skin movement and soft tissue deformation.
96 Designing Biomechanical Models

Version 3.5 BodyBuilder for Biomechanics

Choice of Origin and Axes

When defining segments, the model writer is free to choose any point
within the segment to be the origin of that segment, and any set of
mutually perpendicular directions as the axes. However, there are a few
guidelines which simplify these choices.
The majority of models in biomechanics involve linked segments which
form a chain, such as Pelvis - Femur - Tibia - Foot, and such models
describe the movements of each segment relative to the more proximal
segment. For example, a model might be written with the purpose of
describing the movement of the tibia with respect to the femur, in terms
of rotations about the knee joint.
In such models, it is necessary to define the location of a joint centre and
axes of rotation. In the case of the knee, for example, a kinematic model
might attempt to describe the movement of the tibia segment in terms of
rotation about a knee flexion axis which is fixed in the femur.
In such cases, it is convenient to define the femur segment such that the
knee joint centre is the origin of the femur segment. It may also be
convenient to define the axes of the femur segment so that one of them
coincides with the knee joint axis of rotation.
Generally, it is recommended to write segment definitions so that:

the origin of the segment is the centre of rotation of the distal

joint

the first axis of the segment coincides with the line between the
centres of rotation of the distal and proximal joints linking the
segment to its neighbours (ie. it is the long axis of an elongated
segment such as a limb segment)

if compatible with the above, the second axis coincides with the
most significant axis of rotation of the distal joint

While these are only guidelines and will not apply in all cases, certain
BodyLanguage functions (especially kinetic functions) assume that they
are followed unless otherwise specified. If you decide not to follow these
guidelines, pay particular attention to the calculation of force, moment
and power quantities in your model.
Version 3.5 BodyBuilder for Biomechanics

Designing Biomechanical Models 97

These guidelines cannot be used in all cases, for example segments, such
as the pelvis, which have more than one distal segments attached. The
treatment of such segments is illustrated in the example model scripts
supplied with BodyBuilder and discussed later in this manual.

Rotations
To describe the attitude of one segment relative to another, it is
necessary to choose a mathematical convention for the description. For
example, if we choose to model the elbow as a simple hinge joint,
knowing that it can only flex within a limited angular range, all we need
to choose is the position we call zero, and a sign convention to describe
flexion and extension. However, if the model is more complex, we must
use a more sophisticated definition. To describe ball-and-socket joints,
we must find an unambiguous convention for describing a particular
orientation using three angles.
The convention most relevant to biomechanics is called the Euler angle
convention, after the mathematician Leonhard Euler. Euler angles
correspond best to the concepts of flexion, abduction and rotation which
are used in anatomy and biomechanics. The use of this approach to
define rotations between segments is illustrated in all the example
models supplied. A ball-and-socket joint capable of rotating about three
different axes from any given position will be described using three Euler
angles; a joint with fewer degrees of freedom (for example, a hinge joint)
is equivalent to a ball-and-socket joint in which one or two of the angles
is given a fixed value. It is a useful simplification to describe a joint
using the minimum number of variables necessary for the model to fulfil
its purpose. For example, if it is acceptable to describe the knee as a
simple hinge joint with only flexion/extension movement permitted, ie.
no valgus/varus or rotation movements, then this will simplify the model
and reduce the number of markers required.
The characteristics of Euler angles, their full mathematical definition,
and an explanation of the effect known as gimbal lock, are given in
textbooks of mathematics and biomechanics, and will not be repeated
here.

98 Designing Biomechanical Models

Version 3.5 BodyBuilder for Biomechanics

BodyLanguage

Overview
BodyLanguage is an interpreted programming language for defining
kinematic and kinetic models of complex moving objects, such as the
human body. BodyLanguage is designed to be used by non-programmers
who have a reasonable grasp of geometry, but not necessarily of vector
algebra.
BodyLanguage scripts are read by VICON BodyBuilder and used to
process motion data, generating virtual trajectories, kinematic angles,
moment and power quantities, and other outputs of interest in
Biomechanics.
This section, inevitably, resembles a mathematics textbook; however,
every effort has been made to express meaning as clearly as possible and
to illustrate each technique with diagrams and examples.

Kinematic Modelling with BodyLanguage

BodyBuilder can generate output files which contain the locations and
relative orientations of body and limb segments, calculated on the basis
of the user-defined relationships of rotation centres to physical markers.
The user-defined model is contained in a BodyLanguage text file with
the extension .MOD, also referred to as a script, in which the
relationships between physical and virtual points are stated in general
terms. Numerical constants are contained in a separate text file with the
extension .MP, so that these parameters can be adjusted without
changing the general properties of the model itself.

Version 3.5 BodyBuilder for Biomechanics

BodyLanguage 99

Before Starting
The first step in using motion capture for computer animation is to
decide on the kinematic model to be used. This means choosing the
number and type of body segments which are to be defined and
measured, and the relationships between them. It also involves deciding
the locations of markers to be placed on the body of the subject or
patient, whose motion is to be captured; and writing down, in a
BodyLanguage script, the relationship between those real points and the
kinematic model body segments which are subsequently calculated.

Writing the Model Script

Models are written using BodyLanguage, which has been specially
designed to make kinematic and kinetic modelling as clear and concise
as possible. Complex mathematical operations can be accomplished with
plain, one-word functions. It is perfectly possible, using the information
given in this manual, to write a biomechanical model script from the
beginning, and several examples of such models are supplied. In
addition, Oxford Metrics encourages the exchange of model scripts
between users, and will circulate scripts with permission.
However, rather than writing a new model from scratch, it is often
quicker to start with an existing model and modify it to suit a new
purpose. Often, parts of one model can be copied into another.
BodyBuilder makes this easy by providing a model editing window in
which changes can be made, and immediately applied to experimental
data to see if the intended effect has been obtained.

Verifying Model Scripts

When a model has been written, it is necessary to test it with
experimental data to verify that the outputs are suitable for their purpose.
This may mean making an assessment of whether the assumptions made
about body segments and joints are realistic enough to give meaningful
results, and assessing the significance of various kinds of error.
A wide variety of models have been used in clinical gait analysis, the
purpose of which is to describe the subjects motion while walking, with
sufficient detail and accuracy to provide the basis for diagnostic and
100 BodyLanguage

Version 3.5 BodyBuilder for Biomechanics

treatment decisions. Obviously, any model which is to be used for a

purpose of such importance should be thoroughly verified by a properly
controlled study, before it is used routinely for assessing patients.

Using Kinetic Data: Terms and Definitions

BodyBuilder version 3.5 implements a range of new extensions to
BodyLanguage, which allow segments to be assigned mass and inertia,
and which allow moment and power values to be calculated from force
plate data, if available. All popular makes of force plate are supported:
Kistler, AMTI and Bertec.
The interpretation of kinetic quantities calculated by modelling is beyond
the scope of this manual. Also, the laws of motion and the general
principles of biomechanics are covered in textbooks and will not be
repeated here. However, the following basic terms and definitions, which
are used in BodyLanguage, may be useful.

Force
Force is a vector quantity, ie. one which has a magnitude and a direction.
Forces acting on a rigid body may be added and subtracted to each other
to obtain the net force on the body. All forces may be broken down into
three components which are parallel to any given set of mutually
perpendicular axes. The total, or net, force acting on a body is the sum of
the different forces acting on it at any given time, such as gravity, ground
reaction forces, and forces from other bodies linked to the body being
considered. If the net force acting on a body is zero, the body will remain
at rest or move at a constant velocity. If the net force on a body is nonzero, the body will be accelerated. Some forces can be measured directly
(eg. weight, ground reaction forces), others (eg. muscular forces) can be
estimated using appropriate kinetic models. The SI unit of force is the
Newton (N). Weight is an example of a force; it is the effect of gravity
on mass. A mass of 1kg has a weight of about 9.8N. Note that although a
force may be fully specified by a magnitude and a direction as far as the
strict definition is concerned, the needs of kinetic modelling may require
additional information such as the point of application of a force.

Moment

Version 3.5 BodyBuilder for Biomechanics

BodyLanguage 101

Moment is also a vector quantity. It describes the ability of a force to

make a body rotate. It is the (vector) product of the tangential component
of force acting on a body, and the distance separating the line of action
of the force from a defined reference point. Moment can also be broken
down into three components. For example, the vertical component of a
moment is the part which tends to make the body rotate around a vertical
axis. The SI unit of moment is the Newton-metre (Nm); in biomechanics,
the most widely used unit is the Newton-millimetre (Nmm). 1Nm =
1000Nmm. In BodyBuilder, it is assumed that the unit of moment is
Nmm.

Reaction
In mechanics, a reaction is a kind of force. When a body presses against
another, it experiences an equal and opposite force from that body. This
is the reaction. In biomechanics, the term is normally used to describe the
force exerted by the ground on the foot (or other body part) in contact
with it.
Ground reaction force vectors can be directly measured by force plates.
Strictly speaking, a reaction is a three-component force, but the quantity
measured by a force plate has an additional three moment components as
well, which are measured round a calibrated forceplate centre.
In BodyLanguage, a Reaction groups together a force and a moment
with the moment reference point, around which the force is deemed to
act, as a single convenient unit.

Work and Energy

Work is done when a force moves through a distance. If the movement is
in the direction of the force, as in a concentric muscle contraction, the
body applying the force is said to have done work (ie. the work done is a
positive number). If the movement is against the direction of the force, as
in an eccentric contraction, the body applying the force is said to have
work done upon it (ie. the work done is a negative number). Work is a
scalar quantity and cannot be broken down into components. The SI unit
of work is the Newton-metre or Joule (J). Energy is the ability to do
work and has the same units. Energy is also a scalar.

Power

102 BodyLanguage

Version 3.5 BodyBuilder for Biomechanics

Power is the rate of doing work. The power generated by a force acting
in a straight line is the product of the force and its velocity. The power of
a force causing a rotation is the product of the moment and its angular
velocity. Power is a scalar quantity, but sometimes in biomechanics it is
treated as a pseudo-vector by calculating power separately for each
component of a force or moment. The SI unit of power is the Joule per
second (J/s) or Watt (W). In BodyBuilder, the milliwatt is the normal
unit (mW). Ground reaction forces, however strong, do not move
through a distance, and thus do no work and generate zero power.

Moment of Inertia
Inertia is the tendency of a body to maintain a state of rest or constant
motion. It is effectively identical to mass. Moment of inertia is the
tendency of a body to maintain a state of rest or constant rotation about a
specified axis. It is a scalar quantity which depends on the mass of a
body, the way the mass is distributed, and the chosen axis of rotation.
The SI unit of moment of inertia is kgm2. Radius of gyration k is a
related quantity, defined as follows: if a body of mass M has a certain
moment of inertia about a specified axis, a point-like body of mass M
placed a distance k from that axis would have the same moment of
inertia. Radius of gyration is a distance and in biomechanics is generally
measured in millimetres.
The definitions, calculation, measurement, and inter-relationships of
these and other quantities are given in textbooks of biomechanics. The
user should take care to use consistent sign conventions for quantities
such as power, which can be either generated or absorbed by a muscle.
When power is transmitted across a joint, one segment does work on the
other and it is a matter of convention and preference which is considered
to be positive.

Applying the Model

In most cases, the results obtained will depend not only on the
anatomical assumptions made, and the model script used, but on the care
with which markers are placed on the subject prior to measurement.
Data collection, reconstruction and labelling is a function of VICON 370
(or VICON 140) and is described in the documentation supplied with
that equipment. The labels used to identify reconstructed trajectories
should match those mentioned in the model script.
Version 3.5 BodyBuilder for Biomechanics

BodyLanguage 103

The editing functions in BodyBuilder allow the data to be manipulated

prior to applying the model. For example, short breaks in trajectories can
be interpolated; noisy trajectories can be filtered; trajectories can be
created, changed and deleted. Clearly these features should be used with
care if the results are to reflect real motion rather than manipulation.
Users should be aware of the difference between cleaning up data and
changing it.

Displaying the Results

The output of BodyBuilder may take the form of a text (ASCII) file,
listing the locations of various points and segments, and the rotations
between certain segments as required. Alternatively, these quantities can
be stored in the more compact C3D format, and displayed graphically
using Reporter.
Reporter allows the user to open several C3D files at once, and to display
their contents in graphs. Graphs can be laid out on the page according to
preference, and the format can be saved and re-used once it has been
defined. Reports can be printed out or saved on disk. Reports may
include text as well as graphs.
The results of modelling may also be viewed directly in the Workspace
window of BodyBuilder. In many models, virtual points are created for
the sole purpose of making segments more easily visible in the
Workspace. If the virtual points created are listed in the marker label list
file, and stick figure links are defined between them, the segment can be
given a natural appearance, which is often enhanced when the display of
points is turned off and only the stick figures remain. Examples of this
technique are given in the sample scripts which are supplied with
BodyBuilder for Biomechanics.

104 BodyLanguage

Version 3.5 BodyBuilder for Biomechanics

Objects

Types of Object
BodyLanguage models are built up from 5 types of object:

numbers

points

segments

rotations

reactions

Numbers
Numbers are the simplest type of object, from which all other objects are
constructed. Numbers can be variable (such as the height of a point) or
constant (such as a body measurement like knee width). An important
use of constant numbers is for the physical parameters of a measured
subject.

Points
Points are locations in space, specified by Cartesian co-ordinates. Each
point has three ordered components, corresponding to the X, Y and Z
coordinates of the location in space, so a point may also be considered as
a vector. The co-ordinates may be specified relative to the overall
laboratory frame of reference, in which case the point is described as
global, or relative to a particular segment, in which case it is described as
local.

Version 3.5 BodyBuilder for Biomechanics

Objects 105

There are two kinds of point, real and virtual. Real points, derived from
physical markers, are the measured locations of reflective spheres
attached to the subject. Virtual points, created by modelling or other data
manipulation techniques, have all the properties of real points, but may
be in locations where no actual reflective marker existed. Virtual points
can be used:

to specify the location of internal body parts such as joint

centres

to build a mesh of surface points for a more realistic display of

the subject

to re-create, by interpolation or estimation, the location of a real

marker which becomes obscured during part of the motion
capture

Although a virtual point may not describe the position of a physical

marker, the terms point and marker are often used interchangeably.

Segments
A segment is defined by a group of points, both real and virtual, which
move together. A segment can move and rotate with respect to the global
frame of reference.
Each segment has a single point which is defined as the segment origin,
and three segment axes. The orientation of the segment is described by
rotations about the origin, relative to the global frame of reference.
A segment is generally used to describe the position and orientation of a
body part, such as the head, the pelvis, or a limb segment, which can be
considered as a rigid body which moves relative to neighbouring body
segments (although, as human body parts are not perfectly rigid,
allowance is made for the fact that markers placed on a body segment
may move a little relative to each other).

Rotations
A rotation is a quantity with three ordered components, representing
angular movement about 3 specified axes. These ordered angles are
called Euler angles.
106 Objects

Version 3.5 BodyBuilder for Biomechanics

A rotation may describe the orientation of a single segment with respect

to the global frame of reference, or the relative orientation of two
segments (whether or not they are linked by a joint).

Reactions
A reaction groups a Force, and a related moment a reference point
together, all of which are represented as three dimensional quantities.
Reactions are used to describe the kinetic interactions between segments,
and between segments and forceplates. See the kinetic modelling section
fopr more details.

Object Names
Every object has a name, composed of up to 256 letters and numbers,
plus some additional characters such as % and $. There must be no
spaces in an object name. Object names must not start with a number.
The names of real points in the input .C3D file are determined in other
parts of the VICON system (after reconstruction, when trajectories are
given labels) and must match exactly the names used in the .MOD file.
For example, if your BodyLanguage script (.MOD file) uses a point
called "KNEE", the input .C3D data file should contain a trajectory
named "KNEE". (If the trajectory of the relevant marker in the .C3D file
has been given a different label, you can either use BodyBuilder to relabel the trajectory, or edit the script to use the different name.)
BodyLanguage is case-insensitive, meaning that it ignores the difference
between upper and lower case characters in an object name. For
example, LeftKnee and leftknee are recognised as the same object.
To make a long object name more readable, upper case letters may be
used in the middle of a name (for example,
LeftElbowJointCentre).

Limitations of Object Names

Version 3.5 BodyBuilder for Biomechanics

Objects 107

It is not generally possible to identify the type of an object

simply be looking at its name.

Although in general, object names may have up to 256

characters, there is a limit of sixteen characters on the length of
trajectory labels in a .C3D file.

If you use BodyLanguage to create an object (such as a virtual

point) with the intention of saving it in a .C3D file, it should be
given a name of no more than sixteen characters.

Reserved Names
The following reserved names cannot be used for objects, since they are
reserved for special functions (see section on Functions):
ACOS
ALIGN
AND
ASIN
ATAN
ATAN2
ATTITUDE
AVERAGE
BODYMASS
CHORD
COMP
CONNECT
COS
DEADBAND
DEFINE
DIST
DISTANCETHRESHOLD
ELSE
ELSIF
ENDIF
ENDMACRO
EXIST
FIELD
FORCETHRESHOLD
GRAVITY
IF
LAST
MACRO
MOMENT
108 Objects

Version 3.5 BodyBuilder for Biomechanics

NORM
NOT
O (letter "oh")
OPTIONALFORCES
OPTIONALMOMENTS
OPTIONALNUMBERS
OPTIONALPOINTS
OPTIONALPOWERS
OPTIONALREACTIONS
OR
OUTPUT
PARAM
PERP
POWER
REACTION
ROT
SAMPLE
SIN
SINGULAR
SPINE
SQRT
TAN
THEN
VELOCITYTHRESHOLD

Object Assignment and Type Definition

A BodyLanguage model contains assignments by which an object is
defined or modified. Every assignment takes the following form:
ObjectName = Expression
where Expression is made up of a combination of other objects,
using operators, functions, and brackets ( ). Brackets can be nested
((.(.).).).
The type of an object (number, point, segment, or rotation) is determined
by its first assignment in the model, called the "type definition". The type
of the expression on the right-hand side of this first assignment fixes the
type of the new object on the left-hand side. At every subsequent
appearance of an object, its type must remain the same.
Version 3.5 BodyBuilder for Biomechanics

Objects 109

New lines have no structural meaning in BodyLanguage and are used

only to make the script easier to follow.

Inputs
Since BodyLanguage processes VICON motion data, its variable inputs
are real points from VICON three-dimensional data files (.C3D), which
move sample-by-sample. Each point used in the model must be referred
to by the same name in BodyLanguage as the label attached to it in the
.C3D file.
Other fixed inputs, known as "parameters", are constant for an individual
subject and may either have been typed in or calculated from a static
trial.

numbers, points, and segments

from parameter file

points

real or virtual
trajectories, read
from a C3D file

Optional Points
All objects referenced in a BodyLanguage script must be defined. For an
object to be defined, it must either be:

set to a constant, using one or more numbers

present in the list of labels of the input C3D file

calculable from other, previously defined, objects

Any other object found in a script is assumed to be an error (for example

a typing mistake) and is flagged when the model is run.
There is one exception to this rule. It is often convenient to write a script
that is able to run a different part of a model according to which labelled
trajectories are present in the C3D file. Points which may or may not be
present in the input file must be listed as optional, using the

110 Objects

Version 3.5 BodyBuilder for Biomechanics

OptionalPoints() statement. See later section on Non-Assigning

Statements.
Objects may be defined but not exist in the current sample (for example
if a measured point has not been reconstructed in the current sample).
The OptionalNumbers() statement works in the same way as
Optional Points, but declares a number of names as corresponding to
scalar values. Other types may also be defined using
OptionalForces(), OptionalMoments() etc.

Outputs
The purpose of a BodyLanguage model is to generate outputs:

numbers, points, and segments

parameter (.MP) file

(from static trials)

virtual points

as .C3D trajectories
(eg. joint centres)

segment rotations

.C3D (Euler angles)

joint rotations

.C3D (Euler angles)

The outputs, if appropriate, may also be written to .ASF or .AMC file

types. The non-assigning statements PARAM() and OUTPUT() are used
to generate outputs. (See later section on Non-Assigning Statements).
To optimise BodyLanguage execution speed, the sample-by-sample
values of an object are not evaluated unless it either appears directly in
an OUTPUT() or PARAM() statement, or are used in the definition of
another object which appears in an OUTPUT() or PARAM() statement.

Parameters
A BodyLanguage script is divided into two parts, a parameter section
(.MP file) and model section (.MOD file), which are loaded, edited, and
saved separately.

Version 3.5 BodyBuilder for Biomechanics

Objects 111

The Parameter section is intended to provide subject specific information

that is required as input to the model, such as knee width, for example.
When the model is run, the two sections are linked together for
execution, with the parameter section heading the model section.
A model can be run with any parameter section which contains the
required definitions.
BodyLanguage scripts are often divided into two types, static and
dynamic, according to the output they generate. Some models however
do not need a special static trial.
A static, or calibration, script generates a set of parameter values that are
needed for running the main dynamic model. New parameters are
appended at the end of the current parameter section. Assignments to
existing parameters cause the existing parameter value to be overwritten.
The main dynamic model calculates values required from the moving
dynamic trial.
Although both types may be combined in a single script, it may simplify
matters if they are kept separate.

Samples
BodyLanguage differs from programming languages in one fundamental
respect.
The input to a BodyLanguage model is always a series of sampled data
points, equally spaced in time. In a conventional program, there would
need to be a "main loop" containing the instructions:
set first sample number
read sampled data from file
apply model to data in current sample
test for last sample number
loop back to read next sample

112 Objects

Version 3.5 BodyBuilder for Biomechanics

With BodyLanguage, this loop is assumed. The model is written simply

as it is to be applied to each sample in turn. No explicit loop instructions
are needed.
However, it is still possible to create expressions which depend on the
sample number (SAMPLE function - see later section on Number
Functions), or which use the values of objects from samples other than
the current one (sample offset function -see later section on Special
Functions).

Version 3.5 BodyBuilder for Biomechanics

Objects 113

Expressions

Types of Expression
An expression is a combination of objects, operators and functions by
which a new object is defined. Every assignment statement (by which
objects are defined or modified) takes the following form:
ObjectName = Expression
The expression in every assignment in a script must match the type of the
object being assigned. (If it is the first assignment of that object, it will
define the type of the object). The type of an expression is determined as
follows:

Numbers
A number expression can be:

a number input

a single integer or real constant (in the model script or

parameter list)

a valid combination of numbers, number operations, and

number functions

Points
A point describes a position in space. The same point can be described
either:

Version 3.5 BodyBuilder for Biomechanics

Expressions 115

in terms of its position relative to the global reference frame of

the VICON measurements

as a local position relative to the origin of the segment of which

it is a member.

Although it is possible to use the same name for a point in both

circumstances, it is recommended that, when a local definition of a point
is used, its name is prefixed with a "%" character, eg. LSHO (global) and
%LSHO (local).
A pair of braces {} is used to construct a point from 3 numbers. A point
expression can be:

a point input

numbers - {numberA,numberB,numberC}

a valid combination of points, point operations, and point

functions

Segments
A segment is a group of points which remain at fixed distances from one
another. As a segment moves, all the points in it move together. A
segment can move and rotate with respect to the global VICON frame of
reference. Strictly speaking, a segment expression does not require that
the points referred to are absolutely, rigidly fixed relative to each other since human body parts are not mechanically rigid, there must be some
flexibility. However, segment expressions should include points which
move together, at least approximately.
If the global positions of at least 3 points in a segment, (which are not in
a straight line) are known, the segments position (ie. the position of the
segment origin), and orientation, can be determined. Any other local
points in the segment can then be output as global, virtual points (see
section on Operators). This is the method of locating points, such as joint
centres, where a real marker cannot be fixed.
A pair of square brackets [ ] is used to construct a segment from a set of
points. A segment expression can be:

116 Expressions

a point and two lines in square [ ] brackets

Version 3.5 BodyBuilder for Biomechanics

a valid combination of segments, segment operations, and

segment functions

Segment Definition
In a segment definition, one global point defines the segment origin. (If
there is no real point at the desired location of the segment origin, the
segment is first defined with a different origin, and then moved to the
required position).
Up to 4 other global points are used to create two defining lines which
together uniquely describe the segment rotation. Rotation of a segment is
represented by the orientation of its 3 axes, pointing in mutually
perpendicular directions from the segment origin.
The point that defines the segment origin can also be used in the
definition of either defining line. Defining lines may also share a
common point, so a minimum of 3 global points are sufficient to define a
segment.
The global axes X, Y and Z, are established by the VICON calibration.
(Although they can be manipulated in BodyBuilder, for the purposes of
this document, they will be taken as fixed). Co-ordinates of global points
are an ordered triplet of numbers, in the order X co-ordinate, Y coordinate, Z co-ordinate. Segment axes, to avoid confusion with global
axes, are referred to as 1, 2 and 3, rather than X, Y and Z. Local coordinates are an ordered triplet of numbers, in the order 1-axis, 2-axis, 3axis. When a segment is defined, it is possible to control which axis has
which label, as long as the right-hand rule is followed.
One segment axis is set parallel to, or coincident with, the first defining
line (depending whether the segment origin lies on the first defining
line).
A second segment axis is in a direction perpendicular both the first and
second defining lines. The positive direction of the second segment axis
is towards the tip of an imaginary corkscrew whose handle turns, by the
shortest angle, from the direction of the second defining line onto the
first.
A third segment axis is perpendicular to the first two segment axes, and
the positive direction is determined using the right-hand rule.
Version 3.5 BodyBuilder for Biomechanics

Expressions 117

The order in which the global points are entered in the definition of a
segment is critical. If it is intended that:

the origin is defined by pointI

the first defining line is (pointK-pointJ)

the second defining line is(pointM-pointL) (from L to M)

(from J to K)

then the segment definition expression should be:

[pointI,(pointK-pointJ),(pointM-pointL),1]
The 1 at the end of the definition expression contains two pieces of
information. Its value (1) indicates that the first defining line coincides
with (or is parallel to) segment axis 1. Its sign (positive) indicates that
the segment axis constructed to be perpendicular to both the first and
second defining lines is axis 2 (one more than axis 1). The other axis is,
therefore, labelled 3. A token may be substituted for the number as
shown in the following table.
The permitted values for this number are:
Value

118 Expressions

st

1 line defines the

axis labelled

st

nd

1 /2 lines define
the axis labelled

Token
alternative

xyz

-1

xzy

yzx

-2

yxz

zxy

-3

zyx

Version 3.5 BodyBuilder for Biomechanics

Example

The diagram above shows the segment defined by

Pelvis =[CPelvis,LPelvis-RPelvis,FPelvis-BPelvis,yzx]

The virtual point CPelvis is the origin. The first defining line is from
RPelvis to LPelvis. The second defining line is from BPelvis to
FPelvis. The token yzx means that the axis parallel to the first
defining line is Axis 2; Thus Axis 2 is parallel with the first defining line
but originates from the origin at CPelvis. Axis 3 is perpendicular to both
defining lines, and its direction is determined by the right hand screw
rule. Axis 1 is, then, perpendicular to the other two axes, such that the
three axes form a right-handed frame. It is therefore not necessarily
parallel to the 2nd defining line.
This example uses five points to define a segment, since the defining
lines have no common points, and the origin is not part of a defining line
definition.

Segment Definition across Hinge Joints

It is often convenient to define one of the axes of a segment to be aligned
with the axis of a hinge joint. Using this form of definition limits the
degrees of freedom at the joint concerned and allows the segments to be
Version 3.5 BodyBuilder for Biomechanics

Expressions 119

defined using fewer markers than if they were independently defined

using separate markers. This approach is justified if it is acceptable for
the purpose of the model, to make the simplifying assumption that a joint
such as the knee or elbow can only move in flexion. This is equivalent to
assuming that there is no valgus/varus movement. Although this
technique prevents the two segments moving independently, it is not the
same as linking the segments in a hierarchy.
For example, the thigh and lower leg segments on either side of a kneejoint can be defined in terms of just 3 points: hip, knee, and ankle:
LFemur=[LKnee,LHip-LKnee,LAnkle-LKnee,-3]
LTibia=[LAnkle,LKnee-LAnkle,LHip-LKnee,-3]
where, in this example, LFemur is the left thigh segment and LTibia is
the left shank segment. However, two problems arise if the knee
hyperextends (goes beyond straight).
First, while the leg is close to straight, the three points used to define the
segment are almost co-linear. In the unlikely case that the three points are
precisely co-linear, the segment definition is not valid. However, this is
so unlikely that it can be disregarded. The real problem is that when the
three markers are very close to being co-linear, small variations in the
relative positions of these points can cause the direction of the knee axis
to swing wildy.
Second, when the knee goes beyond straight, the positive direction of the
knee flexion axis reverses and the segments "flip" by 180 degrees.

Singularities and Dead Band

To overcome wild swings in the knee axis when the leg is almost
straight, a deadband region can be defined in which the direction of the
axis is not calculated directly from the segment definition. Instead, the
modeller automatically checks the attitudes of the segment on either side
of the fields for which the axis lies in the deadband, and creates a smooth
transition between them.
If required, this automatic action by the model can be tested by using the
special logical function SINGULAR(segmentP). This function is true
if segment P is in the dead band. For example, the statement

120 Expressions

Version 3.5 BodyBuilder for Biomechanics

IF SINGULAR(Tibia) DEAD={1,1,1}
(followed by an OUTPUT statement) would create a point labelled
DEAD at the location 1,1,1 in each field in which the segment Tibia is
in the dead band.
The default value for the dead band is 1 on either side of straight. For
human movement analysis, unless marker positions are adjusted with
great care, this value is often too small to eliminate axis swings. A dead
band value can be set by including the following assignment anywhere in
the script, either as part of the model itself, or more conveniently as a
parameter.
DeadBand=numberA
where numberA is the half-width of the dead band in degrees.
In static trials, if the arms and legs are stretched out, it is possible for the
knees and elbows to lie in the dead band all the time, causing the
expression to be invalid throughout the trial. In this case it is necessary to
set a low value of dead band, or to comment out the line altogether. In
static trials, the problem of axis swing is irrelevant, so a dead band is not
required.

Anti-Flip
In addition to the problem of defining lines which are almost co-linear,
which is addressed using the dead band, there is another potential
problem which may arise if (for example) a knee hyperextends slightly
(goes past the straight position). Because the shortest angle from the
second defining line to the first is now in front of the knee, the knee
extension axis will appear to flip around so that it points inward rather
than outward. To overcome the flip problem, an optional argument can
be added to a segment definition, in the form of an anti-flip line.
To understand the use of the anti-flip line, visualise the 2 segment
defining lines projected into a plane to which they are both parallel.
Next, project the anti-flip line into the same plane. Now move these three
vectors in the plane, without changing their directions, until they
originate at the same point.

Version 3.5 BodyBuilder for Biomechanics

Expressions 121

The segment definition process involves rotating the second defining

line, projected into this plane, onto the first, through the shortest angle.
The second axis of the segment is defined, using this rotation, by a righthand screw rule. If, during this rotation, the second defining line passes
through the projected anti-flip line, the direction of the second axis is
automatically reversed. This has the effect of maintaining the general
orientation of the axis, even if the two defining lines move either side of
the dead band.
For example, a thigh, or femur, segment is conveniently defined using
the lines between hip, knee, and ankle:
LFemur=[LKNE,LHIP-LKNE,LANK-LKNE,zyx]
This works well until the knee becomes hyperextended, as when the
ankle moves in front of the hip-knee line. Without an anti-flip line, the
direction of the shortest rotation of the second defining line (LANKLKNE) onto the first (LHIP-LKNE) is then reversed causing the
horizontal axis of the segment to flip.
However, if the anti-flip line (LTOE-LKNE) is added:
LFemur=[LKNE,LHIP-LKNE,LANK-LKNE,zyx,LTOE-LKNE]
then, if the knee is hyperextended, the second axis rotation passes
through the projection of the line (LTOE-LKNE) and the reversal of the
horizontal axis directions is automatically negated.

Example
The following segment definition is taken from the model script
FULLBODY.MOD which is listed fully in a later section.
RFemur=[RKNE,RHJC-KneeOffset*2(Pelvis)RKNE,RANK-RKNE,zyx,RTOE-RKNE]
The name of the segment defined in this line is RFemur. The expression
in square brackets consists of a real point (RKNE) and two defining lines,
along with the token zyx and the anti-flip line RTOE-RKNE. The first
defining line is from the real point RKNE to the virtual point RHJCKneeOffset*2(Pelvis), which is to the right of the estimated
122 Expressions

Version 3.5 BodyBuilder for Biomechanics

position of the right hip joint centre, by an amount equal to half the width
of the knee joint (the knee offset is a number read from the parameter
file). The reason for this complex line definition is that the virtual point
RKJC at the knee joint centre has not yet itself been defined, so cannot
be used in the simpler definition RHJC-RKJC. The line established
instead is closely parallel to RHJC-RKJC but shifted to the right. The
second defining line is simply RANK-RKNE, and the anti-flip line is from
RKNE to the point RTOE. The token zyx ensures that the first defining
line establishes axis 3, and the axis established by the right hand screw
rule is axis 2. In the normal situation in which the knee is flexed, the
construction is as shown below.

In this diagram, the plane of the paper is the plane containing the two
defining lines; the projection of the point RTOE is also shown. The
curved arrow shows the shortest rotation bringing the second defining
line onto the position of the first. This causes axis 2 to be aligned out of
the paper.
Version 3.5 BodyBuilder for Biomechanics

Expressions 123

If the knee hyperextends, the construction would be as shown:

In this case, the shortest rotation of the second defining line passes
through the anti-flip line, reversing the right-hand screw rule, and
therefore ensuring that axis 2 is still aligned out from the paper.
If a dead band is defined, then in the case of the two defining lines being
co-linear (or close to co-linear), the position of axis 2 will be interpolated
from better-defined positions either side of the frames in which the leg is
straight.

Hierarchical Skeletons
It is not necessary to specify the interconnections of segments in a
kinematic model. Any number of segments may be independently
defined using separate sets of three or more markers, and the movement
of those segments will be completely independent. In some situations,
this may be appropriate and necessary. For example, it is possible to
124 Expressions

Version 3.5 BodyBuilder for Biomechanics

measure the movements of two subjects who are not connected to each
other and whose movements are fully independent. Alternatively, it is
possible to model two indirectly linked body parts of the same subject
(such as the two feet), without modelling all the segments which form the
bridge between them.
However, in many models, especially those which use the kinetic
functions, it is necessary for segments to be linked in specified ways,
corresponding to the actual physical joints between the body parts they
represent. In such a model, there is a hierarchy of segments beginning
with a root segment, from which chains of other segments branch out.
For example, the pelvis may be defined as a root segment, with the legs
and upper body represented by chains branching out from it. Each
segment in such a chain is called a child segment, and must have a
specified parent segment (which may be the root segment, or another
segment one level closer to the root). A segment may have only one
parent, but may have more than one child. In the example of a pelvis root
segment, the left and right thigh segments will both be child segments of
the root. No closed loops are permitted.
Any segment definition which does not state the name of a parent
segment is interpreted as a root segment definition. There is no limit to
the number of root segments which may be defined in one model script
(if the hierarchical scheme is not used, every segment is a root segment).
The choice of root segment does not correspond to any special
anatomical significance. Normally, if a simple diagram is drawn showing
the segments used in a particular model, one segment will suggest itself
as the root.
The naming of a parent for a particular segment does not itself define the
kind of joint between the two; their positions can still be measured
independently, and the distance between them is not fixed by their
hierarchical relationship. In some cases it may be desirable to limit the
degrees of freedom between the parent and the child, but this is
controlled entirely by the kinematic part of the segment definition (the
choice of origin and defining lines) not by the hierarchy. However,
segments which are defined as parent and child will be considered to be
physically linked, so that forces can act directly between the two.
Each child segment is defined by an expression which states the name of
the parent to which it is attached, and the connection point in the child
segment. The segment definition statement syntax is:
segmentS=[pointI,(pointK-pointJ),(pointM-pointL),xyz,<pointA>,
<parent<,pointC>>]
Version 3.5 BodyBuilder for Biomechanics

Expressions 125

where the first five arguments in the expression are the origin, defining
lines, token, and antiflip point; parent is the name of the parent
segment, which must have been defined earlier in the script; and
pointC is the connection point in the child, defined in global space. If
the connection point is not specified, the connection will be at the origin
of the parent segment.
A hierarchical definition may be made by reference to a previously
defined segment, using an assignment statement which adds a parent and
attachment point to an existing free segment
segmentS=[segmentS,parent,pointC]

This statement would replace the previous definition of segmentS by

extending it to include the parent and attachment point. Alternatively, a
previous segment definition may be copied, with the addition of a parent
and attachment point:
segmentS=[segmentR,parent,pointC]
The component function is
described later

The attachment point of a segment may be accessed using the component

function with the value 4:

Attachment=segmentS(4)
The IF ELSE block is
described later

or

4(segmentS)

The definition of segment parents may not be made inside IF ELSE

blocks, preventing the definition of a hierarchy that may change from one
frame to another.

Rotations of Segments
A rotation refers to either:

the orientation of a segment relative to the VICON global space

the orientation of one segment relative to another (joint angles)

Unless otherwise specified, rotations are saved as 3 Cardan (Euler)

angles.
126 Expressions

Version 3.5 BodyBuilder for Biomechanics

Rotation Definition
A special pair of brackets <> is used to define a rotation. A rotation
expression can be:

one segment in <> brackets, plus a token, eg.

<segmentP,xyz>

two segments in <> brackets, plus a token, eg.

<segmentC,segmentP,xyz>

If one segment and a token are enclosed in the <> brackets, the segment
rotation is global. If two segments are enclosed in the <> brackets, the
rotation is relative between the segments.
The first segment in the <> brackets is the child, or moving segment,
whose orientation is to be described relative to the second segment (or
global frame of reference). The second segment, if present, is the parent
or fixed segment.
In addition to the segment(s), a rotation definition includes a token of the
form xyz, which defines the order in which the angles are calculated.
If the token is omitted, the default is xyz.
The rotation is expressed as angles in degress about the fixed axes of the
second segment (or global frame if no second segment is supplied). The
order of the rotations is the same as that given by the axis token.
For a given rotation between two segments, there are twelve possible sets
of Euler angles. BodyLanguage specifically performs a fixed axis
calculation where the three angles are calculated in the given order
around the fixed axes of the parent segment.
However manipulation of the parameters passed to this routine allows
any of the floating axes possibilities to be used. This is described below.

Helical Vectors

Version 3.5 BodyBuilder for Biomechanics

Expressions 127

An alternative to Euler angles is the Helical Vector representation. If the

integer 0 (zero) is placed in the rotation definition instead of the token, a
helical vector is calculated.
This option is provided primarily for users who will make use of helical
vectors in their own software.

Global Rotations
A global rotation is a special case where one of the segments is aligned
with the global frame of reference. In any expression involving segments,
the global unit segment
[{0,0,0},{1,0,0},{0,0,1},xyz]
can be indicated by the numeral 1. For example, the expression
<Pelvis,1>
defines the global rotation of Pelvis, with angles measured about
global axes in the order xyz. This is equivalent to the expressions
<Pelvis,xyz> and <Pelvis,1,xyz>

Rotations about Fixed or Floating Axes

In computer graphics animation, it is usual to express rotations about
axes in the fixed/parent segment. This is the convention in
BodyLanguage, as illustrated above.
In some applications, including biomechanics and clinical gait analysis,
Euler angles are normally expressed as rotations about the moving axes
of the child or floating segment. To find these angles using the fixed
angle calculation in BodyBuilder, you can do the following :1.

reverse the segment order, ie. <segmentP,segmentC>

2. negate the rotation

128 Expressions

Version 3.5 BodyBuilder for Biomechanics

For example,
CG: < LeftShank, LeftThigh,yxz>
Bio: -< LeftThigh, LeftShank,yxz>
The first example gives the fixed axis values, and the second gives
floating axis values from the Thigh to the Shank, which gives quite
different results. For further information about the underlying
mathematics of this operation, please refer to the document
EulerAngles.rtf.

Gimbal Lock
The most widely-used form for recording the rotation between two
segments is as 3 Euler (Cardan) angles. The primary rotation angle
(normally flexion) is defined about one axis (side-to-side, or lateral), a
secondary rotation angle (normally abduction/adduction) is defined about
a second axis (forward, or anterior), and a third rotation angle is defined
about the remaining axis (nominally vertical). This is the method used by
BodyBuilder.
However, Euler angles suffer from one well-known problem. If any of
the rotation angles becomes close to 90 degrees, for example lifting the
arm to point directly sideways (shoulder abduction about a forward axis),
the other two axes of rotation become aligned with one another, making
it impossible to distinguish them from one another (shoulder flexion and
rotation). This is known as gimbal lock.
True gimbal lock is rare, arising only when two axes are perfectly
aligned. A similar effect occurs when a segment spins through more than
one revolution. If the range of all three Euler angles is +/-180, there are
two possible sets of Euler angles which describe a given orientation. This
ambiguity may cause switching between one solution and the other,
resulting in sudden discontinuities. This situation resembles gimbal lock.
To avoid this, one of the angles must be restricted to +/-90 . In
BodyLanguage, the second angle is chosen to be restricted in this way.
This restriction applies to static trials.
In dynamic trials, if a segment rotates continuously, BodyLanguage
prevents discontinuities by keeping an internal record of rotations in a
form which does not suffer gimbal lock.

Version 3.5 BodyBuilder for Biomechanics

Expressions 129

130 Expressions

Version 3.5 BodyBuilder for Biomechanics

Kinetic Modelling

Mass and Inertia Properties of Segments

Mass and inertia can be assigned to each segment for the purposes of
calculating forces and moments. This can be done in two ways: either
directly, by supplying numerical values in a definition expression; or
indirectly, by referring to a table of typical values.

Direct Definition of Mass Properties

These can be made in the same expression as the basic kinematic and
hierarchical definitions, or added as an extension to a previously defined
segment. The mass properties must the last part of the definition, whether
the whole definition is made in one expression, or in parts. The syntax
for extending a previously defined segment is:
segmentS=[segmentS,SegmentMass,CentreOfMassPoint,Inertia]

where

segmentS is the segment name

SegmentMass is a scalar quantity expressing the mass
of the segment (in kg)
CentreOfMassPoint is the location of the centre of
mass of the segment, in the local co-ordinate system of that
segment
Inertia is defined using three terms, like a point,
which correspond to the components of the moment of inertia

Definition using a Table

Version 3.5 BodyBuilder for Biomechanics

Kinetic Modelling 133

The inertial properties can be defined using a table of anthropometric

data based on standard values for the mass and inertial properties of
various body segments. In most cases this will be a close enough
estimate to give useful data. The table must be included in the model
script file before any reference is made to it in segment definitions.
Each entry in the table must include a name and four numbers. The
numbers are:
1.

the segment mass as a proportion of total body mass

2.

the location of the centre of mass as a proportion of the length

of the pricipal (long) axis of the segment

3.

transverse radius of gyration around the centre of mass

4.

longitudinal radius of gyration around the centre of mass

the radii of gyration being quoted as a proportion of the length of the

segment. Note that it is assumed that the segment definition follows the
convention that the origin is at the distal end, with the first (principal)
axis being the length of the segment (origin of segment to attachment
point in proximal segment). The centre of mass is assumed to lie on this
axis (which is a good approximation for human limb segments) and the
three length numbers are all expressed as a proportion of the segment
length.
The table must begin with the word AnthropometricData and end
with the word EndAnthropometricData
Example:
AnthropometricData
DefaultFemur 0.1 0.567 0.323 0
DefaultTibia 0.0465 0.567 0.302 0
DefaultFoot 0.0145 0.5 0.475 0
EndAnthropometricData

In this example, the numbers on each line are taken from published
anthropometric data (Biomechanics and Motor Control of Human
Movement, David A. Winter, publ. John Wiley, p. 56).

134 Kinetic Modelling

Version 3.5 BodyBuilder for Biomechanics

The total body mass must be given, either in the model script or
(preferably, since it will be different for each subject) in the parameter
file, using the name BODYMASS, in a line such as
BODYMASS = 75 {*kilos*}

The longitudinal radius of gyration is used for the inertia calculations

around the principal (long) axis, and the transverse value, around the
other two axes. Reference to the entry values are made by the entry
name. The segment length defaults to the distance from the segment
origin, to the attachment point on the parent segment, a distance which
may vary slightly from frame to frame because of skin movement,
measurement noise, or inappropriate joint centre estimation, but which
will in most cases be nearly constant.
A fixed length may be defined using a value from the parameter file:
segmentS=[segmentS,EntryName<,SegmentLength>]

where EntryName is the reference to the table (eg. DefaultFemur in the

example above), and SegmentLength is an expression for the
segment length (expressed in the units in which the original
measurements were made, normally millimetres).

Correcting for the Mass of a Prosthesis

The tabulated values in the example above refer to the mass of a normal
complete body. If one or more segments have been replaced by a
prosthesis which has a mass greater than the natural segment it replaces,
the BodyMass needs to be corrected to allow for this. The value required
is an estimate of what the body mass of the subject would be if they had
all natural body segments - the equivalent intact body mass.
For example, if the subject has one artificial foot which has a mass of
2kg, and the total body mass of the subject with the prosthesis is 62kg,
then the body mass without the prosthesis is 60kg. From the above table
of normal proportions, this represents (1 - 0.0145) of the total mass of
the body if the subject had a natural foot. To calculate the equivalent
intact body mass, the actual body mass (60kg) without the prosthesis
should be divided by this figure, giving 60/0.9855 = 60.88kg. The
formula in the general case is

Version 3.5 BodyBuilder for Biomechanics

Kinetic Modelling 135

BodyMass (equivalent intact body mass)

= (Total Mass - Mass of Prosthesis)/(1 - Normalised Segment Mass)
where the normalised segment mass is the proportion of normal body
mass which is attributable to the segment replaced by the prosthesis.
The segment in the model which represents the prosthesis, should then be
defined with the specific mass of that prosthesis.

Reactions, Forces and Moments

Reaction, Force and Moment are kinetic objects which can be defined
using BodyLanguage assignment statements.

Force
Force objects have identical properties to points. They can be plotted and
saved as points, using OUTPUT() statements, or stored as parameters
using PARAM() statements. They can be defined from named or
constant numbers in the same way as points:
forceF = {numberA,numberB,numberC}

Forces may be split into components in the same way as points

component1 = 1(forceF)or forceF(1)

Moment
Moments, like forces, have identical properties to points. They can be
plotted and saved as points, using OUTPUT() statements, or stored as
parameters using PARAM() statements. They can be defined from
named or constant numbers in the same way as points:
momentM = {numberD,numberE,numberF}

Moments can be split into components like forces or points.

136 Kinetic Modelling

Version 3.5 BodyBuilder for Biomechanics

Reaction
Reaction is a combination of force, moment, and point of application:
reactionR = |forceF,momentM,pointP|

where pointP is the point (local or global) at which the reaction is

applied. A reaction may be split into its components as follows:
pointP = 1(reactionR) or reactionR(1)
forceF = 2(reactionR) or reactionR(2)
momentM = 3(reactionR) or reactionR(3)

Forces, moments and reactions can all be transformed between global

and local co-ordinate frames of reference using the * and / operators. By
convention local names should begin with the % sign.
A function allows a reaction to be referred to a new point:
reactionR = REFER(reactionR,pointP}

Reactions can be added and subtracted. The result is referred to the point
referenced by the first reaction specified. Reactions can be negated in
sign. Reactions can also be added to the parameters list
PARAM(<. . .,>reactionR<,. . .>)

and they can be output as three trajectories

OUTPUT(<. . .,>reactionR<,. . .>)

The three trajectory labels are generated from the reaction name, with the
suffixes F, M and P applied to the force, moment and point components
respectively, and the force and moment trajectories are marked
accordingly. The moment values are converted to Nm when they are
output, making them less distracting in the workspace view by limiting
the amplitude of their motions.

Version 3.5 BodyBuilder for Biomechanics

Kinetic Modelling 137

Individual forces and moments are distinguishable from points only by

their names within the model. There are no constraints applied to their
use, other than those normally applied to points. If a force is OUTPUT
independently from a reaction, it appears as a point in the workspace,
and in the C3D file if saved.

Force Plate Data

Force plate data, if present in the input C3D file, is automatically
integrated by a kinetic model. When a REACTION function is called
(see below), each of the force plates is deemed to be in contact with one,
and only one, segment, for each frame in the trial. An internal test is
made for each segment that is part of a hierarchy for which reactions
need to be solved.
For any segment to be attached to a force plate, the magnitude of the
force must exceed that of the ForceThreshold, which may be set to any
scalar value. The default value is 10 N.
A segment origin or attachment point must be perpendicularly above the
plate to be considered, at a distance less then the DistanceThreshold,
which may also be set to any scalar value. This has a default of 200 mm.
The closest end of the segment to the plate must also have a velocity less
then the VelocityThreshold. The default VelocityThreshold is set to 2000
mms-1. Note that if this value is too low, it can cause the ends of the
forceplate data to be cut off from the REACTION calculations, which
may lead to subtle changes in graphs of kinetic variables. Great care
must be taken in setting this value. It is deliberatley set to a relatively
high level just for this reason. It most cases, where both feet are
modelled, this value need not be changed.
The segment deemed to be in contact with the plate is the one which has
the shortest perpendicular distance from origin or attachment point to the
plate, and the lowest velocity. Where two segments have the same
shortest distance, the segment with the closest second end (either origin
or attachment point) is taken, preferring those ends above the plate.
The force plate data is available in the script as reaction types. They are
named and numbered consecutively as ForcePlate1, ForcePlate2 etc.

138 Kinetic Modelling

Version 3.5 BodyBuilder for Biomechanics

Segment (free body ) Equations of Motion

A single reaction function solves the equations of motion of a segment,
taking into account all reactions applied to it by its child-segments in the
hierarchy, as well as segment mass distribution, its motion, and gravity.
The result of the function is the reaction applied to the segment, at its
attachment to its parent, which achieves dynamic equilibrium.
ReactionR =

REACTION(segmentS)

where segmentS is the segment in dynamic equilibrium.

The reaction can be referred to a different point in the segment by
providing a point, which is assumed to be local to the segment, as a
second argument to the function.
ReactionR =

REACTION(segmentS, PointP)

Connection of other reactions

CONNECT(Segment,Reaction,ScalarTest)

This function allows the testable application of the Reaction

expression to the Segment. Once this function has been called, the
reaction function is held internally with the segment name, and included
in the list of reactions applied to the segment when a REACTION
function is called for the segment (or any parent segments, for whom this
segments reaction is required to be calculated). Note that although this
can be used to attach force plate reactions to segments, this will not
affect the automatic connection system, which will still apply the force
plate data in addition if appropriate.

Gravity
Gravity is specified internally in a point format
GRAVITY = {0,0,9810}

Version 3.5 BodyBuilder for Biomechanics

Kinetic Modelling 139

This defines gravity as equivalent to an upwards acceleration of 9810

mms-2, assuming that the VICON lab (global) space was calibrated with
Z up. This value can be changed anywhere within the script. Following
REACTION results will be correspondingly affected.
Changing the value of the acceleration due to gravity does not change the
motion of the segments, which is driven only by the measurements of the
trajectories of markers on the subject. Reducing the gravity specification
will not make the subject moonwalk or spacewalk. Although the
function would be useful for kinetic accuracy in the event of data being
captured in space, it is actually provided to cater for situations in which
the Z axis is not up.

Linear Acceleration and Angular Velocity and

Acceleration
These values are calculated using three samples of the segments position
and orientation, centred on the current frame. Samples three frames
before and three frames after are used in the calculation. These give a
reasonable time during which the segments move by an amount
significantly greater than the noise or errors in the positions of the
markers. This sampling period is fixed. The same sampling period is
used for the calculations for the dynamic reactions and the powers.

Intersegmental Power Flow

A new number function is defined to calculate power flow between
segments
powerI =

POWER(segmentA,segmentB)

where segmentA is the segment to which power (+ve or -ve) flows

segmentB is the segment from which power (+ve or -ve) flows.
Since the results are presented as scalar values, output is best performed
by making them the components of a point, which can be output. For
example:
LeftPowers = {POWER(Pelvis,LFemur),
POWER(LFemur,LTibia),POWER(LTibia,LFoot)}
140 Kinetic Modelling

Version 3.5 BodyBuilder for Biomechanics

OUTPUT(LeftPowers)

Units
The following units are assumed within the calculations :
Mass

kilograms

kg

Distance

millimetres

mm

Force Newtons

Newtons

Moment

Newton millimetres

N.mm

Inertia

kilogram.millimetre.millimetre

Power

milliwatts

kg.mm2

mW

So if, for example, the force plate moment data is supplied in the C3D
file in Newton metres, it should be converted to N.mm by a line such as
ForcePlate1 = |ForcePlate1(1),
ForcePlate1(2)*1000, ForcePlate1(3)|

This line will not affect the reactions automatically applied from the
force plates. Instead, automatic application must be disabled, by setting
either the ForceThreshold to a very high value (at least 100*BodyMass
for example), or the DistanceThreshold to zero. Then the reaction from
the force plate can be applied to the segment using the CONNECT
function.
If such corrections to the incoming data are not made, then the output
values should be converted as necessary. Note that in calculating the
moment due to the angular acceleration, the moment is divided by 1000
internally, to convert correctly to N.mm, given that the inertia is supplied
in kg.mm2.
If using tables, the units the inertia are in depends on the units of the
length and mass of the segment, as supplied by BodyMass and the
segment definition of the origin and attachment point or the supplied
length expression.

Version 3.5 BodyBuilder for Biomechanics

Kinetic Modelling 141

142 Kinetic Modelling

Version 3.5 BodyBuilder for Biomechanics

Operators

Types of Operator
Operators are symbols used to combine, select, or compare objects in an
expression.
There are three types of operator: arithmetic, selective, and logical.
Arithmetic and selective operators can be used together in an arithmetic
expression.
The arithmetic operators are +, -, *, and /. They can be used to
combine objects of the same or of different types. The type of an
arithmetic operation is defined by the type of its result.
The selection operator is ?. It is used in an arithmetic expression
between clauses (sub-expressions) of the same type.
The logical operators AND, OR, NOT, <, >, and = are used to
compare numbers, or number expressions, within logical expressions.
Logical expressions are used only in Conditionality Tests.
In an expression, clauses are evaluated according to the order of
precedence:
(used to indicate negation)
/,*
-, +
>=, <=, >, <
<>, ==
NOT, OR, AND
Version 3.5 BodyBuilder for Biomechanics

Operators 145

Number Operations
Numbers can be added (+), subtracted (-), multiplied (*), or divided (/) in
an arithmetic expression. The result is always a number and the normal
arithmetic precedents apply.
Numbers can be compared in a logical expression. The result of a logical
expression is true or false:
numberA AND numberB

is true if numberA and

numberB are both true
(non-zero)

numberA OR numberB

is true if either numberA

or numberB is true (nonzero)

numberA<numberB

is true if numberA is less

than number B

numberA>numberB

is true if numberA is
greater than numberB

numberA==numberB

is true if numberA is equal

to numberB

Paired combinations are permitted, in either order;

<= or =<
>= or =>
<> or ><

less than or equal to

greater than or equal to
not equal to

Point Operations
Points can be added (+) and subtracted (-):
(pointI+pointJ)/2
(pointJ-pointI)

146 Operators

mid-point of pointI and

pointJ
line from pointI to
pointJ.
Version 3.5 BodyBuilder for Biomechanics

Examples:
Point addition and subtraction:
FPelvis=(LFWT+RFWT)/2

defines the virtual point FPelvis as the mid-point of the line joining
the real markers LFWT and RFWT.
LFemur=[LKJC,LHJC-LKJC,LAJC-LKJC,zyx,LTOE-LKJC]

defines the segment LFemur using the lines LHJC-LKJC and LAJCLKJC as defining lines, and LTOE-LKJC as the anti-flip line.
Number comparison:
If
$Static==1
$#Child#Length=DIST(0(Child),0(Parent))
PARAM($#Child#Length)
EndIf

If the variable $Static is set to 1 in the parameter file, the parameter

$#Child#Length is defined. For example, a parameter such as
$TibiaLength might result from this definition. The PARAM
command carries an implicit AVERAGE function, meaning that a single
mean value of $ChildLength would be written to the parameter file. The
EndIf line indicates the end of the conditional section. Not all
possibilities result in actions: if both $VariableBoneLengths and $Static
are both false (set to a value other than 1), no definition is implemented.
Points can also be scaled by numbers. For example, pointI*numberA
scales the position of the point I.

Example:
%LHJC=PelvisDiameter*$%HipOffsetFactor
Version 3.5 BodyBuilder for Biomechanics

Operators 147

In this example, the local point %LHJC is defined by the vector

$%HipOffsetFactor (from the parameter file) multiplied by the
number PelvisDiameter (whose value is calculated in the preceding
line).
The operators * and / have a special meanings in point operations. They
are used to transform a point between its global version in the VICON
calibrated space and its "local" version in a segment, and vice versa;
pointI = %pointI*segmentP

converts local %pointI in

segmentP to global
pointI

%pointI = pointI/segmentP

converts global pointI into

local %pointI in
segmentP

Note that it is the operators in the expression which define the action, not
the % character in the name of the point object.

Segment Operations
Points can be added to (+) and subtracted from (-) segments. The result
is a segment in a new position but with the same rotation.
segmentP = segmentP+pointI
-0(segmentP)

segmentP is moved to
pointI

where 0(segmentP) is the origin of segmentP.

Rotation Operations (none permitted)

Because of the nature of Euler angles, rotations cannot be combined by
any of the arithmetic operators. For example, two rotations cannot be
added together.

Selection Operator

148 Operators

Version 3.5 BodyBuilder for Biomechanics

The selection operator ? is used within an arithmetic expression to

separate alternative clauses of the same type. The expression is set equal
to the first clause which is defined in the current field (sample);
pointI = pointJ ? pointK ?
? pointL

pointI is set to pointJ,

if defined, otherwise
pointK, if defined,
otherwise pointL

The selection ? operator has a lower precedence in an expression than

any of the arithmetic operators.

Version 3.5 BodyBuilder for Biomechanics

Operators 149

150 Operators

Version 3.5 BodyBuilder for Biomechanics

Functions

Types of Function
A number of special functions and constructions may used in an
expression. They are defined according to the type of their result.

Number Functions
1(pointI),2(pointI),

Components of

3(pointI)

pointI

or
pointI(1),..(2),..(3)

Components of
pointI

n(rotation) or

nth angle component

rotation(n)

of rotation

COMP(pointI,pointJ)

Component of pointI in
direction of pointJ

DIST(pointI,pointJ)

Distance between pointI

and pointJ
(either point can be omitted)

SIN(Angle)

Sine of the angle (in degrees)

COS(Angle)

Cosine of angle (in degrees)

Version 3.5 BodyBuilder for Biomechanics

Functions 151

Tangent of the angle (in

TAN(Angle)

degrees). Angle can be any

value except 90, or other
value of which the tangent
is infinite.
Arc-sine function. Value must

ASIN(Value)

be between -1 and +1. Returns

angle in the range -90 to
+90.
Arc-cosine function. Value

ACOS(Value)

must be between -1 and +1.

Returns angle in the range 0
to +180.
Arc-tangent function. Value

ATAN(Value)

may be any number. Returns

angle in the range -90 to
+90.
Arc-tangent function. X-value

ATAN2(x,y)

is the base of the triangle

concerned, Y-value is the
perpendicular. Zero values not
permitted.
Square root function. Value

SQRT(Value)

may be any number greater

than zero. Returns the positive
square root.

Point Functions
O(segmentP), or 0(segmentP)

152 Functions

Point at origin of segmentP

Version 3.5 BodyBuilder for Biomechanics

1(segmentP), 2(segmentP),
3(segmentP), or
segmentP(1), ..(2), ..(3)

Directions of axes of
segmentP

NORM(pointI,pointJ,pointK)

Direction perpendicular to
plane of 3 points I,J,K

PERP(pointI,pointJ,pointK)

Point at perpendicular
bisector from point I to line
J-K

CHORD(numberA,pointI,
pointJ,pointK)

Point at distance A from I in

plane IJK forming a right
angle between I and J on
the opposite side of IJ from K

The CHORD function may be useful in locating the centre of the knee
joint given the hip joint centre and a marker on the mid-thigh and lateral
condyle of the knee. This method is used in VICON Clinical Manager
gait analysis software.

In the illustration above, the green point is created using the CHORD
function. The line between points I and J is used as the diameter of a
Version 3.5 BodyBuilder for Biomechanics

Functions 153

circle. The plane of the circle is the plane of this line and point K. Any
point on the red semicircle will fulfill the right-angle criterion, and the
distance A specifies the point indicated. The distance A is thus used in
the construction as the chord of a circle, hence the name of the function.

Segment Functions
ATTITUDE(segmentP)

Move segmentP to the global origin

{0,0,0} keeping the same rotation
(attitude)

ROT(segmentP,pointI,q) Rotate segmentP about direction of

pointI by q degrees
ALIGN(segmentP,p,q,
pointI)

Rotate segmentP about axis

p (=1,2,3) to align projections of axis
q (=1,2,3) and pointI in plane
perpendicular to p

Rotation Functions
rotation(-n)

Change the sign of the nth angle

(n=1,2,3) in rotation

<numberA,numberB,numberC>
Define a rotation from three numbers. This
function has the same syntax as rotation
definition

Special Functions
LAST()is a special function used to recall the most recent arithmetic
value of an object from the current or any previous field. If the object has
never previously been defined, it remains undefined.
LAST(pointI)

154 Functions

pointI from the last

occasion it was defined

Version 3.5 BodyBuilder for Biomechanics

EXIST() is a special function used in a logical expression to establish

whether or not an object (number, point, segment, or rotation) is defined
in the current field.
true if pointI is defined in
current field

EXIST(pointI)

EXISTATALL() is used in a logical expression to establish whether or

not an object (number, point, segment, or rotation) is defined in at least
one field during the trial. More than one object may be supplied to the
function, in which case all such objects must exist for at least one frame
during the trial.
EXISTATALL(pointI, pointJ)

true if both I and J are ever

defined

EXISTALWAYS() is used to determine whether an object or objects

have values for every frame in the trial.
AVERAGE() is a special function which can be applied to any type of
object (number, point, segment, or rotation) , but which is evaluated in a
different way from all other functions.
Normally, each assigned expression is evaluated once per field through
the full set of data to which the model is applied. However, any
expression containing an AVERAGE() function is evaluated only once
for all fields.
AVERAGE(numberA)

Average numberA over all fields

AVERAGE(pointI)

Average pointI over all fields

AVERAGE(segmentP)

Average segmentP over all fields

AVERAGE(rotation )

Average rotation over all fields

For technical reasons, the AVERAGE() function is not allowed inside IF

blocks. There is more information about this in the file
AverageModifications.txt
MIN() MAX() STDDEV() functions calculate the minimum,
maximum and standard deviation (n-1) values for scalar values over the
whole trial. These functions are not allowed inside IF blocks either.
Version 3.5 BodyBuilder for Biomechanics

Functions 155

[ ] is a special "field offset" post-fix function used to find the final

value of an expression in any field, relative to the current one.
segmentP[-1]

segmentP in previous field

The "sample offset" function has many uses, including the creation of
special filters.
FIELD or SAMPLE, FIRSTSAMPLE and LASTSAMPLE are special
predefined values that can be used in the script to provide the current,
first and last sample numbers in the trial that is being processed. These
are fixed values, and cannot be changed.

Spine
SPINE()is a special segment function for creating new segments based
on the position and orientation of existing ones. As the name implies, it
is designed for creating vertebrae between the segments Pelvis, Thorax
and Head. The general form is
SPINE(<length,><direction,>SegmentL,<location,
>SegmentU<,stiffnessL><,stiffnessU>)
The parameters in <> brackets are optional. The default values listed
below are used if they are omitted:
SegmentL

is the lower segment at one end of the spine

SegmentU

is the upper segment at the other end

length

is the total distance along the curve of the spine

between segmentL and segmentU.

The default length of the spine is the length of the cubic base spline
between the end segments.
direction

156 Functions

is a local line (axis or local point) within both

segmentL and segmentU indicating the local

Version 3.5 BodyBuilder for Biomechanics

directions of the ends of the spine. The same local direction is used for
new segments generated within the spine. Default is the Z or 3 axis.
is the relative distance (0 - 1) along the spine
from SegmentL to SegmentU where the
origin of the new segment will be located. Default is 0.5

location

stiffnessL and stiffnessU set the flexibility at either end of the

spine. The stiffness of any point on the spine is a linear proportion of the
values set for either end. Higher values mean that the spine is stiffer in
the direction of its curve, and the orientation of its created segments
remain closer to the orientation of the end segments. Lower values mean
that the spine is more flexible and its direction and segment orientation
tend towards a straight line connecting the end segments. Default
stiffness is 1.

Length and Stiffness

The SPINE parameters length and stiffness are interdependent.
A spine of unspecified length, with identical stiffness set at either end, is
generated with the same stiffness along its length. As the stiffness is
increased, the spine grows longer, eventually forming a loop between the
ends. If the stiffness is decreased, the spine grows shorter, forming a
straight line between the ends when stiffness is 0.
If length is specified, the absolute stiffness cannot be controlled
independently. In this situation, the specified stiffness parameters
indicate the relative stiffness at either end.

Multiple Segments/Vertebrae Mode

The SPINE function has a special mode which can be used to generate a
series of vertebrae simultaneously:
SPINE(SegmentL,<location1>,Segment1,<location2>,
Segment2,...,<locationN>,SegmentN,SegmentU>)
where

Version 3.5 BodyBuilder for Biomechanics

Functions 157

Segment1,Segment2,...,SegmentN

are new segments

created along the
spine

<location1>,<location2>,...,<locationN>
are the optional relative distances of the
new segments along the spine. Locations always appear before the
segment to which they apply.
The optional parameters length, direction and stiffness can be included
and have the same effect as in the previous mode.
This mode of the SPINE function is used on its own, rather than as an
expression in an assignment. It does not appear on the right of a = sign.

Shorthands and Tokens

When 0 (numeral zero) is used in place of a point, it means {0,0,0}. If it
is a local point, it means the origin of the segment. If it is a global point,
it means the global origin.
When 1 (numeral one) is used in place of a segment, it means:
[0,{1,0,0},{0,0,1},xyz]

the global segment

The following tokens are predefined to the numbers indicated:

xyz
yzx
zxy
xzy
yxz
zyx

=
=
=
=
=
=

1
2
3
-1
-2
-3

Their values may be changed, but they may not be assigned as points,
segments or rotations.

158 Functions

Version 3.5 BodyBuilder for Biomechanics

Non-Assigning Statements
There are three statement lines which do not make assignments.
OUTPUT(pointI,rotation ,..)
Create output records of pointI and rotation for
all the samples for which they exist. Output records are
displayed in the 3D Workspace and can be saved.
PARAM(numberA,pointI,segmentP,rotation )
Append assignments for
numberA,pointI,segmentP and rotation to
parameter section of current BodyLanguage script.
Parameter sections can be saved.
OptionalPoints(pontI,pointJ,..)
Listed points may be referenced in an expression even if
they do not exist in the input C3D file. Any expression
derived a non-existent optional point is not evaluated. There
are also OptionalNumbers, OptionalForces etc. functions
too.

Conditionality Tests
BodyLanguage allows user-specified assignments to be made if, and only
if, the current value of a logical expression is TRUE or FALSE.
The form of a Conditionality Test is:
IF logicalexpression (THEN) assignment...
(ELSIF logicalexpression...) (ELSE
assignment...) ENDIF
where brackets indicate optional elements of the test.

Dealing with Marker Occlusions

Version 3.5 BodyBuilder for Biomechanics

Functions 159

The primary use of Conditionality is to create virtual points in place of

real points that are temporarily missing, for example due to marker
occlusions.
For example;
PelvisOrigin=(RHIP+LHIP)/2
LmRHip=LHIP-RHIP
PelvisABDO=[PelvisOrgin,LmRHip,ABDOPelvisOrigin,2]
%SacrumAvABDO=AVERAGE(SACR/PelvisABDO)
IF EXIST(SACR) ELSE
SACR=%SacrumAvABDO*PelvisABDO ENDIF
Pelvis=[PelvisOrgin,LmRHip,PelvisOrigin-SACR,2]
In this example, the segment Pelvis is normally defined in terms of
three measured points, LHIP, RHIP, and SACR. However, if point
SACR (sacrum, on the back of the pelvis) is occluded, it is automatically
re-created using its local offset, %SacrumABDO, in an alternative
definition of Pelvis based on measured point ABDO (abdomen, on the
front of the pelvis). The same method can easily be extended so that
there are several alternative definitions are used for a segment, according
to what which measured points are available.

160 Functions

Version 3.5 BodyBuilder for Biomechanics

Macros

Uses of Macros
In a BodyLanguage script, many separate sections can end up repeating
the same basic set of instructions. For example, the procedure for filling
gaps in a group of related points may be identical but for the names of
the points involved.
In order to make scripts shorter, easier to read, and more reliable,
BodyLanguage supports the defining and calling of macros. A macro
works like a subroutine in a compiled program. Once defined, a macro
can be called as many times as required, thereby eliminating repetitions
of text. Only when the script is executed, is each macro call
automatically replaced by the lines in the macro definition.
In order to make a macro applicable in different situations, it can be
defined using a set of dummy variables or macro parameters. These
parameters are listed at the start of the macro definition. When the macro
is executed, the parameters are replaced by a matching set of real
variable names.
A macro definition, which must occur earlier in the script than any
corresponding macro calls, starts with:
define macro <macroname>(parameter1,
parameter2, ...)
(although the word define is optional), and ends with:
endmacro
where:
Version 3.5 BodyBuilder for Biomechanics

Macros 161

<macroname> is any unique, valid variable name

A macro call is simply:
<macroname>(variableA, variableB, ...)
where the number and type of variables in the call must match the
number and type of parameters in the definition. A macro call can
constitute a whole line of script, or can appear within an expression, as
long as the substitution results in valid BodyLanguage syntax.

Text Concatenation Operator

To make macros more powerful, a special text concatenation operator, #,
is available for use within macro definitions (but nowhere else in a
BodyLanguage script). Dummy variables within a macro definition can
be constructed of concatenations of parameters and other strings of
characters.
For example:
$#Child#Length=DIST(0(Child),0(Parent))
where: Child is a parameter of the macro definition of which this
assignment is a part.
There are several examples of macro definition and text concatenation in
the example script FULLBODY.MOD, which is listed and explained in a
later section.

162 Macros

Version 3.5 BodyBuilder for Biomechanics

Other Expressions

Comments
Comments are encouraged. Each comment string starts with characters
{* and ends with characters *}. Comments can be "nested", ie. a
complete section of script can be commented out although it includes
comments. This requires strict matching of the {* and *} symbols in
pairs. If an unmatched comment symbol causes a model script to fail to
run, an error message will indicate the cause of failure, and the cursor
will be placed at the first unmatched {*symbol.

Error Codes
Every time a BodyLanguage script is run, it first checks the parameters
and model for errors.
If an error is found, a dialog box displays the error message. The line
containing the error is highlighted and diplayed in the appropriate text
window. If necessary, the text editor window will be opened, and the text
will be scrolled to make the line visible. The error message also appears
in the status bar at the bottom of the main application window. If you
change windows of scroll the text, pressing the "show last error" button
will re-display the offending line, and the error message.
If the cause is in a macro expansion, pressing the "show last error"
button, or selecting the menu command, will display the line in the macro
where the error occured. Pressing the button further will alternate
between the two lines, to allow you to check both the macro code, and
the arguments you are passing to the macro.

Version 3.5 BodyBuilder for Biomechanics

Other Expressions 163

Example Model - FOOT

Anatomical Structure
The model FOOT divides the foot into several segments with limited
degrees of freedom between them. The first segment defined is the tibia.
Beneath this, and related to it by a simple hinge joint about an
intermalleolar axis, is the talus segment. The position and orientation of
the talus is deduced entirely from the segments around it - no markers are
attached to it directly. The calcaneus is defined below the talus and
related to it by a simple hinge joint, the subtalar joint, about an axis
which is defined by the placement of a marker on the instep. The central
part of the foot is represented by a midfoot segment, and the toes by a
hallux segment.

Axis Definitions
The axes of rotation for the tibia-talus joint (ankle flexion joint) and the
subtalar joint, in this model, are not derived from any assumed
relationship between exterior landmarks and interior anatomy. The
locations of these axes are determined entirely by marker placement. It is
assumed, for example, that the ankle flexion joint axis lies between the
malleoli, and it is suggested that the two markers labelled LMAL and
MMAL are placed on these exterior landmarks, however, if they are
placed elsewhere, the axis will be located on a line between them. Thus,
the user has the freedom to define the location of this axis by placing the
markers where they choose on the subject.
This contrasts with the assumptions made in the kinematic model used in
VICON Clinical Manager, for example, where it is assumed that the
markers will be placed on stated landmarks (such as the anterior superior
iliac spines) and a theory of anatomy (based on cadaver studies) is used
to derive the locations of the hip joint centres. In such a model,
misplacement of the markers will invalidate the assumptions, and lead to
erroneous interior points being calculated. In FOOT, there are no such
Version 3.5 BodyBuilder for Biomechanics

Example Model - FOOT 165

assumptions, and if the user has their own opinion about the location of
the axes concerned, they can place the markers accordingly. Users of
models like this should be aware of the implications for comparability of
data from different workers.

Handedness
This model has two equivalent sections, one for the left foot, dealing
with all the markers whose labels begins with L, and one for the right
foot, dealing with the markers whose labels begin with R. The two
sections are very similar, but not quite identical - the corresponding
segments on either side cannot be mirror images of each other, because
of the requirement that all segment axes form a right handed system.

Model Script
Comment Section
The following comment section describes the markers used.
{*VICON BodyLanguage*}
{*copyright Oxford Metrics 1997*}
{*Foot.MOD, for use with Foot.MP paramter file*}
{*This a sample file for BodyBuilder for
Biomechanics. It is supplied to illustrate some
of the range of modelling techniques made
possible by this program. It should NOT be used
for clinical or research purposes without
independent verification. Oxford Metrics
accepts no liability for its performance.*}
{*The model uses a total of 28 markers:
Lateral and Medial Epicondyles of the Knee
RLEPC, RMEPC, LLEPC, LMEPC
Tibial Tuberosity
L/RTTUB
Shin
L/RSHN1, L/RSHN2
Lateral and Medial Malleoli L/RMMAL, L/RLMAL
Lateral and Medial Calcaneus L/RMCAL, L/RLCAL
166 Example Model - FOOT

Version 3.5 BodyBuilder for Biomechanics

Proximal and Distal 2nd and 5th metatarsals

L/R P/D2MT,P/D5MT
Hallux
L/RHLX
Medial epicondyle and medial malleolus markers
are required only for static trials, however if
they are present, they will be used.
1) collect static and motion trials, using above
markers
2) set $static = 1 in .MP file and process
static trial
3) adjust rotation parameters in .MP file until
foot posture is as measured
4) set $static = 0 in .MP file and process
motion trial
5) write output angles (ANKA,STLA,MDFA,HLXA) to
C3D or ASCII file*}

Macro Substitute4
{*Start of macro section*}
{*======================*}
macro Substitute4(p1,p2,p3,p4)

This line begins the definition of the macro named Substitute4.

s234 = [p3,p2-p3,p3-p4]

This line defines the segment s234, whose origin is at p3, whose Axis
1 is parallel to the line from p3 to p2, and whose second defining line is
the line from p4 to p3. This segment will exist in every frame in which
the points p2, p3 and p4 are all present.
p1V = Average(p1/s234)*s234

The above line defines the global point p1V in the following way. First,
the expression in () brackets is evaluated in every frame for which it is
valid. p1/s234 is the local position of p1 relative to the segment s234.
Therefore, the expression is valid in each frame in which all four points
are present. Then, the average of this throughout the trial is evaluated,
resulting in a single averaged local point (ie. not a separate value for
each frame). Finally, this is converted to a global point by the *s234
operator, and this is evaluated in each frame, as the segment s234 is not
fixed. The result is a new point, p1V, which is fixed relative to segment
Version 3.5 BodyBuilder for Biomechanics

Example Model - FOOT 167

s234, and exists in every frame in which s234 exists. The averaging
process acts as a kind of filter, in which the movement of p1 is smoothed
by relating it to p2, p3 and p4. The result is that p1V will behave more
smoothly than p1. Also, p1V will exist in frames in which p1 itself does
not exist. This is the key feature of the operation.
s341 = [p4,p3-p4,p4-p1]
p2V = Average(p2/s341)*s341
s412 = [p1,p4-p1,p1-p2]
p3V = Average(p3/s412)*s412
s123 = [p2,p1-p2,p2-p3]
p4V = Average(p4/s123)*s123
p1 = (p1+p1V)/2
p2 = (p2+p2V)/2
p3 = (p3+p3V)/2
p4 = (p4+p4V)/2
endmacro

?
?
?
?

p1
p2
p3
p4

?
?
?
?

p1V
p2V
p3V
p4V

The last four expressions redefine p1 - p4 using the selection operator. In

a frame in which p1 and p1V both exist (ie. all four original points exist),
p1 is redefined to be the mid-point of the line joining p1 and p1V. This
will have some filtering effect on the movement of p1, while allowing it
to remain reasonably true to the original measurements. If p1V does not
exist in a particular frame (it exists only in frame in which p2, p3 and p4
exist), the measured value of p1 is left unchanged. If p1 does not exist,
but p1V does exist (ie. points p2, p3 and p4 only are present), then p1V
is used to fill the gap in p1. This operation, therefore, modifies p1 by
both smoothing its trajectory, and extending it into frames in which p1
originally did not exist. The result is that there will be a point p1 in any
frame in which at least three of the four original points existed. In the
following three lines, the same redefining expressions act on the other
points. The result is that all four points are smoothed, based on the
presumption that they are fixed to the same body segment and so move
together; and gaps in the trajectories are filled in, unless more than one
marker is missing, in which case there is insufficient data to reconstruct
the segment.
{* End of macro section *}

Optional Points
{*Points which may not be present in every
trial*}
OptionalPoints(RMEPC,RMMAL,RP5MT,RTTUB,RSHN2)
OptionalPoints(LMEPC,LMMAL,LP5MT,LTTUB,LSHN2)
168 Example Model - FOOT

Version 3.5 BodyBuilder for Biomechanics

Segment Definitions
{* Tibia segment *}
{* ============= *}
{* This segment uses 7 markers in static trials
(L/MEPC,TTUB,SHN1/2,L/MMAL), with medial markers
(MEPC and MMAL) removed for motion trials*}
{*Minimise dropouts of RLEPC and RLMAL*}
SUBSTITUTE4(RLEPC,RTTUB,RSHN1,RSHN2)
SUBSTITUTE4(RLMAL,RTTUB,RSHN1,RSHN2)
{*Create a dummy segment using most visible
tibia markers, present in all trials*}
DummyTibia = [RLMAL,RLEPC-RLMAL,(RLMAL+RLEPC)/2RSHN1]

The segment DummyTibia is defined with its origin at the marker

RLMAL, and uses in its definition the points RLEPC and RSHN1. These
markers will remain in position throughout the experiment, including
static and dynamic tests. The segment DummyTibia itself is not
interesting in biomechanical terms, but is used to derive some local
points as follows:
{*For static trial in which medial markers are
present, save key anatomical points and Tibia
scale as parameters*}
If $Static == 1
{*Find mid-points of knee and ankle*}
RKJC = ((RLEPC+RMEPC)/2)
RAJC = ((RLMAL+RMMAL)/2)
$%RKJC = RKJC/DummyTibia
$%RAJC = RAJC/DummyTibia
$%RMMAL = RMMAL/DummyTibia
$RTibiaScale = DIST(RKJC,RAJC)/100
PARAM($%RKJC,$%RAJC,$%RMMAL,$RTibiaScale)
EndIf

The segment DummyTibia is used to obtain the local co-ordinates of

the marker MMAL and the virtual points KJC and AJC, so that when the
markers MEPC and MMAL are removed for dynamic trials, we can recreate their positions relative to the remaining markers. The If
Version 3.5 BodyBuilder for Biomechanics

Example Model - FOOT 169

expression tests whether the parameter $Static has been set to 1. If

so, that is a sign that the trial is a static one, and the virtual points are
calculated and written (by the PARAM command) to the parameter file. If
the test is not satisfied, because $Static is not set to 1, the section is
not acted on.
{*Create global positions of key anatomical
points from parameters and dummy tibia segment*}
If (Exist(RMMAL) AND $Static == 0) Then
RAJC = ((RLMAL+RMMAL)/2)
Else
RAJC = $%RAJC*RDummyTibia
RMMAL = $%RMMAL*RDummyTibia
EndIf
If (Exist(RMEPC) AND $Static == 0) Then
RKJC = ((RLEPC+RMEPC)/2)
Else
RKJC = $%RKJC*RDummyTibia
EndIf

In this part, the marker RMMAL and virtual points RAJC and RKJC are
recreated from the parameters calculated earlier.
{*Define Tibia segment with third axis aligned
with long axis of tibia*}
RTibia = [RAJC,RKJC-RAJC,RMMAL-RLMAL,zxy]

In this definition, the segment origin is at the ankle centre, and the first
defining line is the line from the ankle centre to the knee centre. This line
(because of the token zxy) becomes the third axis. The second defining
line is from the lateral to the medial malleolus. Because of the token, this
means the second axis of the tibia section is in the plane defined by the
first axis and the line RMMAL-RLMAL, and is positive in the lateral-tomedial direction (inward). This segment is of genuine interest, unlike
DummyTibia, which is not referred to again.
{*Draw Tibia, using 16 vertices, scaled to
length of Tibia*}
RTIB1 = $RTibiaScale*{10,0,95}*RTibia
RTIB2 = $RTibiaScale*{-4,-10,100}*RTibia
RTIB3 = $RTibiaScale*{-4,0,100}*RTibia
RTIB4 = $RTibiaScale*{-4,10,100}*RTibia
RTIB5 = $RTibiaScale*{3,0,80}*RTibia
170 Example Model - FOOT

Version 3.5 BodyBuilder for Biomechanics

RTIB6
RTIB7
RTIB8
RTIB9
RTB10
RTB11
RTB12
RTB13
RTB14
RTB15
RTB16

=
=
=
=
=
=
=
=
=
=
=

$RTibiaScale*{0,-8,80}*RTibia
$RTibiaScale*{-3,0,80}*RTibia
$RTibiaScale*{0,3,80}*RTibia
$RTibiaScale*{3,0,20}*RTibia
$RTibiaScale*{0,-6,20}*RTibia
$RTibiaScale*{-3,0,20}*RTibia
$RTibiaScale*{0,3,20}*RTibia
$RTibiaScale*{10,0,10}*RTibia
$RTibiaScale*{0,-10,0}*RTibia
$RTibiaScale*{-5,0,10}*RTibia
$RTibiaScale*{0,10,4}*RTibia

OUTPUT(RKJC,RAJC)
OUTPUT(RTIB1,RTIB2,RTIB3,RTIB4,RTIB5,
RTIB6,RTIB7,RTIB8)
OUTPUT(RTIB9,RTB10,RTB11,RTB12,RTB13,
RTB14,RTB15,RTB16)

This section defines sixteen new virtual points for the purpose of
drawing a simulacrum of the tibia in the Workspace display. The points
will be joined together when a suitable MKR file is selected with the
required links.
{*Draw y-axis of Tibia*}
RAKJ1 = RAJC+100*2(Tibia)
RAKJ2 = RAJC-100*2(Tibia)
OUTPUT(RAKJ1,RAKJ2)

In this section, two points are defined to illustrate the second axis of the
tibia section. Note that the above two sections contained OUTPUT
commands, which means that they actually generate new data points in
the C3D file.
RTibia2=[RAJC,RLMAL-RMMAL,RAJC-RKJC,yxz]

In this segment definition, the intermalleolar axis is used as the first

defining line, and becomes the second segment axis. This means that the
second defining line (knee to ankle) is not normally parallel to the third
axis, and the knee joint does not therefore lie on an axis. However,
despite this difference, this segment cannot rotate relative to the segment
RTibia. RTibia2 will be used later for defining the ankle flexion.

Version 3.5 BodyBuilder for Biomechanics

Example Model - FOOT 171

{* Talus *}
{* ===== *}
{* This segment uses 3 real (RL/RMMAL,RP2MT) and
one virtual (RCCAL) markers*}
{*Find mid-point of Calcaneous*}
RCCAL = (RLCAL+RMCAL)/2
{*Minimise dropouts of LEPC and LMAL*}
SUBSTITUTE4(RLMAL,RMMAL,RCCAL,RP2MT)
{* Draw Malleolar axes along y-axis of Tibia*}
RMALC= (RLMAL+RMMAL)/2
RMAL1 = RMALC+(RLMAL-RMMAL)
RMAL2 = RMALC-(RLMAL-RMMAL)
OUTPUT(RMAL1,RMAL2)

In this section, two points are defined which illustrate the inter-malleolar
axis. This axis is not parallel to the tibia lateral axis.
{*Define Upper Talus segment with lateral(y)
axis along inter-malleolar (RLMAL-RMMAL) line*}
RTalusU = [RAJC,RMMAL-RLMAL,RP2MT-RCCAL,yzx]

The Upper Talus segment is defined with its origin at the same point as
that of the tibia, and with the intermalleolar line as its second axis.
If $Static ==1
{*Save Upper Talus scale as parameter*}
$RTalusScale = ((DIST(RLMAL,RMMAL)$MarkerDiameter)/1.5)/100
PARAM($RTalusScale)
EndIf

The TalusScale parameter is one-hundredth of the distance between the

lateral and medial malleolus markers.
{*Reposition RIGHT Upper Talus, maintaining
attitude*}
%RSTJ = {0,0,-20*$RTalusScale}
RSTJ = %RSTJ*RTalusU
RTalusU = RSTJ+Attitude(RTalusU)
172 Example Model - FOOT

Version 3.5 BodyBuilder for Biomechanics

RTalusU=ROT(RTalusU,1(RTalusU),-$TalusRotation)

The TalusScale parameter is used to shift the segment down. It is then

rotated by a variable parameter TalusRotation.
{*Draw Talus, using 8 scaled vertices*}
RTAL2 = $RTalusScale*{30,30,45}*RTalusU
RTAL1 = $RTalusScale*{30,-30,45}*RTalusU
RTAL4 = $RTalusScale*{-30,-30,80}*RTalusU
RTAL3 = $RTalusScale*{-30,30,80}*RTalusU
RTAL6 = $RTalusScale*{65,50,-50}*RTalusU
RTAL5 = $RTalusScale*{65,-50,-50}*RTalusU
RTAL8 = $RTalusScale*{-65,-50,0}*RTalusU
RTAL7 = $RTalusScale*{-65,50,0}*RTalusU
OUTPUT(RTAL1,RTAL2,RTAL3,RTAL4,RTAL5,
RTAL6,RTAL7,RTAL8)

This section creates virtual points which are used to draw a box shape to
represent the talus in the Workspace window.
{*Define Lower Talus segment with anterior(x)
axis along subtalar (RP2MT-RCCAL) line*}
RTalusL = [RSTJ,RP2MT-RCCAL,RMMAL-RLMAL,xzy]
{*Draw Subtalar axis along x-axis of Lower
Talus*}
RSTJ1 = RSTJ+100*1(TalusL)
RSTJ2 = RSTJ-100*1(TalusL)
OUTPUT(RSTJ1,RSTJ2)

This section defines another segment which has a different origin and
orientation to Upper Talus, but which does not move relative to Upper
Talus.
{* Calcaneus *}
{* ========= *}
{* This segment has 3 real (RL/RMCAL,RP2MT)
markers*}
If $Static ==1
{*Save Calcaneus scale as parameter*}

Version 3.5 BodyBuilder for Biomechanics

Example Model - FOOT 173

$RCalcaneusScale = ((DIST(RP2MT,RCCAL)$MarkerDiameter)/3)/100
PARAM($RCalcaneusScale)
EndIf
{*Define Calcaneus segment with anterior(x) axis
along subtalar (P2MT-CCAL) line*}
RCalcaneus = [RCCAL,RMCAL-RLCAL,RP2MT-RCCAL,yzx]

This segment is defined with its origin at the point RCCAL (mid-point of
calcaneus markers).
{*Apply rotation offset parameters*}
Calcaneus =
ROT(Calcaneus,2(Calcaneus),$CalcaneusFlexion)
Calcaneus =
ROT(Calcaneus,3(Calcaneus),$CalcaneusAbduction)
Calcaneus =
ROT(Calcaneus,1(Calcaneus),$CalcaneusInversion)

{*Draw Calcaneus, using 8 scaled vertices*}

RCAL2 = $RCalcaneusScale*{210,45,10}*RCalcaneus
RCAL1 = $RCalcaneusScale*{210,-45,10}*RCalcaneus
RCAL4 = $RCalcaneusScale*{-50,
-55,110}*RCalcaneus
RCAL3 = $RCalcaneusScale*{-50,55,110}*RCalcaneus
RCAL6 = $RCalcaneusScale*{235,55,-45}*RCalcaneus
RCAL5 = $RCalcaneusScale*{235,-55,
-45}*RCalcaneus
RCAL8 = $RCalcaneusScale*{-90,-95,
-15}*RCalcaneus
RCAL7 = $RCalcaneusScale*{-90,95,-30}*RCalcaneus
OUTPUT(RCAL1,RCAL2,RCAL3,RCAL4,RCAL5,
RCAL6,RCAL7,RCAL8)

{* Midfoot *}
{* ======= *}
{* This segment has 3 real (RD5MT,RP/RD2MT)
markers*}

174 Example Model - FOOT

Version 3.5 BodyBuilder for Biomechanics

{*Define Midfoot segment with lateral (y) axis

along metatarsal (RD5MT-RD2MT) line*}
RMidfoot = [RD2MT,RD2MT-RP2MT,RD5MT-RD2MT,xzy]
If $Static == 1
{*Save Midfoot scale as parameter*}
$RMidfootScale = DIST(RD2MT,RP2MT)/100
PARAM($RMidfootScale)
EndIf
{*Draw Midfoot, using 8 scaled vertices*}
RMDF2 = $RMidfootScale*{8,-84,0}*RMidfoot
RMDF1 = $RMidfootScale*{8,16,0}*RMidfoot
RMDF4 = $RMidfootScale*{8,-84,15}*RMidfoot
RMDF3 = $RMidfootScale*{8,16,20}*RMidfoot
RMDF6 = $RMidfootScale*{-112,-111,-74}*RMidfoot
RMDF5 = $RMidfootScale*{-112,-11,-74}*RMidfoot
RMDF8 = $RMidfootScale*{-112,-111,-49}*RMidfoot
RMDF7 = $RMidfootScale*{-112,-11,-44}*RMidfoot
RMTJ1 = (RD5MT+RD2MT)/2+$RMidfootScale*(RD5MTRD2MT)
RMTJ2 = (RD5MT+RD2MT)/2-$RMidfootScale*(RD5MTRD2MT)
OUTPUT(RMDF1,RMDF2,RMDF3,RMDF4,RMDF5,RMDF6,RMDF7
,RMDF8)
{*Draw Metatarsal joint axis*}
OUTPUT(RMTJ1,RMTJ2)

{* Hallux *}
{* ====== *}
{* This segment has 1 real (RHLX) marker*}
{*Apply toe width offset*}
RD1MT=RD2MT-$ToeWidth*2(RMidfoot)
{*Define Hallux segment with lateral (y) axis
aligned with Midfoot y-axis*}
RHallux=[RHLX,-2(RMidfoot),RHLX-RD1MT,yxz]
Version 3.5 BodyBuilder for Biomechanics

Example Model - FOOT 175

If $Static ==1
{*Save Hallux scale as parameter*}
$RHalluxScale = DIST(RHLX,RD2MT)/150
PARAM($RHalluxScale)
EndIf
{*Reposition Hallux, maintaining attitude*}
%RDHLX = {-5*$RHalluxScale,0,0}
RDHLX = %RDHLX*RHallux
RHallux = RDHLX+Attitude(RHallux)
{*Draw Hallux, using 8 scaled vertices*}
RHLX2 = $RHalluxScale*{-20,70,40}*RHallux
RHLX1 = $RHalluxScale*{-15,-20,0}*RHallux
RHLX4 = $RHalluxScale*{-15,10,80}*RHallux
RHLX3 = $RHalluxScale*{-20,70,80}*RHallux
RHLX6 = $RHalluxScale*{-30,70,40}*RHallux
RHLX5 = $RHalluxScale*{-20,-20,-20}*RHallux
RHLX8 = $RHalluxScale*{-40,-10,80}*RHallux
RHLX7 = $RHalluxScale*{-40,70,80}*RHallux
OUTPUT(RDHLX,RHLX1,RHLX2,RHLX3,RHLX4,RHLX5,
RHLX6,RHLX7,RHLX8)

Angle Output Section

{* Angle Outputs *}
{* ============= *}
{*Calculate joint angles, using Grood&Suntay
sequence - flexion,abduction,rotation*}
RANKA = <RTalusU,RTibia2,yxz>
RSTLA = <RCalcaneus,RTalusL,yxz>
RMDFA = <RMidfoot,RCalcaneus,yxz>
RHLXA = <RHallux,RMidfoot,yxz>
{*Output angles for plotting and saving*}
OUTPUT(RANKA,RSTLA,RMDFA,RHLXA)

176 Example Model - FOOT

Version 3.5 BodyBuilder for Biomechanics

The use of the segment RTibia2 in the definition of RANKA means that
the two segments in the angle definition have a common axis, the
intermalleolar axis, so the relative rotation of the two segments is forced
to be around this axis. Only one component of RANKA should have a
significantly non-zero value, as a result.

Left Foot Script

The rest of the script is a duplicate of the above, with the replacement of
L (for Left) prefixes in all labels, and with some defining lines changed
to maintain right-handed systems. For example, the tibia segment
definition is:
LTibia = [LAJC,LKJC-LAJC,LLMAL-LMMAL,zxy]

The order of points in the second defining line being the reverse of that
in the corresponding right foot definition.

Version 3.5 BodyBuilder for Biomechanics

Example Model - FOOT 177

178 Example Model - FOOT

Version 3.5 BodyBuilder for Biomechanics

Example Model - Kinetic Leg Model

Kinematic Principles and Limitations

The kinematic parts of this model use a minimal marker set to model the
pelvis and lower extremities using seven segments.
The pelvis segment is defined using three markers, one on each anterior
superior iliac spine, and one on the back at the same height as the
posterior iliac spines. A simple hip centre estimation model generates hip
centres relative to the pelvis segment.
The thigh segments are defined using the knee and mid-thigh markers
plus the estimated hip centres. The knee marker should be placed on the
lateral epicondyle, and the mid-thigh marker should be placed on the
thigh, just below the hand swing level, and in the plane containing the
hip centre and knee flexion axis.
The tibial segment is defined in a similar way, with an ankle marker on
the lateral malleolus, and a mid-tibia marker placed in the plane defined
by the knee centre and ankle flexion axis.
The foot, although technically a segment, does not have rotations about
three axes fully determined. Only one additional marker is used to define
the foot segment, meaning that ankle flexion and rotation can be
measured, but ab/adduction (pronation/supination in foot terminology)
are not measured.
This marker set is widely used in clinical gait analysis, and similar
modelling methods are used in VICON Clinical Manager (VCM) gait
analysis software. However, there are important differences. The model
within VCM is fixed and cannot be adjusted, while this model can be
edited. VCM modifies the timebase of the data to match the gait cycle,
which this model does not do. In this process of timebase modifying,
Version 3.5 BodyBuilder for Biomechanics

Example Model - Kinetic Leg Model 181

VCM interpolates between data points, which this model does not. Also,
VCM uses a static trial to determine certain parameters, while this model
is only able to process walking data. This model will not, therefore,
replicate the results of VCM precisely.
In addition, it should be noted that while the models used in gait analysis
software products such as VCM are fixed, the model described here is
open to editing. Also, while the model in VCM has been verified by
widespread testing and use, any reproduction of similar methods in
BodyLanguage will not be so well verified. The intention of this model is
to illustrate modelling methods, and to provide a starting point for further
developments. It should not be used for clinical gait analysis.

Force Vectors
{*VICON BodyLanguage (tm)*}
{*For use only with BodyBuilder Version 4.0, or
higher*}
{* Show the force plates *}
if EXIST( ForcePlate1 )
Force1 = ForcePlate1(1)
Moment1 = ForcePlate1(2)
Centre1 = ForcePlate1(3)

The quantity ForcePlate1 is a Reaction. If it exists (ie. there is data

from a force plate), the quantities Force1 , Moment1 and Centre1
are defined equal to the components of the reaction.
if ( ABS ( Force1 ) > 10 )
Point1 = Centre1 + {-Moment1(2)/Force1(3),
Moment1(1)/Force1(3), -Centre1(3) }
else
Point1 = Centre1
endif
Point1 is defined as the centre of the force plate plus an amount equal
to the centre of pressure location relative to the centre of the plate - that
is, Point1 is the centre of pressure.

182 Example Model - Kinetic Leg Model

Version 3.5 BodyBuilder for Biomechanics

Force1 = Force1 + Point1

OUTPUT ( Point1, Force1, Centre1 , Moment1 )
endif
{*
if EXIST( ForcePlate2 )
Force2 = ForcePlate2(1)
Moment2 = ForcePlate2(2)
Centre2 = ForcePlate2(3)
if ( ABS ( Force2 ) > 5 )
Point2 = Centre2 + { Moment2(2)/Force2(3), Moment2(1)/Force2(3), Centre2(3) }
else
Point2 = Centre2
endif
Force2 = Force2 + Point2
OUTPUT ( Point2, Force2, Centre2 )
endif
*}

Segment Definitions
{*Pelvis*}
{*======*}
PEL0=(LASI+RASI)/2
Pelvis=[PEL0,LASI-RASI,PEL0-SACR,yzx]

The Pelvis segment is defined using the markers LASI , RASI and
SACR if all three are present. The right-to-left direction between the
ASIS markers is the second axis of the segment. The plane of all three
markers is the plane containing the first and second axes, the first axis
pointing in an anterior direction.
{*Hip Joint Centres are positioned within the
Pelvis segment by user-set offsets, scaled
by inter-ASIS distance*}
InterASISDist=DIST(LASI,RASI)
Version 3.5 BodyBuilder for Biomechanics

Example Model - Kinetic Leg Model 183

LHJC=(InterASISDist*$%LHipOffsetFactor)*Pelvis
RHJC=(InterASISDist*$%RHipOffsetFactor)*Pelvis

The HipOffsetFactor parameter can be set by the user according to the

anatomical model they prefer. It can be seen that in this case, the crucial
biomechanical definition is made by setting a parameter, rather than by
re-positioning markers as in the foot model.
{*Pelvic Tilt can be adjusted*}
Pelvis=ROT(Pelvis,2(Pelvis),$PelvisTilt)
{* Add its mass etc. *}
Pelvis = [Pelvis, BodyMass*0.142, {0,0,0},
{0,0,0}]

{*Femora*}
{*======*}
KneeOffset=($MarkerDiameter+$KneeWidth)/2
LKJC=CHORD(KneeOffset,LKNE,LHJC,LTHI)
RKJC=CHORD(KneeOffset,RKNE,RHJC,RTHI)
LFemur=[LKJC,LHJC-LKJC,LTHI-LKJC,zxy]
RFemur=[RKJC,RHJC-RKJC,RKJC-RTHI,zxy]

The femur segment definition uses the CHORD function to locate the
knee centre. This virtual point is then used as the origin in the femur
segment definition.
{*Femoral Rotation can be adjusted*}
LFemur=ROT(LFemur,3(LFemur),$LFemurRotation)
RFemur=ROT(RFemur,3(RFemur),$RFemurRotation)

The attitude of the femur segment can be adjusted using a thigh rotation
parameter, allowing the user to compensate for mis-positioning of the
thigh marker.
LFemurLength=DIST(LKJC,LHJC)
RFemurLength=DIST(RKJC,RHJC)
184 Example Model - Kinetic Leg Model

Version 3.5 BodyBuilder for Biomechanics

{* Add the hierarchical and inertial

characteristics *}
LFemur=[LFemur, Pelvis, LHJC,
0.1*BodyMass, LFemurLength*{0,0,0.567},
LFemurLength*LFemurLength*{0,0.292,0.292}
*0.1*BodyMass ]
RFemur=[RFemur, Pelvis, RHJC, 0.1*BodyMass,
RFemurLength*{0,0,0.567},
RFemurLength*RFemurLength*{0,0.292,0.292}
*0.1*BodyMass ]
{*LFCoM = LFemurLength*{0,0,0.567} * LFemur
OUTPUT( LFCom )*}
{*Tibiae*}
{*======*}
AnkleOffset=($MarkerDiameter+$AnkleWidth)/2
LAJC=CHORD(AnkleOffset,LANK,LKJC,LTIB)
RAJC=CHORD(AnkleOffset,RANK,RKJC,RTIB)
LTibia=[LAJC,LKJC-LAJC,LTIB-LAJC,zxy]
RTibia=[RAJC,RKJC-RAJC,RAJC-RTIB,zxy]

The tibial segments are defined similarly to the femur segments.

{*Tibial Rotation can be adjusted*}
LTibia=ROT(LTibia,3(LTibia),$LTibiaRotation)
RTibia=ROT(RTibia,3(RTibia),$RTibiaRotation)
LTibiaLength=DIST(LAJC,LKJC)
RTibiaLength=DIST(RAJC,RKJC)
{* Add the hierarchical and inertial
characteristics *}
LTibia=[LTibia, LFemur, LKJC,
0.0465*BodyMass, LTibiaLength*{0,0,0.567},
LTibiaLength*LTibiaLength*{0,0.279,0.279}
*0.0465*BodyMass ]
Version 3.5 BodyBuilder for Biomechanics

Example Model - Kinetic Leg Model 185

RTibia=[RTibia, RFemur, RKJC, 0.0465*BodyMass,

RTibiaLength*{0,0,0.567},
RTibiaLength*RTibiaLength*{0,0.279,0.279}
*0.0465*BodyMass ]
{*Feet*}
{*====*}
LFoot=[LTOE,LTOE-LAJC,LKJC-LAJC,xyz]
RFoot=[RTOE,RTOE-RAJC,RKJC-RAJC,xyz]

The foot segments are defined using the line between the knee and ankle
joint centres, with the result that the foot segment does not have three
rotational degrees of freedom relative to the tibia.
{*Apply Static Trial Offsets*}
LFoot=ROT(LFoot,2(LFoot),$LStaticPlantarFlexion)
RFoot=ROT(RFoot,2(RFoot),$RStaticPlantarFlexion)
{* Add the hierarchical and inertial
characteristics *}
LFoot=[LFoot, LTibia, LAJC, 0.0145*BodyMass,
DIST(LTOE,LAJC)*{0.5,0,0},
DIST(LTOE,LAJC)*DIST(LTOE,LAJC)*{0,0.226,0.226}*
0.0145*BodyMass]
RFoot=[RFoot, RTibia, RAJC, 0.0145*BodyMass,
DIST(RTOE,RAJC)*{0.5,0,0},
DIST(RTOE,RAJC)*DIST(RTOE,RAJC)*{0,0.226,0.226}*
0.0145*BodyMass]

Definition and Output of Rotations

{*Angles*}
{*======*}
PELA=<Pelvis,1,yxz>
PELA=<1(PELA),2(PELA),3(PELA)>
LHPA=<Pelvis,LFemur,yxz>
LHPA=<1(LHPA),2(LHPA),3(LHPA)>
RHPA=<Pelvis,RFemur,yxz>
186 Example Model - Kinetic Leg Model

Version 3.5 BodyBuilder for Biomechanics

RHPA=<1(RHPA),-2(RHPA),-3(RHPA)>
LKNA=<LFemur,LTibia,yxz>
LKNA=<-1(LKNA),2(LKNA),3(LKNA)>
RKNA=<RFemur,RTibia,yxz>
RKNA=<-1(RKNA),-2(RKNA),-3(RKNA)>
LANA=<LTibia,LFoot,yxz>
LANA=<1(LANA),-2(LANA),3(LANA)>
RANA=<RTibia,RFoot,yxz>
RANA=<1(RANA),-2(RANA),-3(RANA)>
OUTPUT(PELA,LHPA,RHPA,LKNA,RKNA,LANA,RANA)
{*Segment Axes*}
{*============*}
PEL1=PEL0+50*1(Pelvis)
PEL2=PEL0+50*2(Pelvis)
PEL3=PEL0+100*3(Pelvis)
LFE0=0(LFemur)
LFE1=LFE0+50*1(LFemur)
LFE2=LFE0+50*2(LFemur)
LFE3=LFE0+LFemurLength*3(LFemur)
RFE0=0(RFemur)
RFE1=RFE0+50*1(RFemur)
RFE2=RFE0+50*2(RFemur)
RFE3=RFE0+RFemurLength*3(RFemur)
LTI0=0(LTibia)
LTI1=LTI0+50*1(LTibia)
LTI2=LTI0+50*2(LTibia)
LTI3=LTI0+LTibiaLength*3(LTibia)
RTI0=0(RTibia)
RTI1=RTI0+50*1(RTibia)
RTI2=RTI0+50*2(RTibia)
RTI3=RTI0+RTibiaLength*3(RTibia)
LFO0=0(LFoot)
LFO1=LFO0+50*1(LFoot)
LFO2=LFO0+50*2(LFoot)
LFO3=LFO0+100*3(LFoot)
RFO0=0(RFoot)
Version 3.5 BodyBuilder for Biomechanics

Example Model - Kinetic Leg Model 187

RFO1=RFO0+50*1(RFoot)
RFO2=RFO0+50*2(RFoot)
RFO3=RFO0+100*3(RFoot)
{*Virtual Points Output*}
{*=====================*}
OUTPUT(PEL0,PEL1,PEL2,PEL3,LHJC,RHJC)
OUTPUT(LFE0,LFE1,LFE2,LFE3,RFE0,RFE1,RFE2,RFE3,L
KJC,RKJC)
OUTPUT(LTI0,LTI1,LTI2,LTI3,RTI0,RTI1,RTI2,RTI3,L
AJC,RAJC)
OUTPUT(LFO0,LFO1,LFO2,LFO3,RFO0,RFO1,RFO2,RFO3)

These virtual points are defined to make the segments visible in the
Workspace window, when a suitable MKR file is selected.
r3 = REACTION( LFemur )
FP1 = | ForcePlate1(1), ForcePlate1(2),
ForcePlate1(3) |
CONNECT( LFoot, FP1, 1 )
{* ABS( ForcePlate1(1) ) > 5 ) *}
%r2 = REACTION( LFoot )
r2 = %r2 * LFoot
Force = r2(1)
Moment = r2(2)
Centre = (r2(3) - { Moment(2)/Force(3), Moment(1)/Force(3), 0 })
Force = Force + Centre
M2 = %r2(2)/(BodyMass)
output( Force, Centre, M2 )
P2 = { POWER( Pelvis, LFemur )/BodyMass, POWER(
LFemur, LTibia )/BodyMass,POWER( LTibia, LFoot
)/BodyMass }
output( p2 )

188 Example Model - Kinetic Leg Model

Version 3.5 BodyBuilder for Biomechanics

Glossary of Terms

Acclaim
File formats .AST, .ASF and .AMC were devised by Acclaim Corp. for
the description of kinematic models and motion data.

BodyLanguage
The language in which kinematic models for BodyBuilder are written.

Browse box
Also called a Browser. A small window which allows rapid search of
directory trees to find particular files.

Cartesian frame of reference

A system of three perpendicular axes which meet at an origin. The
position of any point relative to these axes can be specified by an ordered
triplet of numbers.

Current field
The field displayed in the Workspace window. The number of the
current field is shown under the replay slide bar. May be referred to as
Current Frame or Current Sample.

Dongle
A hardware key which must be plugged into a computer before
BodyBuilder can be run. Supplied to licensed users by Oxford Metrics
Ltd.

Field
A time-sample of kinematic data. In standard video terminology, a
"frame" is composed of one even- and one odd-numbered field. In
kinematic modelling, as in cine film, the distinction between even and

Version 3.5 BodyBuilder for Biomechanics

Glossary of Terms 191

odd fields is lost, and the word "frame" is often used interchangeably
with "field".

Gait analysis
The study of human movement for medical purposes.

Global point
A point which is defined in terms of the VICON reference axes, which
are constant throughout a trial.

Interpolation
Filling a gap in a trajectory by inventing new points. Small gaps in
smooth trajectories may be interpolated reliably. Large gaps and
trajectories which are not smooth are more difficult to interpolate, and
the results may be unrealistic. Interpolation should be used with caution.

Inverse Kinematics
Deducing the movements of segments from the desired overall result
rather than measured motion. For example, deducing the movements of
leg segments from the requirement that the feet do not move relative to
the floor. This is an inverse problem without a unique solution.

Kinematic angles
Numerical description of the angular relationship between connected
body segments of a kinematic model. Stored as three numbers.

Kinematic model
A numerical description of a moving object, composed of segments and
links.

Label
A name by which a point or trajectory is identified. Limited to 16
characters.

Local point
A point defined in terms of the axes of a particular segment, which is
itself able to move during the trial.

Marker
A reflective ball fixed to the performer. Also called a real marker, or
physical marker, to distinguish between trajectories which result from
actual measurements, and virtual ones created by modelling.
192 Glossary of Terms

Version 3.5 BodyBuilder for Biomechanics

Operating system
Software which controls the operation of a computer. BodyBuilder
requires a 32-bit operating system, which may be either Windows NT
(preferred) or Windows 95.

Passband
The range of frequencies allowed through a filter. Motion at a nearly
constant speed has low frequency components; motion involving high
accelerations has high frequency components which may fall outside the
passband of a filter.

Point
A location in space, specified by 3D co-ordinates. A trajectory (or
segment of a trajectory) consists of a time-series of points. A point is
stored in a .C3D file as three spatial co-ordinates and a residual,
identified by a label. Points may represent the measured positions of real
markers, or may be virtual (created by modelling). Point and marker
are often used interchangeably.

Pointer
Screen symbol (by default, an arrow) which is controlled by moving the
mouse.

Reconstruction
The calculation of the position of a marker by a VICON 370 system.

Script
A set of BodyLanguage definitions and functions which can be run by
BodyBuilder. Scripts are contained in .MOD files.

Segment
In a kinematic model, body parts are represented by segments, which are
assumed to be rigid elements linked by joints. Segments have both
position and orientation. (The term "trajectory segment" is sometimes
used to describe a short or interrupted marker trajectory.)

Spike
A point which lies to one side of an otherwise smooth trajectory. Spikes
can occur as a result of a mis-resconstruction in a single field, perhaps
caused by video noise or marker obscuring.

Version 3.5 BodyBuilder for Biomechanics

Glossary of Terms 193

Static trial
A short capture during which the performer stands still. Used for creating
Acclaim skeleton files and for deriving subject-specific parameters.

Stick
A line connecting two points as displayed in the Workspace window.
Defined in the current .MKR file, sticks are a useful graphic aid, but
have no significance above that of the points they link.

System memory
The working memory (RAM) of a computer. Data and programs in
current use are held in system memory, and will be lost if the computer is
shut down before they are written to disk.

Toggle
A command, button or key which causes a particular display, function or
feature to change between its two possible states.

Trajectory
The path through space followed by a marker, whether real or virtual.
Stored in a .C3D file as a time-series of points with the same label. May
consist of several trajectory segments separated by gaps, or a single,
uninterrrupted trajectory, depending on marker visibility. Displayed in a
Workspace window as a line through the position of the marker in the
current field.

Trial
A single data capture. The word also refers to the .C3D file resulting
from a data capture.

Virtual point
A point produced by kinematic modelling, in a position where no real
marker existed during motion capture. Virtual points may represent
internal features such as joint centres, where it is impossible to place a
real marker.

194 Glossary of Terms

Version 3.5 BodyBuilder for Biomechanics