The aim of this tutorial is to help Odin users build their own protocol. At the end of this tutorial, the user will have used most of the Odin functions (pointer landmark, filtering, Euler angles, graph creation, 3D view configuration, etc).
This protocol focuses on the thigh and shank tracking and the calculation of the knee joint angle.
- 1 Creating a new protocol
- 2 The acquisition profile
- 3 Configuring a layout for realtime
- 4 Adding calculation script to the protocol
- 5 Adding stick figure on the 3D view
- 6 Preparing an acquisition
- 7 Doing an acquisition
- 8 Displaying the results
Creating a new protocol
A protocol menu is automatically displayed when ODIN is launched. This menu gives the user the possibility to either open an existing protocol or create a new protocol
To create a new protocol, simply click on “New Protocol”, indicate a name for your protocol and click on “OK”
Odin will be opened on a complete new and empty template.
The acquisition profile
A new protocol doesn’t contain an acquisition profile. The best way to create an acquisition profile is to connect Odin to the hardware (Coda-hub or mini-hub). Odin will automatically select the different parameters of the acquisition profile in line with the hardware setup. To do so, simply click on “Hardware / select hardware server”, choose the server to connect and then the hardware configuration you need to use for your experiment. In the event that you cannot connect Odin to the hardware, you can create / add a new profile by right clicking on “Acquisition Profiles” and select “Add New …”
A new menu will appear.
You may create an acquisition profile by selecting a combination of hardware that you will use during your experiment.
Here are three different examples of hardware combination:
- CX1 + GS Analog Board. Choose this configuration if you want to collect data of marker position (CX1) and analogue channels / force plate data (analogue plate) using an old active hub (hub with mouse, keyboard and screen).
- CX1 + National instruments Analog Board. Choose this configuration if you want to collect data of marker position (CX1) and analogue channels / force plate data (analogue plate) using the new generation of Coda-Hub (hub with little touch screen integrated)
- CX1. Choose this configuration if you want to collect marker data only (mini or Coda-hub).
In our example, we will only choose “CX1”. To do it, tick the “CX1” option and click on “OK”. A new window will appear.
This window is used to set the names of the markers, the sampling rate, the acquisition time, start delay. Note that the red cross on the CX1 tab indicates that Odin is not connected to the system. For our quick protocol, first indicate a name for your protocol. Secondly rename the markers 1 to 4 with the following name: “RThigh.0”, “RThigh.1”, “RThigh.2”, and “RThigh.3” and markers 5 to 8 by “R.Shank.0”, “R.Shank.1”, “R.Shank.2”, and “R.Shank.3” (Note that you can use the define cluster option to rename marker having the same prefix in a quicker way). Then untick marker 9 to 56. Choose the sampling rate of 100Hz and set the recording time to 10 seconds. Then click on “OK” to validate the changes.
A new item will appear on the “Acquisition Profile” section as show Figure 6.
The acquisition profile can be modified at any moment by right clicking on it and selecting “Edit …”.
Configuring a layout for realtime
It is possible to configure as many layouts as you want in Odin; each of them focussing on a particular point of interest. We strongly recommend creating a first layout dedicated to realtime work which could be used to check marker names and position on the patient. Then, change the name of the current layout for “01 – Realtime” by right clicking on the layout called “loayout 01” (in the tree menu) and by selecting “Edit …”. A new window will appear, change the name and click on “OK”.
Configuring a 3d view
By default, no 3D view is defined in ODIN. The user can set a 3D view at anytime. Different 3D views can be displayed in ODIN and at the same time. The users just need to set them up. To define a 3D view, simply right click on “3D view” in the tree menu and select “Add new” as shown.
By default, a 3D view is configured to only display real marker and in green. The user can decide to individually choose the marker colour by clicking on the “+” button in the “New 3D panel” section and by selecting one by one the different marker and the colour. By default, the 3D view won’t display virtual markers (pointer landmarks, centroids or virtual markers). The user needs to add them. Odin only gives the user the possibility to set what is available at the configuration time. Because we haven’t defined any virtual marker at this time, the virtual marker option is not available in the list. The user can still write it manually. For that click on the “+” button in the “New 3D panel” section and write “RefPoint” in the group column and set the colour as red as shown.
Give a name to the 3D view such as “Realtime 3D view”, tick the “Show Coda Units” and close the window by clicking on “OK”. A new item called by the 3d view name will be available in the 3D view section of the tree menu.
The user can modified any 3D view at anytime by right clicking on it and by selecting “Edit …”.
The 3d view has just been created but we haven’t still decided where to display it. For it, select the top bar of the layout by clicking on it.
The top bar should become highlighted.
Then double click on the “Realtime 3D view” item in the tree menu. The 3D view will automatically appear in the selected panel.
Adding marker position text table
Odin can display the 3D position of each individual marker in a table. To display it, firstly split the current layout in two by clicking on one of these icons . Then select the top bar of the empty panel and double click on the “Marker text” item in the tree menu. The table will automatically appear in the selected panel.
Adding calculation script to the protocol
Odin has several built-in calculation scripts and other can be programmed and added by the user. Odin can run them as a pipeline in order to treat and analyse your data.
Creating the pointer landmarks
For this protocol, we will need a set of 5 pointer landmarks: 3 attached to the thigh (greater trochanter, medial and lateral epicondyle) and two attached to the shank (medial and lateral malleolus). To create a pointer landmark simply click on “calculation / new pointer landmark” (in the top bar). A new window will pop-up. Fill the different option as shown below:
Click on OK to validate and create the Pointer Landmark. Odin automatically adds an item called “R.GT” under the pointer landmark section in the tree menu. The user can modify it at anytime by simply clicking on the item and by selecting “Edit …”. Note that at this precise moment the user only created the pointer definition. A second step consisting in digitizing the pointer will be required later. Repeat the process 4 times with the following information:
Note that markers selected in the cluster section are different for R.MM and R.LM compare to R.GT, R.FME and R.FLE. Those two pointer landmarks are attached to the shank markers and not the thigh markers.
Creating the centroid markers (knee and ankle joints)
On the pointer landmarks have been created, we can use them to calculate the position of the joint centre (defined as the middle between two points). Two centroids need to be created the knee and the ankle.
To create a centroid, simply click on “calculation / New centroid …” and fill the panel as shown below. The knee joint here is considered as the mid-point between the “R.FME” and the “R.FLE”. Those two makers are stored in the “RefPoint” group.
Repeat the process for creating the right ankle joint but this time by choosing the “R.MM” and “R.LM” landmarks.
Odin automatically adds an item with the name of the centroid under the “calculations” section in the tree menu. The user can modify it at anytime by simply clicking on the item and by selecting “Edit …”. By default Odin does not calculation centroid position in realtime. To turn on this option, one by one right click on the script and tick the “Real-Time option”.
To filter the data, click on “Calculations / Set Marker Filter …”. A new dialog box will pop-up.
By default, the filter options are set to filter the marker (real and virtual) data at 50Hz and to calculate the marker velocities and accelerations. Also the interpolation is set as linear. The changes will be done once the dialog box is closed by clicking on “OK”. Odin automatically adds an item called “Marker Data” under the “calculations” section in the tree menu. The user can modify it at anytime by simply clicking on the item and by selecting “Edit …”. This script won’t affect the raw data. The raw data are still stored in the “Marker” and “RefPoint” sections. The filtered data are stored in the “MFilter” and “RefPointFilter” sections. Odin can display in the 3D view and graphs both non filtered and filtered data at the same time. The user can then visually see the difference between the non filtered and filtered data.
Calculating Segment Orientation
To call the function dedicated to the segment orientation calculation, click on “Calculations / New Coordinate Basis …”. For this quick protocol, there are two segments that we can calculate the orientation: the thigh and the shank.
The longitudinal axis (y) of the shank is going from the ankle joint to the knee joint. The anterior-posterior axis (x) is orthogonal axis to the plane defined by the R.Knee, R.LM and R.MM markers pointing forward. The medio-lateral axis (z) is line perpendicular to both x-and x-axis, pointing to the right.
To do so, click on “Calculation / New Coordinate Basis …” and fill the dialog box as indicated below:
Odin automatically adds an item with the name of the coordinate basis (“R.Shank”) under the “calculations” section in the tree menu. The user can modify it at anytime by simply clicking on the item and by selecting “Edit …”.
Usually, the longitudinal axis (y) of the femur bone goes from the knee joint to the hip joint. Because we don’t have the hip joint centre position in this protocol, we considered for this protocol that the axis going from the R.LFE to the R.GT was parallel. Therefore the longitudinal axis is defined from the RLFE to R.GT markers. The anterior-posterior axis (x) is orthogonal axis to the plane defined by the R.GT, R.LFE and R.MFE markers pointing forward. The medio-lateral axis (z) is line perpendicular to both x-and x-axis, pointing to the right.
To do so, click on “Calculation / New Coordinate Basis …” and fill the dialog box as indicated below:
Calculating Euler angle between the Thigh and the Shank
To calculate the Euler angle between the right thigh and the right shank, click on “Calculations / New Euler Angle …” and set the dialog box as shown below:
Odin automatically adds an item with the name of the Euler angle (“EA-R.Knee”) under the “calculations” section in the tree menu. The user can modify it at anytime by simply clicking on the item and by selecting “Edit …”.
Adding stick figure on the 3D view
Stick figures are used to graphically / visually link markers between each others on the 3D views. Adding a stick figure requires two steps: 1) creating its definition and 2) applying it on a 3D view.
Creating a stick figure definition
The user can create as many stick figures as he wants. To create a stick figure, right-click on the “Stick figure Joins” and select “Add new …”.
A new dialog box will appear. Let’s set this dialog box for a stick figure displaying the cluster outlines.
Odin automatically adds an item with the name of the stick figure (“Cluster”) under the “Stick figure joins” section in the tree menu. The user can modify it at anytime by simply clicking on the item and by selecting “Edit …”. Another stick figure linking the virtual marker of a segment can be created. For this repeat the process: right-click on the “Stick figure Joins” and select “Add new …”. Then fill the dialog box as shown below:
Applying a stick figure on the 3D view
To apply a stick figure to a 3d view, the user need to open the dialog box of the 3D view. To do so, right click on the 3D view item and select “Edit …”. The middle panel of the 3D view dialog box has now two stick figure items: “Clusters” and “Leg”. Tick them and click on “OK” to validate the changes. The 3D view will now display the stick figures.
Preparing an acquisition
Doing an acquisition requires some prerequisites. The name of the patient / trial needs to be indicated before the acquisition because Odin saves the trial automatically in the database at the end of the acquisition. Also when using pointer in your protocol the landmark need to be digitized before the acquisition. Firstly, check that the system is on the live mode. To do so, check if the “Live” button is active. If not, click on it.
Indicating the patient / trial information
The patient / trial information can be inserted in the ambient trial in the trial list.
By default, a protocol contains only three fields: Subject ID, Date and RepLabel. The user can add as many fields as he wants. Fields can be very useful to filter trials when opening them. For this protocol, we will add two more fields: subject height and the name of the experimenter. To do it, click on “View / Trial Viewer Configuration …” and field the new dialog box as shown Figure 27
The trial list should be affected by the changed and should now show 5 fields. Fill the different fields. Note that only Subject ID is compulsory and RepLabel and date are automatically filled by ODIN.
Digitizing the pointer landmarks
Once the “Subject ID” field is filled, click on “Hardware / Acquire Pointer”. A window with the landmark name should appear (see Figure 29). Digitize every landmark one by one using the pointer
Once every landmark has been digitized, all names should be green as shown Figure 30. Click on “Close” to close the window.
The trials list should show 5 trials (one per landmark acquired) and the ambient trial. The 3D view should now show the stick figure of the Leg.
Doing an acquisition
To start an acquisition, click on the “record” button. The acquisition will automatically start and stop once the time set in the acquisition profile elapsed.
The trial is automatically saved at the end of the acquisition. At the end of the acquisition, Odin displays the marker visibility summary (see Figure 32). The playback of the trial can be played by switching to the playback mode and using the play toolbar.
The next trial is reading to be recorded. Simply click on the record button. The RepLabel is automatically incremented by 1.
Displaying the results
Odin can be customized to present the results as the user want. In this example, a special layout will be created to display a 3D view and two graphs: marker positions and knee angles. First, click on the playback button to switch in the playback mode. Secondly, create a new layout (right click on the “layout” item in the tree menu and select “Add New”). Change the name of the layout (right on the newly creation layout in the tree menu and select “Edit”) for “02 – Post treatment”. Divide the layout as shown Figure 36and place the 3D view on the left panel.
The next step consists of creating the graph definitions. Let’s start with the marker position (Z-axis) graph. Right click on the “Graph” item and select “Add New …”.
Indicate a name for the graph “Knee and Ankle Position – Z axis” and click on the “+” button on the “All Plots” panel. And fill the new panel as shown below:
Click on “Ok” to close the first dialog box, tick “Show value at cursor” and “Show time at cursor” and close the dialog box by clicking on “OK”.
Select an empty panel of the layout (select the top bar) and double click on the created graph item in the tree menu.
Repeat the process for the Knee angle. The Euler angles are stored in the “JointAngle” section as shown below
Allocate the new graph to the last empty panel of the layout. The layout should now look as below:
User can switch from one layout to another by simply double clicking on the layout name in the tree menu.
Don’t forget to regularly save your changes regularly. Have fun.