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Tips and tricks for Qualisys Track Manager (QTM)

Matthias Thelen 1

Last updated on April 30, 2020

In this article we will give you a short introduction to the workflow of Qualisys Track Manager (QTM) to make it easier to get started with the program. You will learn the following:

  1. The correct folder structure

  2. Start QTM

  3. Open individual measurements

  4. Automatic marker labeling (batch processing)

  5. Manual marker labeling

  6. Training the AIM Model

  7. Export C3D files

1. The correct folder structure

For Qualisys to work as desired, your project folder (here CarbonInserts) should have the following folder structure. Under AIM models you can save marker models. The data of the test persons should always be saved in Data as shown on the right.



2. Start QTM

When you start Qualisys the following window will appear. Choose your project folder (e.g. CarbonInserts) from step 1 by either selecting it from the list or by searching for it with the Browse button.



3. Open individual measurements

After you have selected the right project, the following window will open. Under Project automation, double-click on the subject you want to edit (A). Next, under Project automation the measurements of the respective subject with all single measurements will appear (B).

Under Project automation (B), select the measurement you want to edit and double-click the green label of the measurement (C). The single measurement is loaded and the unlabeled markers are displayed as a point cloud (D). Every already named marker (in this case none) are displayed in the window Labeled trajectories (E) and all markers that are not yet labeled are displayed under Undefined trajectories (F).



4. Automatic marker labeling (batch processing)

In order to label the markers as quickly as possible and to fill small gaps of markers, the so-called batch processing is used. To do so, press STR + SHIFT + R and the following window will open. In this window, select the settings and check the boxes as shown in the red box (G). Then, the 3 tabs on the left side (H) will appear.

Now select each of the three tabs (H) one after the other to make more precise settings. 3D Tracking: Here you can set the Prediction error and Maximum residual (I). The range of values is between 0 and 25. Here you should try out at which values most markers are automatically detected.

ATTENTION: The Max frame gap (J) should not be greater than 10.

Trajectories: Here the settings should be as follows (K). Max frame gap = 20 and Default interpolation gap = Polynominal.

AIM: This is about selecting the Aim Model (Marker Model) (L) (here e.g. a static model), which you want to apply to the data. The better the Aim Model is, the more markers are automatically detected. You can remove the current Aim Model with the Remove button (M) and add a new one with the Add Model button (N). This will automatically put you into the Aim Models folder from step 1.

If you have checked all settings, you can press the OK button and the automatic marker labeling will start. You will then return to the original view and you will see that parts of the marker point cloud have already been detected automatically (D1). Other parts, however, have not yet been detected (D2). All markers that have already been labeled are listed under Labeled trajectories (E). Repeat the batch processing so often that as many markers as possible are already labeled.



5. Manual marker labeling

If, despite batch processing, not all markers have been named for the whole measurement, you have to label the remaining markers manually. Click on Fill Level (O) to reorder the markers according to their percentage name (P). This gives you an overview of which markers still need to be labeled.

Select the ID button (Q) and then click on a marker that is still at 0% (R) in the Label trajectories window (E). Now you can search for the corresponding marker in the cloud and click on it in order to give it its label (S). Once you have labeled it, the ID function will automatically select the next marker. You can always see which marker it is in the Label trajectories window (E). So you can continue to name markers directly without selecting the marker in the Label trajectories window (E).

If you want to rename a marker that has been given a wrong label by the batch processing, select the arrow key (T), click on the marker and press U on your keyboard. This will delete the existing marker name. 

TIP: If you have clicked once, you can undo your last action by pressing STR+Z.

If you now have a marker that is already named by a certain percentage, e.g. 88.2%, then select this marker in the Label trajectories window by clicking on it (U). Press STR+T on your keyboard to open the Trajectory Editor (V). The Trajectory Editor shows the X, Y and Z progression of the marker you selected. The orange areas (W) indicate time ranges where the marker was not automatically detected. Click on the upper part of the cursor (X), hold down the mouse button and drag it to the point where the marker gap begins or ends. Then press the arrow keys on your keyboard to move from frame to frame and find the exact point in time where the marker disappears. Now you can control if the marker jumps, changes by mistake or disappears completely.

If you now want to fill the gap of the marker (W), select Relational (Y) in the Trajectory Editor and choose 3 adjacent markers that were attached to the same segment (Y) for the reconstruction. Also, set a check marker at Rigid Body. The Relational function calculates the position of the marker from the positions of the other markers. Here there are more options that can be used to fill the marker gap. The choice of these options is a matter for the user. We will write an separate article about this at a later time.

ATTENTION: The other 3 markers must be 100% present for the period of the gap.

If there are several gaps, you can jump from gap to gap with STR+K in the Trajectory Editor (V).

When you have labeled all markers for the entire measurement period, i.e. when in Labeled trajectrories (E) is a 100% behind each marker, you should run through the entire individual measurement again and check whether markers jump or get mixed up. If this is not the case and all markers are 100% and correctly labeled, you can save the single measurement with STR+S. Then the asterisk (Z) next to the name of the single measurement disappears.

ATTENTION: If you use Batch Processing again after manual marker labeling, all manually named markers will be lost. Therefore first use Batch Processing and then name the rest manually.



6. Training the AIM Model

Each Aim Model (Marker Model) can be trained with data sets to make it work better in future applications, so that more markers are automatically detected during batch processing. To train the Aim Model, you need a single measurement where each marker is named 100% CORRECTLY (check in the E subwindow). Close the single measurement by double clicking on another measurement (AA). Then click on the AIM tab and then on Generate From Multiple Files… (BB)

ATTENTION: If the single measurement is not 100% correctly named, you will train your Aim Model with wrong data and it will be worse than the previous one. 

After you have clicked on Generate From Multiple Files… (BB), the following window will open. Select Add to existing models (CC) here. Then click on the Aim Model (DD) you want to train and click the Next button (EE).

The following window will open. In the Project folder (here Carboninserts) select the Data folder and click through (FF) to the single measurement where each marker is named 100% CORRECTLY (here Static.trial_LS1.qtm). Select this single measurement (GG) by clicking on it and then press the Open button (HH).

If the following window appears, the training of the model has worked. For future batch processing the improved Aim Model will be used automatically.



7. Export C3D Files

To continue working with the motion capture data it is possible to convert the Qualisys data into C3D data. Select File, Batch Processing (II).

The following window will appear. Select all single measurements you want to convert into C3D files at once (JJ) (in this case only Static.trial_LS1.qtm) and press the Open button (KK).

Now select Calculate force data (LL), inclusive project (MM) and Export to C3D files (NN). The tab Force Data (OO) should appear. Click on Force Data (PP) and check if the Word Lab is selected as the coordinate system (QQ). Then press the Ok button (RR). The single measurements you selected will now be converted to C3D files. You can check in your folder structure (SS) if the files have been converted to C3D files (TT) as shown in the second picture below.

Now you can continue working with the C3D data e.g. in Matlab or similar programs.


  1. Yuvaraj Ramasamy Yuvaraj Ramasamy

    Thank you for having this blog/website. It’s very helpful to understand better about biomechanics.

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