Loading and Tracking Data

This tutorial provides step-by-step instructions on how to load sample data from Slicer and track it in Autoscoper.

Downloading Sample Data

Some short sample data is included within the SlicerAutoscoperM extension. To load this data, open Slicer and switch to the Sample Data module. This is located in the module drop down menu, in the top left corner of the Slicer window, under the Informatics section.

In the Sample Data module, scroll down the left-hand side until you see the Tracking section. Select your desired data by clicking on the icon for that data.

Available sample data includes:

AutoscoperM - Wrist BVR
AutoscoperM - Knee BVR
AutoscoperM - Ankle BVR

Once downloaded, switch to the AutoscoperM module to begin tracking. This module is located in the module drop-down menu, under the Tracking section.

Launching Autoscoper and Loading Sample Data

Warning

Launching Autoscoper for the first time on Windows may require you to allow the program to run.

Once the AutoscoperM module is open, click the Launch Autoscoper button to launch Autoscoper. This will open a new window with the Autoscoper interface. Once Autoscoper is open, you can load the sample data by clicking one of the buttons in the Sample Data section of the interface. The buttons are labeled Load Wrist Data, Load Knee Data, and Load Ankle Data.

After loading the sample data, the Autoscoper window should look like this:

To zoom in on the radiographs and see the details, you can use Control + Mouse Wheel to zoom in and out. To adjust the position of the radiographs, you can use Control + Left Mouse Button to pan the radiographs.

Tracking a Skeletal Structure

Warning

The filters provided with the sample data may not be the optimal filters. Since the filters play an important role in the tracking process, you may need to adjust the filters to get the best results. Please see the Rendering and Filters tutorial for more information on filters and how to adjust them.

Aligning a Volume

Warning

The current version of AutoscoperM only supports tracking a single volume at a time. If you wish to track multiple volumes, it is recommended to align and track one volume all the way through before moving on to the next volume.

The first step in tracking a skeletal structure is aligning a volume to a set of bi-plane radiographs. Start by selecting the volume you wish to align from the volumes list in the lower-left corner of the screen. In this example, we will align the radius or the rad_dcm_cropped volume. To align the volume, move the mouse over one of the radiograph images and use the Left Mouse Button to move the volume around.

You can press E to switch to rotation mode or W to return to translation mode. Use D to move the location of the pivot point if needed. Use S to set a keyframe, which is used as a reference point in the tracking process. Pressing C will perform optimization on the current frame, which can be useful for snapping the volume to radiographs.

Tip

For help with aligning a volume, please see the Ticks and Tricks for Aligning Partial Volumes tutorial.

Tracking the volume

Warning

Once OK is pressed in the tracking dialog, the tracking process will begin. This process can take a long time, and the program will be unresponsive until the tracking is complete.

To view the output of the tracking process, you can open the Python terminal in 3D Slicer by hitting Control + 3. The output will be printed to the terminal.

Once the volume is aligned with the radiographs, you can press the Tracking Dialog button on the Toolbar to open the tracking dialog. The dialog will look like this:

The dialog has several options. The first option is the Tracking Range which allows you to specify the range of frames you wish to track. The default is to track all the frames in order. The second option is Initial Guess, changing this will change how the initial position of the volume is determined. The default is to use the position of the volume in current frame. The third option is Optimization method, you can choose between particle swarm optimization (PSO) or downhill simplex. The default is PSO. You can also specify the number of time you want the optimization to run on each frame. The default is 1. The fourth option is PSO Algorithm Parameters, you can change the parameters for the optimization here. The default values are usually good enough. The last option is Cost Function, you can choose between the normalized cross correlation (NCC) or the sum of absolute differences (SAD). The default is NCC.

Once you have set the options, you can press the OK button to start tracking. The tracking will take a while to complete, and trials with lots of frames will take even longer. Once the tracking is complete, the dialog will close.

For more information see the Tracking Dialog section of the user interface page.

Viewing the tracking results

Once the tracking is complete, you can view the tracking results by moving the slider at the bottom of the screen.

You can also view the tracking results in the 3D view by going to View -> Show World View in the main menu. You can use Control + Middle Mouse Button to pan the 3D view, Control + Left Mouse Button to rotate the 3D view, and Control + Right Mouse Button + Drag to zoom in and out. Move the view so you can see all of the volumes and radiographs at once. Using the slider at the bottom of the screen, you can move through the frames and see the tracking results in the 3D view.

Saving the tracking results

Once you are satisfied with the tracking results, you can save the tracking results by clicking the Save Tracking button. This will open a dialog where you can specify the name of the file you wish to save the tracking results to. The file will be saved as a .tra file. This file can be loaded back into Autoscoper at a later time by clicking the Load Tracking button.

Once the file name is specified, you can click the OK button and the tracking import/export dialog will open.