Tutorial

Tutorial

This tutorial will walk you through the steps to use SAM to track a 3D motion of a skeletal structure from a single bi-plane video radiography image set.

Prerequisites

SAM is a 3D Slicer extension. Therefore, you will need to install 3D Slicer first. The preview version of Slicer is required, which can be found here. SAM is currently only available for Windows and Linux operating systems. MacOS support is planned for the future.

Installation

SAM is available as a 3D Slicer extension. You can install it from the 3D Slicer extension manager. To open the extension manager, go to View -> Extension Manager in the main menu. In the extension manager, search for AutoscoperM and click Install to install SAM. Once SAM is installed, switch to the AutoscoperM module by clicking Modules -> AutoscoperM in the main menu.

Loading Sample Data

Once the module is loaded, you can launch the module by clicking the Launch Autoscoper button. The module will open in a separate window.

SAM ships with several sample data sets. To load a sample data set, go to Help -> Open Sample - Wrist. There are also datasets for the Knee and the Ankle. You can load them by going to Help -> Open Sample - Knee or Help -> Open Sample - Ankle. Once the data is loaded, you should see the following screen:

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.

Loading Custom Data

Preparing the Data

SAM requires the following data to track a skeletal structure:

• One or more radiograph series
• A 3D volume of each bone in the skeletal structure you wish to track
• A camera calibration file for each radiograph serires

Camera Calibration File

The camera calibration file should be in the following format:

image size
width,height

camera matrix
fx,0,cx
0,fy,cy
0,0,1

rotation
r11,r12,r13
r21,r22,r23
r31,r32,r33

translation
t1
t2
t3

Creating a Configuration File

SAM uses a .cfg file to specify the location of the radiographs, volumes, and camera calibration files. You can create a .cfg file by going to File -> New. This will open up the configuration dialog:

From the dialog you can create as many cameras as needed. Where the Calibration File points the the camera calibration file and the Video Path points to the folder containing the radiographs for each camera.

You can also create as many volumes as needed. Where the File points to the volume file. and the Scale XYZ is the scale of the volume in the x, y, and z directions. The Scale XYZ is used to scale the volume to match the size of the radiographs. The ` Flip XYZ indicates whether the volume should be flipped in the x, y, and z directions. The Flip XYZ` is used to match the orientation of the volume to the radiographs.

Once everything is set in the dialog you can press Ok to automatically load the trial into SAM. Inorder to save the configuration file, you can go to File -> Save Trial as. This will save the configuration file to the specified location. You can also press Crtl + Shift + S to save the configuration file.

Tracking a Skeletal Structure

Aligning a Volume

SAM tracks a skeletal structure by aligning a volume to a set of bi-plane radiographs. To align a volume, start by selecting the volume you wish to align from the volumes list in the lower left corner of the screen. In this case, we will align the radius or the rad_dcm_cropped volume. Once the volume is selected, you can move your mouse over to 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 go back to translation mode. If need you can press D to move the location of the pivot point. If you wish to set a keyframe, this can be done by pressing S. Keyframes are used as reference points in the tracking process. Pressing C will perform the optimization on the current frame, this can be useful for snapping the volume to the radiographs.

You may find it easier to align the volume with one of the radiographs first, then make sure the volume is aligned with all the radiographs.

Tracking the volume

Once the volume is aligned with the radiographs, you can press the Tracking Dialog button 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 Intial Guess, changing this will change how the intial position of the volume is determined. The default is to use the position of the volume in current frame. The third option is Optmiziation method, you can choose between partical swarm optmiziation (PSO) or downhill simplex. The default is PSO. You can also specifiy the number of time you want the optmization to run on each frame. The default is 1. The fourth option is PSO Algorithm Parameters, you can change the parameters for the optmization 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.

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.