How to Use the Example Application

Introduction

The generic navigation application that comes with the SIGN can be used to test the functionality of the framework and act as an example for how to create more advanced applications. In the following, we will describe how to use this application. For information about implementation details, please check the code.

Starting the software

The application is started by entering the command line:

The configuration files

The contents of the three configuration files are explained in the application tutorial. If you would like to navigate using an existing DICOM study, the MRML file can look like this

This will let an optical tracker control a model with the name 'Probe1' and the three orthogonal 2D viewers. See this config file.

An important element of the mrml file is related to the registration. This indicates that the probe named 'Probe1' will be used as registration source and the dataset named 'BrainData' will be registration target. The fiducial sets from the registration source and the registration target will be aligned when enough fiducial points are available, and the resulting transformation will be applied to the probe pipeline (the tracker coordinates will be transformed to the image space).

Registering the physical space to the image space

To register the coordinate space of the tracking system to the coordinate space of the images, fiducial markers have to be placed. First the markers in the images should be placed. This is done in the 2D viewers using the sliders to find the appropriate slices and clicking on a marker (or anatomical feature) with the middle mouse button. It is recommended to zoom into the images with the right mouse button to get accurate definitions. Upon placing a marker, it will be identified in the 2D images with a thin crosshair, in the 3D viewer with a small colored sphere, and in the menu on the left as an item in a list. At least 4 markers should be placed. The markers have to be touched with the tip of the tracked probe in the same order as they were identified in the images. The colored markes in the 3D view may help in identifying the location of each marker. When the probe is touching a marker, the footswitch of the tracker can be pressed, or the GUI button labeled 'Footswitch' can be used. As soon as 4 pairs of markers are identified, the system will calculate a registration transformation. If more markers are used, the transformation will be recomputed (and hopefully improved) for each new pair of markers. There is no feedback of registration accuracy in this application, although that can easily be added.

Navigating

This application allows the probe to be moved around, while driving the three orthogonal views. Such basic navigation can be done once the registration is complete.

Transfer function manipulation

The image data is shown in the 3D viewer using volume rendering. The transfer function, which is used to map intensity values to color and opacity, can be edited by going into the 'View' menu and clicking 'Transfer function...'. A simple widget is displayed that allows interaction with the transfer function.