Begin by loading the images of both modalities. To do so, open the analysis software. To load the CT image A as underlay, go to File followed by Underlay and click Load underlay.
In the dialogue that appears, choose and open the image file. Similarly, to load the PET image A as an overlay, click File, Overlay, Load overlay and choose the image file to open it. For marker-based fusion, hide the underlay by navigating to Menu, View and Layer visibility.
Then uncheck Overlay and keep Underlay. Switch the selected layer to the underlay if required. To show multiple slice views, press Alt plus A for the axial, Alt plus S for the sagittal, and Alt plus C for the coronal views.
If necessary, press Control plus W and adjust the left and right vertical bars in the windowing dialogue to better see the fiducials. Click on OK to close the dialogue. Click the marker symbol on the vertical toolbar on the left side to activate the mouse action mode, Create Marker.
Navigate to one fiducial of the phantom. Place the mouse pointer in its center and left click. Select OK to save the marker.
Place the mouse pointer over the view of a plane and use Alt plus mouse wheel to slice through the planes. Adjust the viewing settings by navigating to Menu, View, Layer visibility, and check Overlay to show the overlay. Switch the selected layer to Overlay.
Adjust the windowing as demonstrated if necessary. Navigate to each fiducial of the phantom. Place the mouse pointer in the center of the fiducial and left click.
Click on OK to save the marker. Place the mouse pointer over the view of a plane and use Alt plus mouse wheel to slice through the planes. Align the markers of Underlay and Overlay by navigating to Fusion, followed by Register overlay to underlay and selecting Compute rotation and translation.
Note this measurement and click OK.Check the result of the alignment. As demonstrated previously, activate the views of underlay and overlay layers. Click on the symbol on the left side vertical toolbar to activate the mouse mode interactive image fusion.
Check Overlay, uncheck Underlay and segmentation. Perform translation by placing the mouse pointer near the center of a view. Hold the left mouse button and move the mouse to move the overlay.
Perform rotation by placing the pointer near the edge of a view, axial, coronal, or sagittal. Hold the left mouse button and move the mouse to rotate the overlay. Keep performing rotations and translations on the different views until the underlay and overlay are aligned as best as possible.
Create and save the differential transformation by navigating Fusion, Overlay transformation, and select Create and save differential transformation. In the first dialogue, select the original overlay file and click on Open. In the second dialogue, enter a file name for the differential transformation and press Save.
