Image Overlay

You can overlay one or more images on top of the main displayed image, subject to all the images having the same number of rows, columns and slices.

Start the image overlay from the View menu: .

This brings up the Overlay Image dialog:

Each overlaid image can be selected from an overlay image tab. With a tab selected, the image to overlay is selected by clicking on the icon. This will pop up a file chooser for you to select the overlay image. Alternatively, hold down the right mouse button inside the image selection panel, to see a list of recently-selected images from which you can select one.

Note: The overlay image must have the same number of rows, columns and slices as the current loaded image, or an error message will be displayed in the status bar of the Overlay Image dialog.

Note: If the overlay image does not have the same pixel sizes as the displayed image, it will still be shown, but the scaling will be incorrect (i.e., it will be shown at the incorrect size in comparison to the displayed image). A warning message will be shown in the status bar if this is the case.

The image you just selected will now be shown on top of the current loaded image. The overlaid image is transparent, and you can change its opacity from 0 (completely transparent) to 1 (completely opaque) using the Opacity slider. The figure below shows an MRI head image with an extracted brain overlaid using the green colour mapping. To select the colour mapping for an overlaid image, first make sure that the tab for the overlay image is selected, and then choose the colour mapping from from the View menu of the Overlay Image dialog.

Effect of varying opacity.

Opacity=0.3	Opacity=0.5	Opacity=0.7

You can also make the background of the overlaid image completely transparent, regardless of the setting of the Opacity slider by checking the check box. Any pixels which have an intensity value below the Min contrast slider value will be completely transparent. You may want to mask the overlaid image to obtain pixel intensities of zero in the background using either the ROI Toolkit or the Masker. Below you can see a masked T₂-weighted image overlaid on a T₁-weighted image, with a completely transparent background.

You can adjust the contrast and brightness settings for the overlaid image (independent of the current loaded image) using the sliders in the Contrast panel as usual. When you have finished with the overlay image, click on the button.

You can rapidly toggle the overlay image on and off using the check box.

Note: you can overlay images onto movies as well, from the Movie frame.

Overlaying More Than One Image

You can overlay as many images as you wish. To add another overlay image, select from the File menu in the Overlay Image dialog. This creates a new tab in which you can select a new image to overlay as above. The images will be displayed with the image in the main display drawn first, which is overlayed by the image in the first overlay tab, which is overlaid by the image in the second tab etc. If any overlay image is completely opaque, the images drawn underneath will not be visible.

Setting Default Colour Mappings

If you find yourself repeatedly setting the same colour mappings for the overlay images after you have loaded them, you can do this automatically. Select from the View menu. This brings up a dialog in which you can set up to three default colour mappings to use for the first three overlay images.

To select a colour mapping to load for one of the three overlays, click the button. To go back to the default colour mapping, select the button when the colour mapping selection dialog pops up.