Hello,
I'm looking to make some animations and was wondering if there is any way to clip the overlays as you can with the main image volume. Any help would be much appreciated.

There are a couple ways to do this:

1.) Use the shader pull down menu at the top-left corner of the shader panel to select a shader that clips the overlay. For example, use the "edge_phong" shader instead of the "default" shader.

2.) Put a Shader into your shader folder that allows you to explicitly control whether or not the overlay should be clipped. For example, I have attached a modified version of the "Default" shader named "defaultClip" that includes a new checkbox named "overClip" - clicking this checkbox will set whether the overlay is clipped. Note you can also control this shader feature with a script, which makes creating animations easy (choose View/Scripting and then select "Shader.gls" from the Scripting window's "File" menu to see how to do this). By the way, if you use MacOS, the shader folder is hidden - you have to select the MRIcroGL application in the finder and then choose to "Show Package Contents".