Hi Sam,
As you mentioned, you can't mix opacities between background and foreground planes. Colors from each of the two stacks are mixed separately then the resultant foreground is attenuated by the average intensity of the resultant background.
However this might work for what you want:
1- Make a convexity dataset on the command line: SurfaceMetrics -conv on the smoothwm surface (that's the LocalDomainParent surface in the spec file). SUMA computes the convexity dataset automatically when it launches using the same function but it also smoothes the output a little.
2- Turn off background attenuation or you will get very confused very quickly
3- Load the manually created convexity dataset into SUMA and color it the same way the background convexity is colorized. Match the colormap, ranges, and 'Col' option. If you really want the smoothed look then run about 4 nearest neighbor smoothing iterations with SurfSmooth.
4- Now you can load two different copies of your activation dataset and do what you were trying to do. You can also load a third copy, and set the color map so that blobs are shown with just one color then display that plane with contours only. This way you can also have contours to accentuate the bright spots.
I hope this helps.
cheers
z
