Hi, 

I was wondering if it is possible to scale the opacity of my overlay based on the strength of my overlayed activation? What I mean is for e.g. I have a color bar ranging from 3.3 to 14.5. With that I have a big part of the standard overlayed with "activations" so it is not very visible what parts of the brain are underneath the color.  I would love to scale the opacity of the overlay so that the values closer to 14.5 would have the highest opacity (no transparency) and the closer we would get to 3.3 in my overlay the lower the opacity would be (overlay gets more and more transparent). Would something like this be possible in MRIcroGL, either in GUI or in scripting?


Thank you for your help,
Marta

You may want to look at NiiVue which provides the ability to outline clusters above a threshold with opacity fading out with significance
  https://niivue.github.io/niivue/features/alphathreshold.html