Hello! This is my first time using QuickNII, and I have noticed that the transparency adjustment feature is not functioning as expected. I would like to understand the possible reasons for this issue. Thank you!

Hi, the transparency slider sets transparency of the entire overlay, including its background (QuickNII actually doesn't know which part of the overlay belongs to the atlas, and which part is just background). And this also applies to the outline view.

Even if you don't plan to deal with nonlinear adjustments, you may want to try opening your alignment data with VisuAlign ( https://www.nitrc.org/projects/visualign... ), simply because it provides a better view of the result.