I recently (last Friday) added a requested feature to the AFNI time series graph viewer -- the ability to mark sub-graphs of those voxels that are below threshold -- that is, those voxels that are un-colored when See Overlay is turned on.

To enable this feature in a particular graph window, you can type the F key while the mouse focus is in the graph window, or you can use the new item 'Thresh Fade' in the Opt menu (just below 'Show Text'). You can also turn this option on for all graph windows by setting the environment variable AFNI_GRAPH_FADE to YES in your ~/.afnirc file.

"Fading" is only on when See Overlay is on. It should work OK with Clusterize and InstaCorr, but I haven't tested it under all conditions -- so if you change the way the overlay is viewed, the graph window may not update properly without you manually forcing a redraw. I'll fix such problems as they arise (Insh'Allah).

I've attached an image showing how the faded sub-graphs look -- the background is set to a grayish color.