Hey, if it's okay, I just thought I'd jump in and say that I also get this error.  I'm only trying to do a tutorial (this one: https://andysbrainbook.readthedocs.io/en/latest/FunctionalConnectivity/CONN_ShortCourse/CONN_09_2ndLevel_Analysis.html), and I'm doing it with three subjects rather than six (because it seemed like CONN was having trouble seeing files in some of the directories -- it was strange).  All my first levels seem like they have all their voxels.  

I'm mostly trying to get oriented and start the process of generating a model struct I can then use as an example for my own data, so I'll see if it persists when I'm trying to get my own study to work.  For now I just wanted to report that I also see it.