>"Are you saying that an fMRI, when taken of a subject at rest, twice - then what the data here show - is that this is likely to be interpreted as a subject in two different states?"

Yes, that is what they seem to be saying. I didn't read the code, or even the paper very closely. However, from what I quoted, they seem to be saying there is some assumption about autocorrelation that introduces what they call "false positives".

I am saying they have mischaracterized the problem. These are true positives.