Also consider aligning the images to process them all with a single model, the different sized/shaped heads in the world and correcting for their different angles and little bits of movement. That's not even considering differences between brains.

I am continually amazed at the level of automated preprocessing tools to deal with this alignment problem. You can play around with fMRI data using some popular packages without thinking too hard about it and produce visualizations almost as nice looking as the ones in the article.

Much of the day-to-day variation concerns uncontrolled variability in blood pressure, arousal and attention. Those factors have enormous influence on the blood-oxygen-level-dependent signal.