The following is my understanding, but I could be wrong:

When neurons activate, they release a neurotransmitter (typically glutamate) that then binds to nearby astrocytes. Astrocytes then increase their intracellular calcium levels which in turn causes vascular dilation of the nearby area, thus increasing blood flow to that area.

Thanks, this was what I was looking for. So I guess this pathway is not very predictable, hence the variations in subsequent measurements of the same subject.

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.

The most sensitive fMRI methods don't do alignment at all, they do all data processing in the individual subject's brain space.

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.

The term you are looking for is neurovascular coupling [1]. The increase in blood flow allows more oxygenated hemoglobin to flow through the capillary bed where the neuronal activity is taking place. This increases oxygen availability, which is necessary to maintain homeostasis and replenish the membrane potentials of the neurons, given that the brain has (essentially) no energy storage. There are multiple signalling pathways that control the mechanism, many of which are still poorly understood - for a review see [2].

I should add that every full moon a study comes out criticizing fMRI or drawing attention to its limitations, but researchers are very well aware of that. The fMRI response* to a task is neither temporally nor spatially specific, and it is confounded by anything that could remotely influence blood flow and blood volume. Figuring out how to deal with these issues is an active area of research - see an informal discussion here [3].

It's really a shame that the field is purported so negatively by the press, given it's the only thing we have to study brain function in humans with sub-millimeter spatial resolution non-invasively in-vivo.

[1] http://scholarpedia.org/article/Neurovascular_coupling [2] https://www.cell.com/neuron/pdf/S0896-6273(17)30652-9.pdf [3] https://practicalfmri.blogspot.com/2017/08/fluctuations-and-...

* Assuming the conventional Blood Oxygenated Level Dependent contrast used for functional imaging.

There is almost irrational glee expressed whenever an article like this comes out, not just by the press, but also by HN commenters, who seem primed to pounce on any evidence that supports their preconceived negative views on neuroscience. I often wonder why this is the case.

Disclaimer: I have an interest in neurosciece but not expertise on fMRI. I also haven't had time to read the article closely (yet). I'm sure others are better equipped to answer the question, so please jump in.

Anyway, here's my impression at a high level: neurons need energy to spike, and increased brain activity in a particular brain region ought to translate to higher metabolic activity, and ultimately to higher blood flow (to deliver e.g. oxygen). However, what one can infer about neural activity from e.g. blood oxygen level is still a matter of debate, precisely because (again as you suggested) the relevant mechanisms are complicated and AFAIK not completely understood. Other factors besides metabolism may also come into play.

I suppose this article is a reasonable start:

  https://en.wikipedia.org/wiki/Blood-oxygen-level-dependent_imaging

Despite these reservations fMRI remains popular, at least in part because it is non-invasive and is one of the few tools we have for studying humans.

Edit: more disclaimers. :-)