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fMRI is not measuring neural activity but rather blood oxygenation (BOLD signal) in a region. Its not well understood why/how increased neural activity would require more oxygenated blood or produce more deoxygenation blood. It has been established using optogenetics (it allows you to control neural activity) that increased neural activity results in an increase in an increased BOLD signal. It was a nice relief to those using the BOLD signal to study brain activity, but no one seemed to notice that it took a solid 30 seconds of brain activity to increase the signal even though most studies use its second-to-second fluctuations. Plus, what if a region actually shuts itself down by increasing inhibitory activity. Wouldn't that show up as an increased in the BOLD signal?
