It’s no secret in cognitive neuroscience that some brain regions garner more attention than others. Particularly in fMRI research, we’re all too familiar with certain regions that seem to pop up in study after study, regardless of experimental paradigm. When it comes to areas like the anterior cingulate cortex (ACC) and insula (AIC), the trend is obvious. Generally when I see the same brain region involved in a wide a variety of tasks, I think there must be some very general level function which encompasses these paradigms. Off the top of my head, the ACC and AIC are major players in cognitive control, pain, emotion, consciousness, salience, working memory, decision making, and interoception to name a few. Maybe on a bad day I’ll look at a list like that and think, well localization is just all wrong, and really what we have is a big fat prefrontal cortex doing everything in conjunction. A paper published yesterday in Cerebral Cortex took my breath away and lead to a third, more sinister option: a serious methodological confound in a large majority of published fMRI papers.
Neurovascular coupling and the BOLD signal: a match not made in heaven
An important line of research in neuroimaging focuses on noise in fMRI signals. The essential problem of fMRI is that, while it provides decent spatial resolution, the data is acquired slowly and indirectly via the blood-oxygenation level dependent (BOLD) signal. The BOLD signal is messy, slow, and extremely complex in its origins. Although we typically assume increasing BOLD signal equals greater neural activity, the details of just what kind of activity (e.g. excitatory vs inhibitory, post-synaptic vs local field) are murky at best. Advancements in multi-modal and optogenetic imaging hold a great deal of promise regarding the signal’s true nature, but sadly we are currently at a “best guess” level of understanding. This weakness means that without careful experimental design, it can be difficult to rule out non-neural contributors to our fMRI signal. Setting aside the worry about what neural activity IS measured by BOLD signal, there is still the very real threat of non-neural sources like respiration and cardiovascular function confounding the final result. This is a whole field of research in itself, and is far too complex to summarize here in its entirety. The basic issue is quite simple though.
End-tidal C02, respiration, and the BOLD Signal
In a nutshell, the BOLD signal is thought to measure downstream changes in cerebral blood-flow (CBF) in response to neural activity. This relationship, between neural firing and blood flow, is called neurovascular coupling and is extremely complex, involving astrocytes and multiple chemical pathways. Additionally, it’s quite slow: typically one observes a 3-5 second delay between stimulation and BOLD response. This creates our first noise-related issue; the time between each ‘slice’ of the brain, or repetition time (TR), must be optimized to detect signals at this frequency. This means we sample from our participant’s brain slowly. Typically we sample every 3-5 seconds and construct our paradigms in ways that respect the natural time lag of the BOLD signal. Stimulate too fast, and the vasculature doesn’t have time to respond. Stimulation frequency also helps prevent our first simple confound: our pulse and respiration rates tend oscillate at slightly slower frequencies (approximately every 10-15 seconds). This is a good thing, and it means that so long as your design is well controlled (i.e. your events are properly staggered and your baseline is well defined) you shouldn’t have to worry too much about confounds. But that’s our first problematic assumption; consider for example when one’s paradigms use long blocks of obscure things like “decide how much you identify with these stimuli”. If cognitive load differs between conditions, or your groups (for example, a PTSD and a control group) react differently to the stimuli, respiration and pulse rates might easily begin to overlap your sampling frequency, confounding the BOLD signal.
But you say, my experiment is well controlled, and there’s no way my groups are breathing THAT differently! Fair enough, but this leads us to our next problem: end tidal CO2. Without getting into the complex physiology, end-tidal CO2 is a by-product of respiration. When you hold your breath, CO2 blood levels rise dramatically. CO2 is a potent vasodilator, meaning it opens blood vessels and increases local blood flow. You’ve probably guessed where I’m going with this: hold your breath in the fMRI and you get massive alterations in the BOLD signal. Your participants don’t even need to match the sampling frequency of the paradigm to confound the BOLD; they simply need to breath at slightly different rates in each group or condition and suddenly your results are full of CO2 driven false positives! This is a serious problem for any kind of unconstrained experimental design, especially those involving poorly conceptualized social tasks or long periods of free activity. Imagine now that certain regions of the brain might respond differently to levels of CO2.
This image is from Change & Glover’s paper, “Relationship between respiration, end-tidal CO2, and BOLD signals in resting-state fMRI”. Here they measure both CO2 and respiration frequency during a standard resting-state scan. The image displays the results of group-level regression of these signals with BOLD. I’ve added circles in blue around the areas that respond the strongest. Without consulting an atlas, we can clearly see that bilateral anterior insula extending upwards into parietal cortex, anterior cingulate, and medial-prefrontal regions are hugely susceptible to respiration and CO2. This is pretty damning for resting-state fMRI, and makes sense given that resting state fluctuations occur at roughly the same rate as respiration. But what about well-controlled event related designs? Might variability in neurovascular coupling cause a similar pattern of response? Here is where Di et al’s paper lends a somewhat terrifying result:
Di et al recently investigated the role of vascular confounds in fMRI by administrating a common digit-symbol substitution task (DSST), a resting state, and a breath-holding paradigm. Signals related to resting-state and breath-holding were then extracted and entered into multiple regression with the DSST-related activations. This allowed Di et al to estimate what brain regions were most influenced by low-frequency fluctuation (ALFF, a common resting state measure) and purely vascular sources (breath-holding). From the figure above, you can see that regions marked with the blue arrow were the most suppressed, meaning the signal explained by the event-related model was significantly correlated with the covariates, and in red where the signal was significantly improved by removal of the covariates. The authors conclude that “(results) indicated that the adjustment tended to suppress activation in regions that were near vessels such as midline cingulate gyrus, bilateral anterior insula, and posterior cerebellum.” It seems that indeed, our old friends the anterior insula and cingulate cortex are extremely susceptible to neurovascular confound.
What does this mean for cognitive neuroscience? For one, it should be clear that even well-controlled fMRI designs can exhibit such confounds. This doesn’t mean we should throw the baby out with the bathwater though; some designs are better than others. Thankfully it’s pretty easy to measure respiration with most scanners, and so it is probably a good idea at minimum to check if one’s experimental conditions do indeed create differential respiration patterns. Further, we need to be especially cautious in cases like meditation or clinical fMRI, where special participant groups may have different baseline respiration rates or stronger parasympathetic responses to stimuli. Sadly, I’m afraid that looking back, these findings greatly limit our conclusions in any design that did not control for these issues. Remember that the insula and ACC are currently cognitive neuroscience’s hottest regions. I’m not even going to get into resting state, where these problems are all magnified 10 fold. I’ll leave you with this image from neuroskeptic, estimating the year’s most popular brain regions:
Are those spikes publication fads, every-task regions, or neurovascular artifacts? You be the judge.
edit:As many of you had questions or comments regarding the best way to deal with respiratory related issues, I spoke briefly with resident noise expert Torben Lund at yesterday’s lab meeting. Removal of respiratory noise is fairly simple, but the real problem is with end-tidal C02. According to Torben, most noise experts agree that regression techniques only partially remove the artifact, and that an unknown amount is left behind even following signal regression. This may be due to slow vascular saturation effects that build up and remain irrespective of shear breath frequency. A very tricky problem indeed, and certainly worth researching.
Note: credit goes to my methods teacher and fMRI noise expert Torben Lund, and CFIN neurobiologist Rasmus Aamand, for introducing and explaining the basis of the C02/respiration issue to me. Rasmus particularly, whose sharp comments lead to my including respiration and pulse measures in my last meditation project.