The Challenge of fMRI Interpretation

Functional Magnetic Resonance Imaging (fMRI) is one of the most popular imaging modalities used to investigate the brain.  A 2008 review of fMRI relates that, at the time of its publication, over 19,000 peer-reviewed fMRI articles had been published, and new publications were coming out at a rate of approximately eight per day in 2007.  For all of its ubiquitous popularity, however, there are a number of issues surrounding fMRI, including not only the temptation to use dubious statistical methods to ensure finding some results (possibly through a lack of statistical understanding as well as malicious disregard for scientific ethics) but also the more fundamental question of just what can be concluded from changes to the fMRI BOLD signal.  Given that the aforementioned 2008 review estimated that approximately 43% of fMRI studies were involved in “functional localization and/or cognitive anatomy associated with some sort of cognitive task or stimulus”, the interpretation of fMRI results with respect to cognition is clearly an important question.

The question of the meaning of BOLD response has come once more to prominence, thanks to a recent Nature paper by Lee et al. that combines the promising new optogenetic technique with fMRI.  Optogenetics involves introducing light-activated transmembrane ion channels to specifically targeted cells via a viral vector.   The virus can be tailored to target specific cell-types, allowing much more control over neuronal activation than other techniques such as implanted electrodes.  Mo Costandi’s excellent (and more timely) review has already been posted, but there are a few aspects of the study that deserve to be specifically highlighted, so I will briefly go through the methods and results again.

Lee et al. first injected the virus into the motor cortex of mice targeting excitatory neurons.  Following the injection, they anaesthetized the mice and optically stimulated the targeted neurons while gathering fMRI readings.  Nicely fitting with expectations, the increased activity of the optically stimulated neurons resulted in a corresponding increase in the BOLD signal 3-6 seconds following the stimulation onset, while there was no change in BOLD signal for control mice injected with a saline solution.  The BOLD signal again began to drop within 6 seconds of stimulus cessation, returning to baseline after approximately 20 seconds.  The researchers next repeated the experiment, only this time targeting inhibitory neurons.  Once again, optically driving the infected neurons resulted in an increase in the BOLD signal, but this time the zone of increased activity was surrounded by a smaller area of decreased BOLD response.  Importantly, as Chris Chatham rightly points out, the result of optically driving inhibitory neurons is still a net increase in the BOLD signal.  Unfortunately, much of this aspect of the experiment was relegated to the supplementary information, leading to an incorrect report by Scicurious that optically driving inhibitory neurons actually decreased the BOLD response.

While the study showed that increased neuronal activity reliably evokes a BOLD response, that does not necessarily mean that an evoked BOLD response is always due to increased neuronal activity.  In fact, as Mo Costandi briefly mentioned in his post, Yevgeniy B. Sirotin and Aniruddha Das performed an experiment showing that the BOLD response could be preemptively evoked irrespective of actual neuronal activity.


Researchers should continue to be careful while interpreting fMRI data.  The BOLD response is a measure of haemodynamic changes rather than neuronal activity, and though this study does suggest that increased activity in a neuronal population fairly reliably evokes a BOLD response, the converse is not necessarily true.  Likewise, the activity of neurons driving the fMRI signal could be from inhibitory as well as excitatory neurons, complicating functional interpretations of BOLD responses.  Inhibiting inhibition to yield excitation is a valid computational strategy (and one which is commonly proposed for functional models of the basal ganglia and its role in voluntary movement), which provokes the question of whether regions of reduced BOLD response are still vital to the cognitive function in question or if they are simply the result of metabolic conservation resulting from increased load elsewhere.  Furthermore, if a region is undergoing a careful balance of excitatory and inhibitory input it might show only marginal haemodynamic alterations despite having a functional role in cognition.

Thus, while Lee et al. have provided an excellent study demonstrating powerful applications of optogenetic techniques as well as providing support for fMRI data, their study does not actually validate fMRI interpretations.  Further combining of optogenetic and fMRI techniques will likely allow more detailed probing of the complex relationship between BOLD response and neuronal mechanisms.  For now neuroscientists must still be careful of the underlying assumptions and possible alternatives involved in the interpretation of fMRI data.  Caution is particularly warranted in relation to fMRI since its aesthetic appeal tends to be hard to resist*.

*If anyone could send me a link of a similar study performed on neuroscientists as opposed to undergraduate students, it would be much appreciated.


7 Responses to The Challenge of fMRI Interpretation

  1. Paul says:

    Nice review.

    Personally I am skeptical of the fMRI potential for cognition research for the reasons you mention. The complexity hidden behind the simplistic BOLD signal is staggering and I don’t see how one can extract *reliable* information from it beyond the simple “X area registers a BOLD signal when the subject does Y”.

    I prefer no data to unreliable data and no conclusions to unreliable conclusions.

    • I would argue against Paul: It is better to do the best we can with current methods, as long as we all understand their limitations.

      When we come up with better methods of imaging the brain in the future, we won’t be starting from scratch, and we will at least have hints at where to look in more detail, and at least vague hypotheses of what could be going on.

      But of course if all of this is true then any fMRI study with conclusions that go beyond “there is more BOLD signal there and there when we do this and that” should immediately raise a flag.

      • caldenwloka says:

        Your are correct, Andrej, that fMRI can give us a starting point, and I find good fMRI studies combine it with other imaging or recording methodologies (for example, using fMRI with EEG (or, even better, MEG) or single cell recordings). That said, there are large numbers of fMRI studies that do not try to corroborate fMRI findings with any other modality, and this is a huge problem for the field of cognitive neuroscience. fMRI is not the only imaging modality to suffer from interpretation problems (for example, references to wave types, which are essentially frequency ranges, being responsible for different cognitive tasks is endemic to EEG, even though there are numerous issues with such claims), but the prettiness of the pictures produced by fMRI makes it much wider reaching, and thus more easily misinterpreted.

  2. […] However, there are good reasons to be skeptical.  Interpretation of fMRI images is still a challenge, and the images gained for ‘lying’ via fMRI have shown to be culturally varied.  For […]

  3. […] On a general note (no fMRI study is complete without it!) we have to be wary when interpreting fMRI data as there are differing views on its meaning; active processing or active inhibition? […]

  4. […] about what ‘activity’ in a certain region even means… For examples, see here, here and here – a more scientific explanation of some of the issues behind imaging experiments can be found […]

  5. […] Among the many issues facing fMRI lie detection is the fact that the interpretation of fMRI images remains a persistent challenge for experts in the field. We still can’t measure ‘brain activity’ directly, instead researchers are limited to monitoring blood flow – which may be telling them something different altogether. […]

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