Course Content
What is fNIRS?
Where fNIRS comes from, what it measures in principle, and where it sits among other neuroimaging tools.
0/5
How does fNIRS work?
The physical logic from light entering tissue to a number quantifying the detected light in an fNIRS device
0/4
Brain Hemodynamics and Neurovascular Coupling
NIRS does not measure neural activity directly; it measures the vascular response that follows it. This unit builds the physiological bridge between the two. We start at the level of neurons and synapses, trace the cascade through metabolism and blood flow regulation, and arrive at the haemodynamic signals we actually record: changes in oxyhaemoglobin (ΔHbO) and deoxyhaemoglobin (ΔHbR). We examine what these signals represent biophysically, how to interpret them, and what the canonical Hemodynamic Response Function looks like. A recurring theme is the distinction between different physiological quantities that are often conflated: CMRO₂, cerebral blood flow, blood volume, oxygen saturation, and hemoglobin concentration are related but not equivalent, and confusing them leads to misinterpretation.
0/3
Collecting fNIRS Data
Not all fNIRS systems are the same. This unit provides a broad overview of the hardware landscape, from the ubiquitous Continuous Wave (CW) systems to Frequency Domain (FD) and Time Domain (TD) instruments, and the emerging class of speckle-based devices that measure blood flow rather than hemoglobin concentration. A central message is that the choice of hardware determines what you can and cannot measure: for example, TD and FD systems can independently quantify absorption and scattering, and therefore provide absolute hemoglobin concentrations, while CW systems are almost always limited to relative changes and must assume a fixed DPF. We also cover the practical side: how sources and detectors are arranged on the head (the montage), and what "good coupling" between optode and scalp actually means.
Processing fNIRS Data
Collecting fNIRS data is relatively accessible, but clean, interpretable data is not. This unit confronts the reality that the fNIRS signal is dominated by noise: physiological fluctuations from the heart, respiration, and slow vasomotion can be an order of magnitude larger than the neural signal of interest. Motion artifacts are arguably one of the defining challenges of the modality. We work through the major noise sources and introduce strategies to address each before considering statistical analysis. On the way, you will understand why simple averaging over blocks is insufficient, and why the General Linear Model (GLM) has been the standard framework. The unit closes with an overview of alternative quantification approaches for data analysis, including inter-subject correlation and functional connectivity, and the broader challenge of pipeline standardization.
fNIRS Challenges and Future Frontiers
The final unit steps back from technical details to consider the bigger picture: what fNIRS uniquely enables, and what still stands in its way. We explore three of the most exciting directions in the field: hyperscanning and social/developmental neuroscience, ecological validity through wearable deployment, and the study of populations that other neuroimaging modalities struggle to accommodate. We also return to the challenge of pipeline standardization and reproducibility as an open problem that newcomers entering the field have an opportunity (and a responsibility!) to address.
Introduction to fNIRS (English)

Neurovascular Coupling

🎯 as you read, try to

  • Describe the physiological chain from neural activity to the vascular response that fNIRS detects
  • Define cerebral blood flow (CBF), cerebral metabolic rate of oxygen (CMRO₂), and oxygen extraction fraction (OEF), and relate them through Fick’s principle
  • Explain why cerebral blood flow increases proportionally more than oxygen consumption during activation
  • Work through, from first principles, why ΔHbR falls during activation even though oxygen is being consumed

Units 1 and 2 established how changes in the concentration of oxy- and deoxy-haemoglobin can be recovered from light attenuation, using the Modified Beer-Lambert Law. Neither unit, however, addressed why those concentrations change in the first place. This lesson introduces neurovascular coupling, the physiological chain linking neural activity to the vascular response that follows it, and the reason light attenuation in tissue carries any information about brain activity at all.

The lesson builds this chain and uses it to resolve a point that trips up almost everyone learning fNIRS for the first time: activation increases oxygen consumption, yet the fNIRS signal most associated with oxygen loss, HbR, decreases rather than increases. By the end of this lesson, that result will follow directly from the physiology rather than needing to be taken on faith.

1. The Neurovascular Unit

The brain has essentially no local energy reserve. It accounts for roughly 2% of body mass but consumes around 20% of the body’s resting oxygen supply, and it cannot store meaningful amounts of glucose or oxygen for later use. Every increase in local neural activity has to be met, in near real time, by an increase in local oxygen and glucose delivery. The system responsible for this matching is the neurovascular unit: neurons, astrocytes, the endothelial cells lining blood vessels, and the smooth muscle and pericytes that control vessel diameter, all working as a coordinated local circuit.

In outline, the sequence runs as follows. Synaptic activity releases neurotransmitters and requires ion pumps to restore resting gradients, both of which consume ATP. This local rise in metabolic activity triggers signalling, substantially mediated by astrocytes, whose processes contact both synapses and the walls of nearby blood vessels. This signalling relaxes the smooth muscle around local arterioles, which dilate; blood flow into the capillary bed downstream increases within one to two seconds of the triggering activity, and continues to rise for several seconds more. This is the process most people mean when they say “neurovascular coupling,” and it is the reason a hemodynamic signal can be used as a proxy for neural activity, despite not measuring neurons directly.

🔬 going deeper

The molecular signalling underlying neurovascular coupling is more plural than any single pathway, and remains an active research area. Candidate signals released by active neurons and astrocytes include potassium ions (which can relax vascular smooth muscle through inward-rectifier channels), nitric oxide (released by a subset of interneurons), and arachidonic acid metabolites such as prostaglandins and epoxyeicosatrienoic acids (produced by astrocytes in response to the calcium signalling triggered by neurotransmitter uptake). These pathways are not mutually exclusive, act on different timescales, and their relative contribution varies by brain region and by the type of neuron driving the response.

Here is a list of must-read papers for a full account on this topic:

💭 pause and think

The neurovascular unit couples local blood supply to local neural activity within a radius of roughly a few hundred microns to a few millimetres. fNIRS, as you know from Unit 2, samples a source-detector volume of several cubic centimetres. What does the mismatch between the true spatial scale of coupling and the spatial scale of a single fNIRS channel imply about what a channel-level signal represents?

2. Delivery, Consumption, and Extraction of Oxygen

Reasoning precisely about what happens when blood flow increases requires three quantities. The first two were introduced informally in Unit 1: cerebral blood flow (CBF), the volume of blood delivered to a tissue per unit time, and cerebral metabolic rate of oxygen (CMRO₂), the rate at which that tissue consumes oxygen. The third, which links them, is the oxygen extraction fraction (OEF): the proportion of the oxygen delivered by the blood that the tissue actually removes and consumes.

Cerebral blood flow (CBF)

The volume of blood delivered to a given mass of tissue per unit time. A delivery quantity: it says nothing, on its own, about how much of the oxygen in that blood is used.

Cerebral metabolic rate of oxygen (CMRO₂)

The rate at which a given mass of tissue consumes oxygen. A consumption quantity: it reflects metabolic demand directly, but says nothing on its own about how that oxygen got there.

These two quantities are related through Fick’s principle, briefly introduced in Unit 1. Stated precisely, Fick’s principle says that the rate of oxygen consumption equals blood flow multiplied by the difference in oxygen content between the blood arriving (arterial) and the blood leaving (venous) the tissue:

💡 fick’s principle

CMRO₂ = CBF × (CaO₂ − CvO₂)

where CaO₂ and CvO₂ are the oxygen content of arterial and venous blood, respectively. The oxygen extraction fraction is the fraction of the delivered oxygen this difference represents: OEF = (CaO₂ − CvO₂) / CaO₂. Combining the two: CMRO₂ = CBF × CaO₂ × OEF. Under normal resting conditions, the brain extracts only a minority of the oxygen delivered to it: normative PET studies place resting OEF at roughly 35-44%, depending on brain region (Leenders et al., 1990). Oxygen supply comfortably exceeds oxygen demand at rest, which gives the system room to respond to changing demand without running out of oxygen.

OEF is the quantity that connects delivery and consumption to oxygenation, which is what fNIRS actually measures, and to oxygen saturation (StO₂) in particular, which represents the fraction of haemoglobin carrying oxygen. Venous oxygen saturation is, to a close approximation, the complement of OEF, since a higher extraction fraction leaves less oxygen in the blood as it exits the tissue. OEF is therefore the variable that sets how oxygenated the blood in a vascular bed is at any moment, and consequently how much of the local haemoglobin pool is HbO₂ versus HbR.

Before we conclude, it is worth noting that Fick’s principle and the extraction fraction derived from it are steady-state relationships, i.e., they describe a tissue mass balance once inflow, outflow, and consumption have reached equilibrium, not an instantaneous relationship valid at any moment during, e.g., a rapidly changing transient. During the first several seconds after stimulus onset, CBF, CBV, and OEF are all changing together, and blood requires a finite transit time to move through the vascular bed. The comparison used throughout this lesson, resting state versus sustained activation, is a comparison of two such steady states, which is exactly how the Fox and Raichle measurements below were collected: each PET value is a block average, not an instantaneous snapshot. Modelling the dynamic transition between these two states requires a more elaborate framework. Two well-known examples are the balloon model (Buxton, Wong & Frank, 1998), which models blood volume and deoxyhaemoglobin content directly as functions of time, and the Windkessel model (Mandeville et al., 1999), which treats the venous compartment as a passive, compliant vessel that inflates under arteriolar pressure and drains more slowly than it fills, accounting for the delayed return to baseline often seen in blood volume after a stimulus ends. Both are widely used in the fNIRS literature specifically, since fNIRS’s high temporal resolution is well suited to testing exactly this kind of dynamic prediction. We will not need this level of detail here, but it is worth knowing these models exist before we discuss the time course of the hemodynamic response itself.

3. Changes in Blood Flow And Metabolism During Activation

Given the relationship above, a natural assumption is that CBF and CMRO₂ increase by roughly the same proportion during activation, leaving OEF, and therefore oxygenation, largely unchanged. However, this assumption is incorrect, and the size of the mismatch between CBF and CMRO₂ during activation is key for interpreting the fNIRS signal.

🎍 landmark paper

Fox, P.T. & Raichle, M.E. (1986). “Focal physiological uncoupling of cerebral blood flow and oxidative metabolism during somatosensory stimulation in human subjects.” Proceedings of the National Academy of Sciences, 83(4), 1140–1144.

Using PET with ¹⁵O-labelled tracers, Fox and Raichle measured CBF and CMRO₂ during somatosensory stimulation in human subjects. At rest, the two were tightly correlated across brain regions, consistent with the naive assumption above. During stimulation, however, this broke down: blood flow to the activated region increased by 29% on average, while oxygen consumption increased by only 5%. This mismatch, sometimes called neurovascular uncoupling (a slightly misleading name, since it is a highly reproducible relationship rather than a breakdown), has since been replicated many times and is the physiological basis of both the BOLD signal and the fNIRS haemodynamic response.

→ doi:10.1073/pnas.83.4.1140

The physiological reason the brain over-delivers oxygen during activation is not fully settled. One account, formalised by Buxton and Frank (1997), holds that oxygen diffusion from capillary blood into mitochondria is itself a limiting step: diffusion depends on the concentration gradient between capillary blood and tissue, so a large increase in flow is needed to raise that gradient enough to support even a modest increase in consumption. A second line of evidence, from Fox, Raichle, Mintun and Dence (1988), found that during activation, glucose uptake and blood flow both rose far more (51% and 50%, respectively) than oxygen consumption (5%), consistent with a transient contribution from non-oxidative glycolysis: glucose metabolised without a matched increase in oxygen use. This remains an active area of study. What matters for interpreting fNIRS is that the CBF/CMRO₂ mismatch itself, whatever its ultimate explanation, is well established and highly reproducible.

4. Consequences to Haemoglobin Concentrations

If a brain region is consuming more oxygen during activation, CMRO₂ has gone up. HbR reflects deoxygenated haemoglobin, the product of oxygen being unloaded from blood into tissue. The standard fNIRS finding, however, is that HbR falls during activation rather than rising.

The explanation for this is the mismatch discussed in the previous section. CMRO₂ rises, but only modestly. CBF rises far more. Because OEF is the ratio between how much oxygen is consumed and how much is delivered, and delivery increases much faster than consumption, OEF falls during activation, even though absolute oxygen consumption is higher than at rest. A smaller fraction of a larger oxygen supply is being extracted. The blood leaving the activated tissue is therefore more oxygen-rich than it was at rest, and the local haemoglobin pool tips further toward HbO₂ and away from HbR.

Rest

CBF: 100 (reference) CMRO₂: 100 (reference) OEF: ≈ 40%

Activation (from Fox & Raichle averages)

CBF: 129 (+29%) CMRO₂: 105 (+5%) OEF: ≈ 33% (falls, despite higher absolute consumption)

Using Fox and Raichle’s own figures as a worked illustration: if OEF at rest is around 40%, and CMRO₂ rises 5% while CBF rises 29%, the new OEF is approximately 0.40 × (1.05 / 1.29) ≈ 0.33. Oxygen extraction drops by roughly a fifth in relative terms, purely because delivery outran consumption. Combined with the accompanying increase in local blood volume, as more of the local vascular bed fills with fresh, oxygenated blood, this produces the canonical fNIRS response: HbO₂ rises, HbR falls, and both changes are consistent with a genuine increase in oxygen consumption.

💭 pause and think

Some studies report a brief, small dip in HbO₂ (or a small transient rise in HbR) in the first second or two after stimulus onset, before the canonical response takes over. Given the logic above, what would have to be true, even transiently, for such an “initial dip” to occur? Which of the two curves, CBF or CMRO₂, would have to lead the other in that brief window?

5. From Physiology to a Measurable Signal

The chain described in this lesson, from synaptic activity, through astrocyte-mediated vascular signalling, to a CBF increase that outpaces the CMRO₂ increase, to a falling OEF and a rising local blood volume, together determine the balance of HbO₂ and HbR in the tissue beneath an fNIRS probe. These are exactly the concentration changes that Units 1 and 2 showed how to recover from light attenuation through the Modified Beer-Lambert Law.

This is why fNIRS functions as a neuroimaging tool at all. A local increase in neural activity triggers a well-characterised, reproducible physiological chain that changes local haemoglobin concentration in a specific and predictable direction. Measuring that concentration change, which is what fNIRS does, therefore provides a usable, if indirect, window onto local neural activity.


📌 Key Takeaways

  • The neurovascular unit (neurons, astrocytes, and blood vessels acting together) links local neural activity to local increases in blood flow, on a timescale of one to a few seconds.
  • CBF (delivery) and CMRO₂ (consumption) are related through Fick’s principle via the oxygen extraction fraction (OEF), the fraction of delivered oxygen actually consumed. Resting OEF is normally around 30–40%.
  • During activation, CBF increases substantially more than CMRO₂ (Fox & Raichle 1986: 29% vs. 5%, on average). This mismatch, not a drop in metabolism, is what causes OEF to fall.
  • A falling OEF means blood leaving the activated tissue is more oxygenated, not less, even though absolute oxygen consumption has risen. This is why ΔHbO₂ rises and ΔHbR falls during activation, consistent with, not contrary to, increased metabolism.
  • This chain, from neural activity to a predictable change in local haemoglobin concentration, is the physiological basis for using fNIRS as a neuroimaging tool.

📚 Further Reading & Key References

  1. Fox, P.T. & Raichle, M.E. (1986). “Focal physiological uncoupling of cerebral blood flow and oxidative metabolism during somatosensory stimulation in human subjects.” Proceedings of the National Academy of Sciences, 83(4), 1140–1144. [doi]The founding demonstration of the CBF/CMRO₂ mismatch that this lesson is built around.
  2. Attwell, D. & Iadecola, C. (2002). “The neural basis of functional brain imaging signals.” Trends in Neurosciences, 25(12), 621–625. — A compact, accessible entry point into the signalling mechanisms behind neurovascular coupling.
  3. Attwell, D., Buchan, A.M., Charpak, S., Lauritzen, M., MacVicar, B.A. & Newman, E.A. (2010). “Glial and neuronal control of brain blood flow.” Nature, 468(7321), 232–243. [doi]The major mechanistic review of astrocyte- and neuron-mediated vascular signalling.
  4. Iadecola, C. (2017). “The neurovascular unit coming of age: a journey through neurovascular coupling in health and disease.” Neuron, 96(1), 17–42. — The most comprehensive modern review; also covers what changes in disease and ageing, relevant background for Unit 6.
  5. Buxton, R.B. (2010). “Interpreting oxygenation-based neuroimaging signals: the importance and the challenge of understanding brain oxygen metabolism.” Frontiers in Neuroenergetics, 2, 8. — A thoughtful discussion of why CBF outpaces CMRO₂, and what remains genuinely unresolved about this question.
  6. Leenders, K.L., Perani, D., Lammertsma, A.A., et al. (1990). “Cerebral blood flow, blood volume and oxygen utilization: normal values and effect of age.” Brain, 113(1), 27–47. — Source for the normative resting OEF range cited in Section 2.
  7. Buxton, R.B. & Frank, L.R. (1997). “A model for the coupling between cerebral blood flow and oxygen metabolism during neural stimulation.” Journal of Cerebral Blood Flow & Metabolism, 17(1), 64–72. — The diffusion-limitation account referenced in Section 3.
  8. Buxton, R.B., Wong, E.C. & Frank, L.R. (1998). “Dynamics of blood flow and oxygenation changes during brain activation: the balloon model.” Magnetic Resonance in Medicine, 39(6), 855–864. — The standard dynamic (non-steady-state) generalisation referenced in Section 2, relevant again in Lesson 3.3.
  9. Fox, P.T., Raichle, M.E., Mintun, M.A. & Dence, C. (1988). “Nonoxidative glucose consumption during focal physiologic neural activity.” Science, 241(4864), 462–464. — The non-oxidative glycolysis account referenced in Section 3.
  10. Mandeville, J.B., Marota, J.J.A., Ayata, C., Zaharchuk, G., Moskowitz, M.A., Rosen, B.R. & Weisskoff, R.M. (1999). “Evidence of a cerebrovascular post-arteriole Windkessel with delayed compliance.” Journal of Cerebral Blood Flow & Metabolism, 19(6), 679–689. — The Windkessel model referenced in Section 2, extensively developed in later fNIRS dynamic-modelling work.