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How is fmri used

Hannah Devlin explains how fMRI is used and answers some common criticisms of fMRI. With additional contributions by Stuart Clare and Heidi Johansen-Berg.

Who works in an FMRI Laboratory?

Neuroimaging is a highly interdisciplinary field, typically bringing together scientists with a wide range of backgrounds. 

The Physics groups focus on designing new ways of using the scanner to acquire data (pulse sequence design), working out what an FMRI measurement corresponds to physically and biophysical modelling.

One of the key roles of the Analysis groups has been developing FMRIB’s in-house software library FSL for analysing FMRI data. These groups continue work to optimise techniques for the analysis of both structural and functional imaging.

The many basic and clinical Neuroscience groups use neuroimaging as a tool to explore how the brain works. Some areas of interest are pain, disease, language, decision-making and development.

 FMRIB Retreat Eynsham Hall

Common Criticisms of FMRI

  1. FMRI only measures the secondary physiological correlates of neural activity, it is not a direct measure. This means it is not a truly quantitative measure of mental activity - when comparing the FMRI response between individuals it is impossible to say whether the differences are neural or physiological in origin.
    Although not a direct measure of neural activity FMRI is still a causal step closer to what is happening in the brain than the behavioural correlates psychologists have traditionally depended on. Although currently qualitative, FMRI is a more objective measure of a person’s mental state than a tick-box questionnaire.The relationship between the FMRI signal and the underlying activity is an active area of research. A variety of techniques have been developed to calibrate an individual’s response in order to obtain a more quantitative measure of neural activity.
  2. Relative to other brain imaging techniques, FMRI has unequalled spatial resolution – at 7T activity can be mapped down to 1mm. However the temporal resolution of FMRI is inherently limited by the slow blood flow response it depends. FMRI cannot uncover the dynamics of mental activity on the sub-millisecond timescale on which neurons operate.
    FMRI can be combined with high temporal resolution techniques, such as EEG to combine the different strengths of each technique. An increasingly popular method is combined EEG-FMRI where the two measurements are made simultaneously.
  3. Critics of the technique complain that FMRI overlooks the networked or distributed nature of the brain’s workings, emphasizing localised activity when it is the communication among regions that is most critical to mental function. This, along with FMRI being an indirect measure of brain activity has led to the charge that FMRI is no more than modern day phrenology - a 19th century pseudo-science which purported to character-type by examining the shape of a person’s skull.
     Any FMRI experiment is only as good as its hypothesis, design and interpretation. Silly FMRI experiments, for instance one showing men’s amygdala’s (which play a key role in generating emotion) light up when viewing Ferraris, are not difficult to find. But such work doesn’t prove any fatal flaw in FMRI, merely poor use of a good tool. Most FMRI investigators seek not to localize brain function but to map the parts of the system that act in different combinations for different tasks.
  4. As FMRI has begun to address more questions, ethical concerns have arisen regarding who should have access to FMRI data.
    Ethical approval, which is required for functional imaging experiments, is only granted if satisfactory procedures are in place to protect the privacy of those taking part in the study.


Clinical and Commercial Use

Patient going into scanner

FMRI now has a small but growing role in clinical neuroimaging. It is used in pre-surgical planning to localise brain function. There is also potential for clinical FMRI in applications including presymptomatic diagnosis, drug development, individualisation of therapies and understanding functional brain disorders. Early studies also suggest that FMRI has the potential to be used as bio-feedback for conditions such as chronic pain.

There have been several early ventures to capitalise on FMRI. Two companies have been setup in North America offering lie detection services using FMRI. There are also several neuromarketing companies using FMRI to gain insights into consumer thought and behaviour.

Other Brain Imaging Techniques


Computed tomography (CT) scanning builds up a picture of the brain based on the differential absorption of X-rays. During a CT scan the subject lies on a table that slides in and out of a hollow, cylindrical apparatus. An x-ray source rides on a ring around the inside of the tube, with its beam aimed at the subjects head. After passing through the head, the beam is sampled by one of the many detectors that line the machine’s circumference. Images made using x-rays depend on the absorption of the beam by the tissue it passes through. Bone and hard tissue absorb x-rays well, air and water absorb very little and soft tissue is somewhere in between. Thus, CT scans reveal the gross features of the brain but do not resolve its structure well.


PET imagePositron Emission Tomography (PET) uses trace amounts of short-lived radioactive material to map functional processes in the brain. When the material undergoes radioactive decay a positron is emitted, which can be picked up be the detector. Areas of high radioactivity are associated with brain activity.



Electroencephalography (EEG) is the measurement of the electrical activity of the brain by recording from electrodes placed on the scalp. The resulting traces are known as an electroencephalogram (EEG) and represent an electrical signal from a large number of neurons. EEGs are frequently used in experimentation because the process is non-invasive to the research subject. The EEG is capable of detecting changes in electrical activity in the brain on a millisecond-level. It is one of the few techniques available that has such high temporal resolution.



Magnetoencephalography (MEG) is an imaging technique used to measure the magnetic fields produced by electrical activity in the brain via extremely sensitive devices known as SQUIDs. These measurements are commonly used in both research and clinical settings. There are many uses for the MEG, including assisting surgeons in localizing a pathology, assisting researchers in determining the function of various parts of the brain, neurofeedback, and others.


Near infrared spectroscopy is an optical technique for measuring blood oxygenation in the brain. It works by shining light in the near infrared part of the spectrum (700-900nm) through the skull and detecting how much the remerging light is attenuated. How much the light is attenuated depends on blood oxygenation and thus NIRS can provide an indirect measure of brain activity.