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Recording policies in functional magnetic resonance imaging


Assume that the areas in a single-subject's brain that are involved in solving a task are supposed to be visualized with fMRI. The dynamics of the task solving process shall not matter (which areas are active first, which second?).

How, i.e. by which policy, are the data collected to give the final image?

I believe to have understood that data are collected per slices (of some millimeters thickness) and later postprocessed to give the final image.

For the sake of definiteness, let $T$ be the overall time it takes to complete the task (e.g. 10 seconds). Let $t$ be the time it takes to simultaneously take the BOLD data of one slice (e.g. 100 milliseconds). Let $N$ be the number of slices to be recorded (e.g. 20). Let $n$ be the minimal number of recordings of one slice that is necessary for statistical analysis ($n=?$). So there are $N n$ recordings of slices necessary which takes $N n t$ milliseconds, if only one slice could be recorded at once. If $T$ is too short, the experiment would have to be repeated $N n t/T$ times to get all of the required $N n$ slice recordings.

If $m$ slices could be recorded simultaneously, a single run of the experiment would suffice, when $m > N n t/T$.

In any case: In which order are the slices to be recorded chosen (in case they cannot be recorded all at once)?

Possible policies:

  1. always from top to bottom (along the z-axis) in time $T$?

  2. repeatedly from top to bottom in some time $T'=T/k < T$?

  3. alternating between top-bottom and bottom-up in repeated experiments?

  4. in a random order?

  5. in an order informed by knowledge of the stages of the task (when different slices are primarly active at different times during the task)

Or is my picture of the recording process all too naive? Or is the question somehow meaningless (for reasons I do not see, but would like to learn about)?


If I recall correctly, in BOLD fMRI an echo-planar imaging (EPI) sequence is typically used. In one example:

44 slices were acquired, every 3 seconds, 96 times in a row, leading to a total number of 4,224 images acquired in 4 minutes and 48 seconds.

- https://www.imagilys.com/functional-MRI-fMRI/

You can read more about EPI here. I think you will find the zig-zag pattern in this link interesting. See also this link for a description of EPI.

fMRI is slow and has a low temporal resolution, because the hemodynamic repsonse of the blood is around 6 second long. This is perhaps a limiting factor for fMRI, which is why there is a limit to optimizing the sequences. However, one real impact of faster sequences is to capture head movement artifacts more accurately. Other sequences are used in anatomical MR imaging, such as FLAIR.


Functional neuroimaging

Functional neuroimaging is the use of neuroimaging technology to measure an aspect of brain function, often with a view to understanding the relationship between activity in certain brain areas and specific mental functions. It is primarily used as a research tool in cognitive neuroscience, cognitive psychology, neuropsychology, and social neuroscience.


Functional magnetic resonance imaging characterization of CCK-4-induced panic attack and subsequent anticipatory anxiety

The main objective of this work was to study the functional markers of the clinical response to cholecystokinin tetrapeptide (CCK-4). Twelve healthy male subjects were challenged with CCK-4 and simultaneously underwent functional magnetic resonance imaging (fMRI) recording. Since anticipatory anxiety (AA) is an intrinsic part of panic disorder, a behavioral paradigm, using the threat of being administered a second injection of CCK-4, has been developed to investigate induced AA. The study was composed of three fMRI scans according to an open design. During first and second scan, subjects were injected with placebo and CCK-4, respectively. The third scan was the AA challenge. CCK-4 administration induced physiological and psychological symptoms of anxiety that met the criteria for a panic attack in 8 subjects, as well as cerebral activation in anxiety-related brain regions. Clinical and physiological response intensity was consistent with cerebral activity extent and robustness. fMRI proved more sensitive than clinical assessment in evidencing the effects of the AA challenge. The latter induced brain activation, different from that obtained on CCK-4 and during placebo injection, that was likely related to anxiety. The method applied in this study is suitable for the study of anxiety using fMRI.


Scientists Say: MRI

This is a magnetic resonance image of the inside of someone&rsquos head. MRI can show the brain in beautiful detail.

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MRI (Magnetic resonance imaging) (noun, “Mag-NEH-tik rez-uh-nunce IM-udj-ing”)

This is a technique scientists use to create very detailed maps of the body.

Your body is full of water. Each molecule of it is made of one oxygen atom and two hydrogen atoms. Hydrogen has just one proton, and that proton has a positive charge. MRI applies a strong magnetic field to the protons of those hydrogen atoms. This makes the hydrogen atom’s protons spin in a direction that aligns them with the magnetic field. Then, the imaging machine applies a radio wave in a perpendicular field — one 90 degrees off of the first field. This makes the hydrogen atoms tip to the side. When the second field is removed, the protons tip back into alignment with the first strong field. As they tip back, they also release energy. The MRI machine can measure this energy to determine the type of tissue the water molecules are in, from brain to liver to bone. MRI’s sensitivity allows scientists to create very specific maps of the human body.

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There is also a type of MRI called functional MRI, or fMRI. Doctors often use it to study the brain. When a part of your brain is very active, more blood will flow there to fuel it. The blood coming in contains oxygen. More blood flowing into an area of the brain sends different signals than does tissue receiving a normal flow of blood. An MRI machine can detect that difference and map where it is. Scientists can compare the same brain area when a person is doing nothing, and again when the person is performing a task, to see how blood flow — and activity — in that brain area changes.

In a sentence

MRI can be used for many things, from studying the aging brain to figuring out how knuckles crack.

Power Words

(for more about Power Words, click here)

brain scan The use of an imaging technology, typically using X rays or a magnetic resonance imaging (or MRI) machine, to view structures inside the brain. With MRI technology — especially the type known as functional MRI (or fMRI) — the activity of different brain regions can be viewed during an event, such as viewing pictures, computing sums or listening to music.

fMRI (functional magnetic resonance imaging) A special type of machine used to study brain activity. It uses a strong magnetic field to monitor blood flow in the brain. Tracking the movement of blood can tell researchers which brain regions are active. (See also, MRI or magnetic resonance imaging)

magnet A material that usually contains iron and whose atoms are arranged so they attract certain metals.

magnetic field An area of influence created by certain materials, called magnets, or by the movement of electric charges.

magnetic resonance imaging (MRI) An imaging technique to visualize soft, internal organs, like the brain, muscles, heart and cancerous tumors. MRI uses strong magnetic fields to record the activity of individual atoms.

molecule An electrically neutral group of atoms that represents the smallest possible amount of a chemical compound. Molecules can be made of single types of atoms or of different types. For example, the oxygen in the air is made of two oxygen atoms (O2), but water is made of two hydrogen atoms and one oxygen atom (H2O).

radio waves Waves in a part of the electromagnetic spectrum they are a type that people now use for long-distance communication. Longer than the waves of visible light, radio waves are used to transmit radio and television signals it is also used in radar.

About Bethany Brookshire

Bethany Brookshire was a longtime staff writer at Science News for Students. She has a Ph.D. in physiology and pharmacology and likes to write about neuroscience, biology, climate and more. She thinks Porgs are an invasive species.

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Integration may provide spatiotemporal snapshot of brain

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The use of scalp electroencephalography (EEG) simultaneously with functional magnetic resonance imaging (fMRI) allows measurement of electrical brain activity in correlation with the hemodynamic response in the brain. Known as EEG-correlated fMRI, or simply EEG/fMRI, this noninvasive multimodal neuroimaging technique is being used at Cleveland Clinic’s Epilepsy Center in an effort to better understand the pathophysiologic mechanisms and patterns of epileptic activities, particularly the generators of interictal discharges (spikes).

Cleveland Clinic is one of only a few clinical centers in the United States to employ EEG/fMRI, which currently serves as a research tool in the study of brain regions involved at the time of epileptic activity.

Eventually, EEG/fMRI may become clinically valuable as a multimodal tool for evaluating individuals with epilepsy, including patients whose seizures are difficult to control with medications and in whom identifying the seizure focus is challenging. Localizing the brain regions that show changes in neuronal activity during interictal spikes through the use of fMRI may one day enhance the evaluation of surgical candidates and may help guide surgical strategies in patients with refractory seizures.

The software used to execute simultaneous EEG and fMRI has been approved by the U.S. Food and Drug Administration for research applications. Cleveland Clinic is in a unique position to validate the clinical use of EEG/fMRI because of the high volume of evaluations and surgeries it performs in patients with seizures refractory to medications.

A Spatiotemporal Snapshot of Brain Activity

Integrating data obtained from EEG/fMRI may provide a spatiotemporal snapshot of brain activity that is not available through either modality alone (see Figures).

FIGURE 1. Schematic illustration of cortical activation revealed with functional MRI within the left basal frontal lobe and anterior insula. Areas of interest are superimposed on sagittal and axial images of the patient’s structural MRI. Red indicates activation green indicates deactivation.

Schematic illustration of an EEG spike predominantly involving EEG electrodes recording from the left frontal and central regions of the patient’s brain. During simultaneously recorded EEG/fMRI, correlation is sought between the time of EEG spike and the brain activation pattern.

With EEG, temporal resolution is excellent because it measures electrical activity in the brain directly, but spatial resolution is poor. Therefore, the accuracy of EEG in localizing the neuronal source from measurements of voltages at the scalp is limited. In contrast, spatial localization of brain activity is much better with fMRI, but temporal resolution is poor. fMRI measures brain activity by detecting associated changes in blood flow. These differing profiles make the two techniques complementary for measuring brain function.

With EEG/fMRI, MRI-compatible EEG electrodes are attached to the patient’s head outside the MRI scanner. Once the patient enters the scanner, these electrodes are connected to an amplifier in the MRI suite and to a recording computer outside the scanner room using a fiber-optic cable. This configuration helps to ensure patient safety during acquisition of the EEG/fMRI study.

Because patients must be placed inside the scanner for this procedure, the duration of the recording is limited to about one hour, so capturing activity during an actual seizure is rare. This duration is usually sufficient, however, to capture several interictal epileptic spikes and record the timing of these activities.

The simultaneous acquisition of data using EEG and fMRI allows measurement of blood oxygen levels in specific brain regions to be correlated with the spike activity, offering evidence of the origin and spread pattern of each spike. The hemodynamic response in the brain is referred to as the blood-oxygen-level-dependent (BOLD) effect. Multiple spikes originating from the same brain region provide important localizing information and represent a strong indication that the epilepsy is focal and potentially amenable to surgical therapy.

Raw EEG data acquired in a 3T Siemens MRI scanner before artifact removal. EEG data after artifact removal showing normal brain activity during wakefulness along with eye movement potentials, which are distributed, as expected, over the most anterior frontal EEG electrodes.

Cleaning Up Signal Artifacts

The EEG recording environment in the MRI scanner is electromagnetically noisy because of the inductive effects of strong switching magnetic gradient fields. Removing artifacts from the EEG recording can be accomplished through several methods that use software to filter or clean up the signal (see Figures). The artifact corrected EEG tracing is reviewed to determine the exact timing of epileptic spikes. The timing is then correlated to changes in the fMRI BOLD signal, which measures the corresponding hemodynamic response.

Studies of focal epileptic spikes caused by different types of brain pathologies have shown reliable activations in the fMRI BOLD signal within the expected location of the epileptogenic focus. In addition, these studies reveal areas of activation and deactivation at locations distant from the pathological focus, and thus provide a unique glimpse into the underlying networks of brain activity. The significance of distant responses in the study of brain connectivity and pathological epileptic networks is one of the issues under active investigation at Cleveland Clinic’s Epilepsy Center.

BOLD response recorded during an EEG/fMRI session. At the time of interictal epileptic spikes, the left anterior insula showed prominent cortical activation (circle), localizing the metabolic origin of the spikes. The posterior BOLD changes are expected in some patients undergoing EEG/fMRI and are not directly related to the origin of the patient’s epilepsy. EEG recorded simultaneously with the fMRI, with artifacts removed offline. The spike predominantly involved EEG electrodes recording from the left temporal region of the patient’s brain, concordant with the cortical activation shown by fMRI.

Dr. Alexopoulous is a neurologist in Cleveland Clinic’s Epilepsy Center. His specialty interests are adult and geriatric epilepsy, seizure manifestations, medical and surgical treatment of seizure disorders, clinical neurophysiology, electroencephalography (EEG), magnetoencephalography (MEG), video-EEG, epilepsy surgery, multimodality non invasive investigations in patients with epilepsy, functional MRI (fMRI), EEG/fMRI, intracranial EEG monitoring for presurgical evaluation, neurostimulation, advancements in noninvasive diagnosis and management of patients with epilepsy.

Dr. Najm is the Director of the Epilepsy Center. His specialty interests are medical and surgical management of adult and geriatric epilepsy, malformations of cortical dysplasia, basic mechanisms of epilepsy, post-traumatic epilepsy.


MRI scanners built for two push limits of neuroimaging

The dark, thumping cavern of an MRI scanner can be a lonely place. How can scientists interested in the neural activity underlying social interactions capture an engaged, conversing brain while its owner is so isolated? Two research teams are advancing a curious solution: squeezing two people into one scanner.

One such MRI setup is under development with new funding from the U.S. National Science Foundation (NSF), and another has undergone initial testing described in a preprint last month. These designs have yet to prove that their scientific payoff justifies their cost and complexity, plus the requirement that two people endure a constricted almost-hug, in some cases for 1 hour or more. But the two groups hope to open up new ways to study how brains exchange subtle social and emotional cues bound up in facial expressions, eye contact, and physical touch. The tool could “greatly expand the range of investigations possible,” says Winrich Freiwald, a neuroscientist at Rockefeller University. “This is really exciting.”

Functional magnetic resonance imaging (fMRI), which measures blood oxygenation to estimate neural activity, is already a common tool for studying social processes. But compared with real social interaction, these experiments are “reduced and artificial,” says Lauri Nummenmaa, a neuroscientist at the University of Turku in Finland. Participants often look at static photos of faces or listen to recordings of speech while lying in a scanner. But photos can’t show the subtle flow of emotions across people’s faces, and recordings don’t allow the give and take of real conversation.

So researchers have crafted real-time encounters in the scanner. In 2002, neuroscientist Read Montague and colleagues at Baylor College of Medicine published the first of many studies to record simultaneously from people in separate, linked MRI machines. The approach can capture neural activity as people play an online game or communicate through an audio or video feed.

Even with that approach, “There’s a huge amount of interpersonal information filtered out,” says Ray Lee, a neuroscientist and MRI physicist at Columbia University. So over the past decade, he has been refining an fMRI setup for two. It requires a specialized pair of head coils that allows researchers to read separate signals from two adjacent brains. These cagelike metal coils encircle participants’ heads as they lie on their sides with their legs touching in the MRI magnet and gaze at each other through a window. In 2012, while at Princeton University, Lee and colleagues published the first paper on the device, which he estimates would cost $200,000 to provide to another lab.

Researchers can disentangle signals from adjacent brains to document the regions active while two people make eye contact.

A second two-person fMRI scanner, developed by Nummenmaa and colleagues in the lab of neuroscientist Riitta Hari at Aalto University in Finland, uses a different type and shape of head coil, but places participants in the same near-cuddling pose. (The team tried a less intimate, sphinxlike pose: bellies down, face to face. But it was “pretty bad for the neck,” Hari notes.)

In a 10 December 2019 bioRxiv preprint, the team describes an early test of the technology: recording neural activity while pairs of friends or intimate partners took turns tapping each other on the lips. With that task, the researchers could verify that the scanner picked up brain activity corresponding to both the touch of the taps and the sight of the tapping finger—along with the sound of recorded instructions.

Lee’s first research questions are also relatively simple: How does brain activity in the shared scanner differ from activity during a remote video connection? What brain networks light up when people make eye contact? He is still analyzing data and submitting publications from his 2012 setup, but in the fall of 2019, his team received nearly $1 million from NSF to design a coil with improved signal quality and scan more brains.

“If Ray can get this system working … he’s got a lot of room to grow,” says Ellen Carpenter, a neuroscientist and program director at NSF. Future studies could, for example, observe the brain as it picks up social cues and decides when and how to convey empathy to a scanner mate, she says.

Of course, researchers can already observe socializing brains by imaging them one at a time. A person being scanned can talk with or even touch a person directly outside the scanner. “Do you actually gain something from observing in real time how the activity is changing in the two brains?” Freiwald wonders. One issue is that fMRI is slow. The changes in blood oxygen that it measures happen on the scale of seconds, which means that in some cases, the precise relationship between the timing of neural firing in the two brains could elude the scanner.

Others say the cozy MRI setup itself could limit the research. “This is more than face to face,” says Uri Hasson, a neuroscientist at Princeton. “You lie next to very particular people in your life.” With other people, the experience could feel threatening. “Have you ever stood in front of a stranger 3 inches from their nose? Probably not on purpose,” says Montague, now at Virginia Polytechnic Institute and State University. “I don’t know where it’s going,” he says of the approach. “On the other hand, I’m a big proponent of the renegade maverick that [does] what they want to do.”

Despite their limitations, Lee thinks two-person MRI scanners will capture aspects of socializing brains long overlooked by neuroimaging. He plans to look at differences in the brain dynamics of children with and without autism as they make eye contact and interact with a parent in the scanner. He expects his first subjects will be sliding into the magnet together by this fall.


Facilities and capabilities

The center boasts the unique capability to simultaneously capture functional magnetic resonance imaging (fMRI), record brain electrical activity and track eye movement. This combination of brain imaging and cognitive assessment equipment could provide groundbreaking findings about brain function’s influence on behavior and performance.


Recording policies in functional magnetic resonance imaging - Biology

EEG, PET, MRI, and fMRI scan the brain through a variety of methods and have varying degrees of specificity and invasiveness.

Learning Objectives

Compare the methods researchers can use to image the brain

Key Takeaways

Key Points

  • Neuroimaging, or brain scanning, includes the use of various techniques to either directly or indirectly image the structure, function, or pharmacology of the brain.
  • Neuroimaging falls into two broad categories: structural imaging and functional imaging.
  • Electroencephalography (EEG) is used to show brain activity under certain psychological states, such as alertness or drowsiness.
  • Positron emission tomography (PET) scans show brain processes by using the sugar glucose in the brain to illustrate where neurons are firing.
  • Magnetic resonance imaging (MRI) scans use echo waves to discriminate among grey matter, white matter, and cerebrospinal fluid.
  • Functional magnetic resonance imaging (fMRI) scans are a series of MRIs measuring brain function via a computer’s combination of multiple images taken less than a second apart.

Key Terms

  • conductivity: The ability of a material to conduct electricity, heat, fluid, or sound.
  • magnetic field: A condition in the space around a magnet or electric current in which there is a detectable magnetic force and two magnetic poles are present.

Neuroimaging, or brain scanning, includes the use of various techniques to directly or indirectly image the structure, function, or pharmacology of the brain. It is a relatively new discipline within medicine, neuroscience, and psychology. Physicians who specialize in the performance and interpretation of neuroimaging in the clinical setting are known as neuroradiologists.

Neuroimaging falls into two broad categories:

  1. Structural imaging, which deals with the structure of the brain and the diagnosis of large-scale intracranial disease (such as a tumor), as well as injury.
  2. Functional imaging, which is used to diagnose metabolic diseases and lesions on a finer scale (such as Alzheimer’s disease), and also for neurological and cognitive-psychology research. Functional imaging allows the brain’s information processing to be visualized directly, because activity in the involved area of the brain increases metabolism and “lights up” on the scan.

Four of the most common types of brain scans are EEG, PET, MRI, and fMRI.

Electroencephalography (EEG)

Electroencephalography (EEG) is used to show brain activity in certain psychological states, such as alertness or drowsiness. It is useful in the diagnosis of seizures and other medical problems that involve an overabundance or lack of activity in certain parts of the brain.

To prepare for an EEG, electrodes are placed on the face and scalp. After placing each electrode in the right position, the electrical potential of each electrode can be measured. According to a person’s state (waking, sleeping, etc.), both the frequency and the form of the EEG signal differ. Patients who suffer from epilepsy show an increase of the amplitude of firing visible on the EEG record. The disadvantage of EEG is that the electric conductivity —and therefore the measured electrical potentials—may vary widely from person to person and also over time, due to the natural conductivities of other tissues such as brain matter, blood, and bones. Because of this, it is sometimes unclear exactly which region of the brain is emitting a signal.

EEG recording: To prepare for an EEG, electrodes are placed on the face and scalp.

Positron Emission Tomography (PET)

Positron emission tomography (PET) scans measure levels of the sugar glucose in the brain in order to illustrate where neural firing is taking place. This works because active neurons use glucose as fuel. As part of the scan, a tracer substance attached to radioactive isotopes is injected into the blood. When parts of the brain become active, blood (which contains the tracer) is sent to deliver oxygen. This creates visible spots, which are then picked up by detectors and used to create a video image of the brain while performing a particular task. However, with PET scans, we can only locate generalized areas of brain activity and not specific locations. In addition, PET scans are costly and invasive, making their use limited. However, they can be used in some forms of medical diagnosis, including for Alzheimer’s.

PET scanner: This is a view of the PET scanner from the outside the radiation detectors are under the covering panel.

Magnetic Resonance Imaging (MRI)

Magnetic resonance imaging (MRI) and functional magnetic resonance imaging (fMRI) scans are the form of neural imaging most directly useful to the field of psychology.

An MRI uses strong magnetic fields to align spinning atomic nuclei (usually hydrogen protons) within body tissues, then disturbs the axis of rotation of these nuclei and observes the radio frequency signal generated as the nuclei return to their baseline status. Through this process, an MRI creates an image of the brain structure. MRI scans are noninvasive, pose little health risk, and can be used on infants and in utero, providing a consistent mode of imaging across the development spectrum. One disadvantage is that the patient has to hold still for long periods of time in a noisy, cramped space while the imaging is performed.

Brain MRI: MRI brain scan (in the axial plane—that is, slicing from front-to-back and side-to-side through the head) showing a brain tumor at the bottom right.

The fMRI is a series of MRIs that measures both the structure and the functional activity of the brain through computer adaptation of multiple images. Specifically, the fMRI measures signal changes in the brain that are due to changing neural activity. In an fMRI, a patient can perform mental tasks and the area of action can be detected through blood flow from one part of the brain to another by taking pictures less than a second apart and showing where the brain “lights up.” For example, when a person processes visual information, blood rushes to the back of the brain, which is where the occipital lobe is located. FMRIs make it possible to show when things happen, how brain areas change with experience, and which brain areas work together. They have been used to study a wide range of psychological phenomena, including (but by no means limited to) the neural activity of telling a lie, the differences between novices and experts when playing a musical instrument, and what happens inside our heads when we dream.

An fMRI of the brain: An fMRI scan showing regions of activation (in orange) including the primary visual cortex.


Recording policies in functional magnetic resonance imaging - Biology

The overall goal of the MRI facility is to provide high resolution/high-throughput imaging and equipment/pulse sequences, delivering sufficient signal-to-noise ratios ( SNR ) as to be able to test novel molecularly targeted MRI agents. The high-field magnet operates at 4.7 Tesla field strength, providing the optimal setup to image both T1 and T2/T2* targeting imaging probes. Furthermore, the magnet facilitates state-of-the art high resolution anatomical and functional imaging of various mouse models for cancer, cardiovascular and neuro-research.

We use tailored MR pulse sequences and high-end, dedicated radio frequency (RF) coils, ranging in size from whole body (rat) to mouse heart, in order to to optimize SNR for each specific application.

To ensure imaging occurs under normal physiologic conditions and to optimize anesthesia, dedicated monitoring systems are used to record the heart and respiratory rate as well as body temperature. The latter is kept within a physiological range through the use of MR-compatible heating systems.


Types of Brain Imaging Techniques

Brain imaging techniques allow doctors and researchers to view activity or problems within the human brain, without invasive neurosurgery. There are a number of accepted, safe imaging techniques in use today in research facilities and hospitals throughout the world.

Functional magnetic resonance imaging, or fMRI, is a technique for measuring brain activity. It works by detecting the changes in blood oxygenation and flow that occur in response to neural activity &ndash when a brain area is more active it consumes more oxygen and to meet this increased demand blood flow increases to the active area. fMRI can be used to produce activation maps showing which parts of the brain are involved in a particular mental process.

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&rsquos 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.

Positron 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.


MATERIALS AND METHODS

Optically pumped atomic magnetometer

The magnetometer is based on a pump-probe scheme to polarize the cesium atomic spins and monitor the Larmor precession. The pump laser is circularly polarized and has a 1/e 2 diameter of

2.7 mm. The central frequency of the pump laser is locked to the D1 transition line (from 6 2 S1/2 F = 3 to 6 2 P1/2 F′ = 4, where F and F′ are the total angular momentum numbers) with dichroic atomic vapor laser lock. The amplitude of the pump beam is modulated with an acoustic-optical modulator at the Larmor frequency. The modulation duty cycle is 20%. The averaged power of the pump laser is

50 μW. The probe laser is linearly polarized and has a 1/e 2 diameter of

1.1 mm. The power of the probe laser is

50 μW. The central frequency of the probe laser is positively detuned by

400 MHz from the D2 transition line (from 6 2 S1/2 F = 4 to 6 2 P3/2 F′ = 5). The cesium vapor cell is antirelaxation-coated and is kept at room temperature, with a typical magnetic resonance line width of

5 Hz. The diameter and the length of the cylinder vapor cell are both 25 mm. The vapor cell, including all the optical components, such as the polarizers, wave plates, mirrors, and the Wollaston prism, is mounted in a three-dimensional printed structure, which has a size of 5 cm by 24 cm by 27 cm. The pump and probe laser beams are coupled into the magnetic sensor with optical fibers. The transmitted probe laser from the vapor cell is fiber-coupled to the sensor and then detected with a balanced photodetector. The output signal from the balanced photodetector is demodulated with a lock-in amplifier (Stanford Research Systems, SR865A, LIA), from which the in-phase component amplitude is proportional to the difference between the Larmor frequency and the modulation frequency of the pump laser.

Frequency response of the atomic magnetometer

To measure the frequency responses of the magnetometers, we use a pair of Helmholtz coils, which has a diameter of 30 cm and is connected in series with a resistance of 500 ohm and is driven with a signal generator (Keysight, 53230A), to generate a sinusoidal magnetic field with an amplitude of 3.7 nT. The readouts of the two magnetometers, together with the sinusoidal signal from the signal generator, are recorded simultaneously with a data acquisition card (National Instruments, USB6363) at a sampling rate of 40 kSa/s. The readouts are demodulated at the frequency of the applied sinusoidal signal to extract the amplitude and phase shift relative to the sinusoidal signal. The frequency responses of the two magnetometers are thus obtained by scanning the modulation frequency from 1 to 2010 Hz and repeating the above measurement procedures. Similarly, we get the amplitude-frequency characteristics of the gradiometer by demodulating the difference of the two OPM sensors’ readouts at the frequency of the applied sinusoidal signal. The frequency dependence of the CMRR of the gradiometer is thus obtained by dividing the amplitude-frequency characteristic of OPM1 by that of the gradiometer.

Magnetic field stabilization

The magnetic noise is compensated using OPM2 and a pair of vertical coils. We use OPM2 as a reference magnetometer to monitor the magnetic field fluctuations. The measured signal from OPM2 is fed into a PID controller (Stanford Research Systems, SIM960), from which the output signal is used to control the current added into the coils. To characterize the ability of rejecting the common-mode magnetic field noise of the field stabilization, we monitor the residual magnetic noise with OPM1. We use the same coils as those for measuring the frequency response to add a white magnetic field noise with a bandwidth of 200 Hz and an amplitude of 58 pT/Hz 1/2 to both of the two OPMs and record the readout of OPM1 at a sampling rate of 40 kSa/s. We divide the noise spectrum density of OPM1 obtained under two different conditions, i.e., without and with field stabilization, to derive the CMRR of the field stabilization.

Measurement of the spontaneous alpha rhythm signal

Each measurement takes 180 s. To avoid the problem of synchronization, the person is asked to open (close) his eyes before recording the data and keep his eyes open (closed) until the recording is finished. The multifunction input/output device USB6363 (National Instruments) is used for data acquisition and is controlled with a LabVIEW program. To further confirm that the peak in Fig. 2A around 10 Hz is related to closing eyes, the participant is required to repeat closing and opening his eyes every 30 s to modulate the alpha rhythm signal. We set a 30-s timer around the unshielded MEG system and generate a tinkling sound every 30 s. The person then opens or closes his eyes once hearing this sound.

Measurement of the AEF signal

For the AEF signal measurement, we need to know the precise time duration between the AEF signal and the auditory stimulus. To do so, we use the MATLAB program to generate auditory stimuli signals in advance and save the sound file to the computer. The time interval between each stimulus is randomly distributed between 0.7 and 1.7 s, and each stimulus is a 440-Hz sinusoidal wave with a time duration of 100 ms. Then, we use the LabVIEW program to play the generated sound file and record the measured magnetic field data at the same time. For each measurement, the time uncertainty between playing the sound and recording the data is less than 1 ms, which has negligible effects for the AEF signal measurement. The transmission of the sound between the loudspeaker and the person makes relatively large but constant time delay, which is

10 ms and can be compensated with proper data processing. The measured data are filtered with a 0.5- to ∼30-Hz band-pass filter.