Scientific Understanding of Consciousness
Consciousness as an Emergent Property of Thalamocortical Activity

Brain Imaging

Current technology for brain imaging studies of consciousness is only crudely productive. The agglomeration of the most incisive of these techniques provide only vague hints of the information flows and processing of consciousness.


A major challenge in neuroscience is to decipher the structural layout of the brain.


Research study — Brain Neuroscience Methods

Research study — Brain Imaging Challenges

Link to — Coordinates in the Brain

Research study — Intracranial Markers of Conscious Access

Research study — Magnetic Resonance Fingerprinting  — The basic structure of a magnetic resonance experiment has remained largely unchanged for almost 50years. Here, researchers introduce ‘magnetic resonance fingerprinting’ (MRF)— a technique that permits non-invasive quantification of multiple important properties of tissue, potentially leading to new diagnostic testing methodologies

Research study — Imaging Large Molecular Complexes via cryo-EM and Computer Processing

Research study — fMRI Imaging of Dopaminergic Signaling


Current imaging techniques are inadequate to capture the recruitment of, say, 10 million cells or more in less than a quarter second and their equally rapid disbanding. (Greenfield; Private Life of Brain, 183)


Brain Imaging Requirements for Consciousness Studies

I can make some crude estimates of what would be desired for information flows and processing for consciousness.

First, we would like to measure the information in the dynamic core and the changes in that information that relate to consciousness. A cubic millimeter of cortex is a good candidate for the size of a computational unit. Take the area of the cortex as 2200 cm2. Assume that each of the six layers represents statistically independent information. The number of information nodes is then

Cortical area granularity of 1 mm2, for all six layers,

Bandwidth centered around 40 Hz, perhaps 35 to 45 Hz,

Spike rate, 5 to 500 spikes/sec, precision about 4 bits.

Fully mature cerebral cortex, mean surface area, Two-thirds of the cortex is hidden in sulci, or fissures. (Changeux; Neuronal Man, 45)

An Ideal Neural Signal Data Recorder

What is the spatial scale in which the subjective just-noticeable differences of spatial location are realized within the phenomenal level?  We may speculate that it must be courser than the spatial scale of single neurons, but certainly much finer than the scale of 1 mm3. (Revonsuo; Inner Presence, 345)

An ideal neural signal data recorder would sample data at the rate of 100 Hz, and could resolve spatial details of activity in volumes of space around 10-4mm3. (Revonsuo; Inner Presence, 345)

An ideal neural signal data recorder would collect signals at the levels where organized electrophysiological patterns are realized in recurrent loops of coherent activity. (Revonsuo; Inner Presence, 345)

An ideal neural signal data recorder would collect signals from a wide range of different frequencies across the whole brain, especially in corticocortical and thalamocortical loops. (Revonsuo; Inner Presence, 346)


Diagram — Confocal Microscopy


Brain Scans

Two types of brain scan: (1) those that respond to some aspect of the static structure of the brain and (2) those that detect activity. CAT scan uses X-rays. MRI records the density of protons, especially sensitive to water, static, do not register activity. (Crick; Astonishing Hypothesis, 115)

Brain imaging techniques (Purves; Neuroscience, 25)

Overall speed of the rostrocaudal scan, which averaged approximately 12.5 msec, corresponded quite closely to half a 40-Hz period. This number is the same as that calculated for a quantum of consciousness in psychophysical studies in the auditory system. (Koch; Large-Scale Neuronal Theories of the Brain; Llinás; Perception as Oneiric-like, 120)

Functional Magnetic Resonance Imaging fMRI

Functional magnetic resonance imaging has become an incisive way to probe the functions of the brain. fMRI is supplemented by traditional techniques, EEG, CAT, PET, fMRI, MEG.

Link to — fMRI Technology Update

Functional Neuroimaging, (Laureys,; Functional Neuroimaging, 31)

When neurons become active, they need more oxygen and glucose. Measure the increased blood flow with PET scans and functional MRI. (Calvin; Neil’s Brain, 107)

Development of MRI and the early 1980s. (Miller; Human Frontal Lobes, 5)

Neuroimaging, PET (positron emission tomography), fMRI (functional magnetic resonance imaging) (Llinás; I of the Vortex, 187)

Exuberant cortical activity does not generate consciousness. (Koch; Quest for Consciousness, 275)


Current imaging techniques are inadequate to capture the recruitment of, say, 10 million cells or more in less than a quarter second and their equally rapid disbanding. (Greenfield; Private Life of Brain, 182)

An especially exciting technique, the Brainbow genetic neuronal labling for analysis of neuronal circuitry,

has been developed by Jeff Lichtman at Harvard.

CT Brain Imaging

CT scanning involved the use of standard x-rays. (Miller; Human Frontal Lobes, 170)

Computed tomography (CT) became widely available in the late 1970s. (Miller; Human Frontal Lobes, 5)

Compared with MRI, CT images are usually lower in resolution. (Miller; Human Frontal Lobes, 170)

CT scans are relatively inexpensive and quick; a complete scan can be obtained in 15 minutes. (Miller; Human Frontal Lobes, 170)

CT scans are safe for patients with metal implants such as pacemakers. (Miller; Human Frontal Lobes, 170)


MRI Brain Imaging

Shows active regions of the brain. Does not vividly show connections between the active regions.

Most current MRI is performed using 1.5 T (tesla) magnets, newer machine using 3 T and 4 T magnets are now in use at many centers. With higher field strength come better signal-to-noise ratio and higher resolution, although images are more susceptible to artifacts induced by idiosyncrasies and variations in tissue. (Miller; Human Frontal Lobes, 165)

Research study — fMRI Description

Research study — fMRI Imaging Techniques

Research study — fMRI Causal Modelling and Brain Connectivity



Magnetoencephalography (Buzsáki - Rhythms of the Brain, 84)

The magnetic fields that emanate from the brain are only 100 millionth to one billionth of the strength of the Earth's magnetic field. (Buzsáki - Rhythms of the Brain, 84)

The sensor that can detect the weak magnetic signals emanating from the brain is known as a SQUID (superconducting quantum interference device), operating at a temperature of -270° C. (Buzsáki - Rhythms of the Brain, 84)

Liquid helium in the SQUID cools the coils to superconducting temperatures. (Buzsáki - Rhythms of the Brain, 84)

For magnetoencephalography, need many sensors around the head to increase spatial resolution. (Buzsáki - Rhythms of the Brain, 84)

For magnetoencephalography, detector coils are placed as close to each other as possible, forming a spherical honeycomb-like pattern concentric with the head. (Buzsáki - Rhythms of the Brain, 84)

Magnetoencephalographic (MEG) signal reflects mostly intracellular currents.

Spatial resolution of MEG is better than EEG mainly because the magnetic fields are not scattered and distorted by inhomogeneities in the skull and scalp. (Buzsáki - Rhythms of the Brain, 84)

Coherence measurements of MEG signals over the hold extent of the cerebral hemispheres indicates that significant coupling in the gamma frequency band is present in the waking brain as well is during REM sleep. (Buzsáki; Rhythms of the Brain, 243)


PET Scans

PET images, seeing words, hearing words, speaking words, generating words - (illustrations) (Calvin; Neil’s Brain, 52)


[paraphrase of (Koch; Large-Scale Neuronal Theories of the Brain;  Posner and Rothbart, Constructing Neuronal Theories of Mind, 187ff)]

Positron Emission Tomography (PET)

Positron emission tomography (PET) is a radioactive tracer method of measuring cerebral blood flow or metabolic activity that provides a means of tracing cerebral activity during sustained cognitive tasks. As used in studies, oxygen-15 labeled water injected into the bloodstream and is carried to various parts of the brain. The distribution of labeled isotope is monitored by radiation generated when positrons are absorbed. The radiation is sensed by an array of de­tectors. While the spatial resolution of this method is limited, the method becomes quite accurate when successive scans are compared. It is possi­ble to compare scans because the data acquired for blood flow images can be obtained within 40 sec. Blood flow activity can be localized to a few millimeters, and changes in activity during experimental tasks lasting less than a minute can be imaged.

The PET spatial imaging method applied to human studies often does not provide sufficient temporal precision for cognitive tasks, where resolution of 20-100 msec is frequently of importance. Event-related electrical activity recorded from the scalp of humans provides one method for providing high-resolution temporal information, although with limited spatial resolution. The use of event-related potentials (ERP) has been quite helpful in linking mental operations studied by chronometric methods to brain systems in general. By combining PET and ERP studies, the two techniques can complement each other.

(end of paraphrase)


Talairach Brain Coordinate System

Talairach coordinate system -- Talairach and Tournoux (1988), the most commonly used standard space, originally created for stereotactically based neurosurgery. (Miller; Human Frontal Lobes, 170)

Talairach grid is a coordinate system that places the brain into a rectangular grid system anchored to the location of the anterior commissure (AC), the posterior commissure (PC), and the outer boundaries of the brain. (Miller; Human Frontal Lobes, 170)

Talairach coordinate system requires that the image be spatially transformed and resampled, so that the line connecting the anterior and posterior commissioners (AC-PC line) is aligned horizontally and along the main horizontal plane of the Talairach reference system, and the interhemispheric fissure is aligned to match the central vertical plane of the system. (Miller; Human Frontal Lobes, 170)

‘Regions of Interest’ for Cortex

Cognitive neuroscientists are interested in how brain functions map onto the structure of the cortex. Regions of Interest (ROI) definitions.  A total of 47 ROIs. (Miller; Human Frontal Lobes, 170)



[paraphrase of Eichenbaum, Cognitive Neuroscience of Memory, 139ff]

Functional neuroimaging in humans, also single neuron probes in animals

Monitoring the ongoing operation of the cortical areas and related brain structures is accomplished using two research techniques: (1) functional neuroimaging methods in normal humans, and (2) recording the activity pat­terns of single neurons in animals.

The functional imaging studies in humans typically use either: (1) positron emission tomography (PET) or (2) functional magnetic resonance imaging (fMRI). The details of these methodologies are discussed in a number of references available via the internet. Both techniques involve measurements of blood flow and brain oxygen consumption, which provide good reflections of the activity level of brain areas encompassing several thousand neurons over a sec­ond-to-second time scale. By indicating, for example, when the medial tem­poral area becomes active, functional neuroimaging studies in humans can provide insight about the functional details of the hippocampal memory.

Single cell recording studies in animals, on the other hand, can provide an even closer look at the inner workings of the hippocampus. This method involves monitoring the action potentials of individual neurons and so allows a major increase in resolution of cellular activity within different parts of the medial temporal area, and even allows us to distinguish particular types of neurons within a specific brain structure. Also, this method has a greater resolution in time, allowing us to capture millisecond-to-millisecond computa­tions by the fundamental elements of neural processing. Thus, these two approaches have complementary strengths and limitations. The strength of functional imaging is that it allows the simultaneous examination of the entire system, but at only a gross level that tells us which structures are activated to major shifts in task demands. Single cell recording methods allow to monitor only one part of the system at any time, but offer insights into the fundamental coding properties of the units of neural computation.

Functional neuroimaging studies of the human hippocampal system

All imaging techniques involve a comparison of activation levels between two conditions, an experimental condition and a control condition. In memory studies, the experimental condition involves the critical memory demand under study, for example, memorizing word lists. The control condition involves the same perceptual and cognitive demands, except without the critical memory demand.

(end of paraphrase)




Continuing Development of Imaging Techniques

Extremely subtle variations in brain structure may be at the root of schizophrenia, autism, and other disorders of the nervous system. Recent developments in computer-aided microscopy offer further help in this research. In one example, a series of 3-D pictures of brain tissue is stained with three types fluorescent dyes to highlight both individual brain cells and the layered organization of the tissue. Software then combines the images into a single seamless composite of 43,500 separate snapshots, requiring 20 hours to acquire and occupying several gigabytes of disk storage space. (Technology Review, published by MIT, January 2007)


“A Better View of Brain Disorders”, Science, Vol 313, 8 September 2006, p.1376.

As imaging methods such as fMRI and PET make their way from lab to clinic, neurologists hope to make earlier and more accurate diagnoses of brain disorders. When magnetic resonance imaging (MRI) came into clinical use in the early 1980s, it gave neurologists more detailed snapshots of the brain's structure. Functional MRI (fMRI), a method used since the early 1990s to infer brain activity in studies of human cognition, now helps neurosurgeons map patients' brains before surgery, and raises the possibility of using fMRI to determine whether a patient in a vegetative state has conscious thought.


Link to — Pathology — Perception Software in Medical Imaging


Brain Research Techniques

In addition to the more recent imaging techniques, traditional techniques of brain research include:

· Classical methods of neuroanatomy: Use neuron and axon staining techniques to determine how the neurons and regions are connected. Pioneered this technique in the early twentieth century.

· Experimentally damage the part of the brain to be studied in research animals.

· Accidental wounds to the human brain can provide similar information. Wounds inflicted by warfare are a rich source of information.

· Brain regions damaged by stroke are also a rich source of information.

· Stimulate certain parts of the brain. This technique has been used as a byproduct of the procedure to locate the focus of epileptic seizures.

· Record the electrical activity of certain clusters of neurons. This technique was used by Hubel and Wiesel to research the visual system of a cat’s brain. They received a Nobel Prize for this work.



    Link to — Consciousness Subject Outline

    Further discussion — Covington Theory of Consciousness