Outline of brain mapping

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The following outline is provided as an overview of and topical guide to brain mapping:

Contents

Brain mapping set of neuroscience techniques predicated on the mapping of (biological) quantities or properties onto spatial representations of the (human or non-human) brain resulting in maps. Brain mapping is further defined as the study of the anatomy and function of the brain and spinal cord through the use of imaging (including intra-operative, microscopic, endoscopic and multi-modality imaging), immunohistochemistry, molecular and optogenetics, stem cell and cellular biology, engineering (material, electrical and biomedical), neurophysiology and nanotechnology.

Broad scope

The neuron doctrine

Map, atlas, and database projects

  • BigBrain A high-resolution 3D atlas of the human brain created as part of the HBP.

Imaging and recording systems

This section covers imaging and recording systems. The general section covers history, neuroimaging, and techniques for mapping specific neural connections. The specific systems section covers the various specific technologies, including experimental and widely deployed imaging and recording systems.

General

Specific systems

Imaging and recording componentry

Electrochemical

  • Haemodynamic response – the rapid delivery of blood to active neuronal tissues. Blood Oxygenation Level Dependent signal (BOLD), corresponds to the concentration of deoxyhemoglobin. The BOLD effect is based on the fact that when neuronal activity is increased in one part of the brain, there is also an increased amount of cerebral blood flow to that area. Functional magnetic resonance imaging is enabled by the detection of the BOLD signal.
  • Event-related functional magnetic resonance imaging can be used to detect changes in the Blood Oxygen Level Dependent (BOLD) hemodynamic response to neural activity in response to certain events.

Electrical

  • Event-related potential – positive and negative 10μ to 100μ Volts (μ is millionths) responses, measured via noninvasive electrodes attached to the scalp, that are the reliable and repeatable results of a certain specific sensory, cognitive, or motor event. These are also called a stereotyped electrophysiological response to a stimulus. They are called somatosensory evoked potentials when they are elicited by sensory (vs. cognitive or motor) event stimuli. The voltage swing sequences are recorded and broken down by positive and negative, and by how long after the stimulus they are observed. For example, [N100] is a negative swing observed between 80 and 120 milliseconds (100 being the midpoint) after the onset of the stimulus. Alternatively, the voltage swings are labeled based on their order, N1 being the first negative swing observed, N2 the second negative swing, etc. See: N100 (neuroscience), N200 (neuroscience), P300 (neuroscience), N400 (neuroscience), P600 (neuroscience). The first negative and positive swings (see Visual N1, C1 and P1 (neuroscience)) in response to visual stimulation are of particular interest in studying sensitivity and selectiveness of attention.

Electromagnetic

  • Magnetoencephalography – a technique for mapping brain activity by recording magnetic fields produced by electrical currents occurring naturally in the brain, using very sensitive magnetometers In research, MEG's primary use is the measurement of time courses of activity. MEG can resolve events with a precision of 10 milliseconds or faster, while functional MRI (fMRI), which depends on changes in blood flow, can at best resolve events with a precision of several hundred milliseconds. MEG also accurately pinpoints sources in primary auditory, somatosensory and motor areas. For creating functional maps of human cortex during more complex cognitive tasks, MEG is most often combined with fMRI, as the methods complement each other. Neuronal (MEG) and hemodynamic (fMRI) data do not necessarily agree, in spite of the tight relationship between local field potentials (LFP) and blood oxygenation level dependent (BOLD) signals

Radiological

  • Positron-emitting radionuclide (tracer). See Positron emission tomography
  • Altanserin – a compound that binds to a serotonin receptor. When labeled with the isotope fluorine-18 it is used as a radioligand in positron emission tomography (PET) studies of the brain.

Visual processing and image enhancement

  • Scientific visualization – an interdisciplinary branch of science primarily concerned with the visualization of three-dimensional phenomena (including medical, biological, and others), where the emphasis is on realistic renderings of volumes, surfaces, illumination sources, and so forth, perhaps with a dynamic (time) component. It is considered a branch of computer science that is a subset of computer graphics. Brain mapping is a leading beneficiary of advances in scientific visualization.
  • Blob detection – an area in computer vision, A blob is a region of a digital image in which some properties (such as brightness or color, compared to areas surrounding those regions) are constant or vary within a prescribed range of values; all the points in a blob can be considered in some sense to be similar to each other

Information technology

  • Determining the number of clusters in a data set – a typical application is in data reduction: as the increase in temporal resolution of fMRI experiments routinely yields fMRI sequences containing several hundreds of images, it is sometimes necessary to invoke feature extraction to reduce the dimensionality of the data space.
  • Fractional anisotropy – a measure often used in diffusion imaging where it is thought to reflect fiber density, axonal diameter, and myelination in white matter. The FA is an extension of the concept of eccentricity of conic sections in three dimensions, normalized to the unit range. Anisotropy is the property of being directionally dependent, as opposed to isotropy, which implies identical properties in all directions.
  • General linear model – a statistical linear model. It may be written as Y=XB +U where Y is a matrix with series of multivariate measurements, X is a matrix that might be a design matrix, B is a matrix containing parameters that are usually to be estimated, and U is a matrix containing errors or noise. It is frequently used in the analysis of multiple brain scans in scientific experiments where Y contains data from brain scanners, X contains experimental design variables and confounds. See also: statistical parametric mapping
  • Resampling (statistics) see section on permutation tests. Nonparametric Permutation Tests are used in fMRI.

Software packages

  • Analysis of Functional NeuroImages – an open-source environment for processing and displaying functional MRI data
  • Cambridge Brain Analysis – a software repository developed at University of Cambridge for functional magnetic resonance imaging (fMRI) analysis under the GNU General Public License and runs under Linux.
  • Statistical parametric mapping – a statistical technique for examining differences in brain activity recorded during functional neuroimaging experiments using neuroimaging technologies such as fMRI or PET. It may also refer to a specific piece of software created by the Wellcome Department of Imaging Neuroscience (part of University College London) to carry out such analyses.
  • ITK-SNAP an interactive software application that allows users to navigate three-dimensional medical images, manually delineate anatomical regions of interest, and perform automatic image segmentation. Its most frequently used to work with magnetic resonance imaging (MRI) and computed tomography (CT) data sets.
  • The Budapest Reference Connectome server generates consensus braingraphs with selectable parameters; the graphs can be downloaded in annotated GraphML format, and can also be viewed instantly on the site.

Scientists, academics and researchers

Journals

See also

See also categories

Notes and references

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    <span class="mw-page-title-main">Cognitive neuroscience</span> Scientific field

    Cognitive neuroscience is the scientific field that is concerned with the study of the biological processes and aspects that underlie cognition, with a specific focus on the neural connections in the brain which are involved in mental processes. It addresses the questions of how cognitive activities are affected or controlled by neural circuits in the brain. Cognitive neuroscience is a branch of both neuroscience and psychology, overlapping with disciplines such as behavioral neuroscience, cognitive psychology, physiological psychology and affective neuroscience. Cognitive neuroscience relies upon theories in cognitive science coupled with evidence from neurobiology, and computational modeling.

    <span class="mw-page-title-main">Magnetoencephalography</span> Mapping brain activity by recording magnetic fields produced by currents in the brain

    Magnetoencephalography (MEG) is a functional neuroimaging technique for mapping brain activity by recording magnetic fields produced by electrical currents occurring naturally in the brain, using very sensitive magnetometers. Arrays of SQUIDs are currently the most common magnetometer, while the SERF magnetometer is being investigated for future machines. Applications of MEG include basic research into perceptual and cognitive brain processes, localizing regions affected by pathology before surgical removal, determining the function of various parts of the brain, and neurofeedback. This can be applied in a clinical setting to find locations of abnormalities as well as in an experimental setting to simply measure brain activity.

    <span class="mw-page-title-main">Functional magnetic resonance imaging</span> MRI procedure that measures brain activity by detecting associated changes in blood flow

    Functional magnetic resonance imaging or functional MRI (fMRI) measures brain activity by detecting changes associated with blood flow. This technique relies on the fact that cerebral blood flow and neuronal activation are coupled. When an area of the brain is in use, blood flow to that region also increases.

    The following outline is provided as an overview of and topical guide to neuroscience:

    <span class="mw-page-title-main">Functional neuroimaging</span>

    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.

    Systems neuroscience is a subdiscipline of neuroscience and systems biology that studies the structure and function of neural circuits and systems. Systems neuroscience encompasses a number of areas of study concerned with how nerve cells behave when connected together to form neural pathways, neural circuits, and larger brain networks. At this level of analysis, neuroscientists study how different neural circuits analyze sensory information, form perceptions of the external world, make decisions, and execute movements. Researchers in systems neuroscience are concerned with the relation between molecular and cellular approaches to understanding brain structure and function, as well as with the study of high-level mental functions such as language, memory, and self-awareness. Systems neuroscientists typically employ techniques for understanding networks of neurons as they are seen to function, by way of electrophysiology using either single-unit recording or multi-electrode recording, functional magnetic resonance imaging (fMRI), and PET scans. The term is commonly used in an educational framework: a common sequence of graduate school neuroscience courses consists of cellular/molecular neuroscience for the first semester, then systems neuroscience for the second semester. It is also sometimes used to distinguish a subdivision within a neuroscience department in a university.

    Neuroimaging is a medical technique that allows doctors and researchers to take pictures of the inner workings of the body or brain of a patient. It can show areas with heightened activity, areas with high or low blood flow, the structure of the patients brain/body, as well as certain abnormalities. Neuroimaging is most often used to find the specific location of certain diseases or birth defects such as tumors, cancers, or clogged arteries. Neuroimaging first came about as a medical technique in the 1880's with the invention of the human circulation balance and has since lead to other inventions such as the x-ray, air ventriculography, cerebral angiography, PET/SPECT scans, magnetoencephalography, and xenon CT scanning.

    <span class="mw-page-title-main">Neural circuit</span> Network or circuit of neurons

    A neural circuit is a population of neurons interconnected by synapses to carry out a specific function when activated. Multiple neural circuits interconnect with one another to form large scale brain networks.

    Functional integration is the study of how brain regions work together to process information and effect responses. Though functional integration frequently relies on anatomic knowledge of the connections between brain areas, the emphasis is on how large clusters of neurons – numbering in the thousands or millions – fire together under various stimuli. The large datasets required for such a whole-scale picture of brain function have motivated the development of several novel and general methods for the statistical analysis of interdependence, such as dynamic causal modelling and statistical linear parametric mapping. These datasets are typically gathered in human subjects by non-invasive methods such as EEG/MEG, fMRI, or PET. The results can be of clinical value by helping to identify the regions responsible for psychiatric disorders, as well as to assess how different activities or lifestyles affect the functioning of the brain.

    <span class="mw-page-title-main">Neuroimaging</span> Set of techniques to measure and visualize aspects of the nervous system

    Neuroimaging is the use of quantitative (computational) techniques to study the structure and function of the central nervous system, developed as an objective way of scientifically studying the healthy human brain in a non-invasive manner. Increasingly it is also being used for quantitative research studies of brain disease and psychiatric illness. Neuroimaging is highly multidisciplinary involving neuroscience, computer science, psychology and statistics, and is not a medical specialty. Neuroimaging is sometimes confused with neuroradiology.

    Brain mapping is a set of neuroscience techniques predicated on the mapping of (biological) quantities or properties onto spatial representations of the brain resulting in maps.

    Event-related functional magnetic resonance imaging (efMRI) is a technique used in magnetic resonance imaging of medical patients.

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    Broadly defined, positive neuroscience is the study of what the brain does well. Instead of studying mental illness, positive neuroscientists focus on valued cognitive qualities that serve to enrich personal life and/or society. Topics in positive neuroscience overlap heavily with those of positive psychology, but use neuroimaging techniques to extend beyond the behavioral level and explain the neurobiology which underpins "positive" cognitive phenomena such as intelligence, creativity, optimism, and healthy aging.

    Robert Turner is a British neuroscientist, physicist, and social anthropologist. He has been a director and professor at the Max Planck Institute for Human Cognitive and Brain Sciences in Leipzig, Germany, and is an internationally recognized expert in brain physics and magnetic resonance imaging (MRI). Coils inside every MRI scanner owe their shape to his ideas.

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    Bruce Rosen is an American physicist and radiologist and a leading expert in the area of functional neuroimaging. His research for the past 30 years has focused on the development and application of physiological and functional nuclear magnetic resonance techniques, as well as new approaches to combine functional magnetic resonance imaging (fMRI) data with information from other modalities such as positron emission tomography (PET), magnetoencephalography (MEG) and noninvasive optical imaging. The techniques his group has developed to measure physiological and metabolic changes associated with brain activation and cerebrovascular insult are used by research centers and hospitals throughout the world.

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    <span class="mw-page-title-main">Russell Poldrack</span>

    Russell "Russ" Alan Poldrack is an American psychologist and neuroscientist. He is a professor of psychology at Stanford University, associate director of Stanford Data Science, member of the Stanford Neuroscience Institute and director of the Stanford Center for Reproducible Neuroscience and the SDS Center for Open and Reproducible Science.