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.
  • Computational anatomy toolbox a software package used for the analysis of structural brain imaging data
  • 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


References