Glossary

-A-

acetylcholine (ACh): An important neurotransmitter used throughout the central and peripheral nervous systems and at the neuromuscular junction. Within the brain, ACh projections from certain cell groups in the basal forebrain may stimulate widespread changes in blood flow.
action potential: A self-propagating wave of depolarization that travels down a neuronal axon.
adaptation: A change in the response to a stimulus following its repeated presentation.
adenosine triphosphate (ATP): A nucleotide containing three phosphate groups that is the primary energy source for cells in the human body.
aerobic glycolysis: The process, consisting of glycolysis, the TCA cycle, and the electron transport chain, that breaks down glucose in the presence of oxygen, resulting in a gain of 36 ATP molecules.
aliasing: The sampling of a signal at a rate insufficient to resolve the highest frequencies that are present. The energy at those frequencies becomes artifactually expressed at lower frequencies, distorting the measured signal.
alpha value: An a priori probability (e.g., 0.001) chosen as the threshold for statistical significance. If the probability that the data would be obtained under the null hypothesis is less than the alpha value (α), the data are considered to be statistically significant.
alternating design: A blocked design in which two conditions are presented one after another for the duration of the experimental run.
γ-aminobutyric acid (GABA): One of the most important inhibitory neurotransmitters.
anaerobic glycolysis: The conversion of glucose to lactate in the absence of oxygen.
anastomosis: The branching and reconnection of blood vessels.
anatomical ROI: A region of interest (ROI) chosen based on anatomical criteria.
angular momentum (J): A quantity given by multiplying the mass of a spinning body by its angular velocity.
anisotropic: Having different properties in different directions; often referenced in the context of anisotropic diffusion, where molecules tend to diffuse along one axis but not others.
anode: A source of positive charge or ions, and an attractor of free electrons.
antiparallel state: The high-energy state in which an atomic spin precesses around an axis that is antiparallel (i.e., opposite) to that of the main magnetic field.
apical dendrites: The dendrites that are distant from the neuronal cell body. For typical pyramidal cells in the cortex, the apical dendrites extend to the superficial layers of cortex, whereas the cell bodies are located in deeper layers.
apparent diffusion coefficient (ADC): The quantification of diffusivity assuming isotropic diffusion.
arachnoid: The middle membrane covering the brain; its name comes from its spider weblike appearance.
arterial spin labeling (ASL): A family of perfusion imaging techniques that measures blood flow by labeling spins with excitation pulses and then waiting for the labeled spins to enter the imaging plane before data acquisition.
arteries: Large, thick-walled blood vessels that carry oxygenated blood from the heart to the rest of the body.
arterioles: Small arteries.
ascending/descending slice acquisition: The collection of data in consecutive order such that slices are acquired sequentially from one end of the imaging volume to the other.
astrocyte: A type of glial cell that regulates the extracellular environment. It is the most prevalent glial cell type in the brain.
autoradiography: Imaging by injecting a radioactive substance into tissue, then exposing the tissue to X-ray-sensitive film.
averaged epoch: The result of averaging a large number of epochs that are time-locked to similar events.
axial: A horizontal view of the brain (along the x–y plane in MRI).
axon: A neuronal process that transmits an electrical impulse from the cell body to the synapse, performing a primarily transmissive function. A neuron typically has a single axon, which in some types of neurons can be extremely long and/or can branch profusely.
axon hillock: A region of the neuronal cell body located at the emergence of the axon. Changes in its electrical potential lead to the generation of action potentials.

-B-

B: The sum of all magnetic fields experienced by a spin.
B₀: The strong static magnetic field generated by an MRI scanner.
B_1eff: The effective magnetic field experienced by a spin system during excitation.
b factor: The degree of diffusion weighting applied within a pulse sequence.
balloon model: A model of the interaction between changes in blood volume and changes in blood flow associated with neuronal activity.
basal ganglia: A set of nuclei in the forebrain that includes the caudate, putamen, and globus pallidus.
base image: The image on which a statistical map is displayed, often a high-resolution anatomical image.
basis functions: A set of functions whose linear combination can take on a wide range of functional forms. In fMRI analyses, researchers often replace a single hemodynamic response function with basis functions in order to improve the flexibility of their design matrices.
beneficence: The principle that research protocols should maximize the potential benefits of research while minimizing the costs to any individual subject.
between-subjects manipulation: A manipulation in which different conditions are assigned to different subject groups.
bias field estimation: A technique for estimating inhomogeneities in the magnetic field based on intensity variations in collected images.
biofeedback: Providing an explicit indicator of some physiological process, such as the beating of the heart or activation within a particular brain region, so that an individual can attempt to regulate that activation or guide behavior.
biomarker: A phenotypic feature, whether physical, physiological, or behavioral, that provides a robust predictor of some experimentally or clinically important outcome.
biophysical property: A biological property (e.g., blood flow) whose physical parameters undergo measurable changes in response to internal processes (e.g., information processing).
Bloch equation: An equation that describes how the net magnetization of a spin system changes over time in the presence of a time-varying magnetic field.
block: A time interval that contains trials from one condition.
blocked design: The separation of experimental conditions into distinct blocks, so that each condition is presented for an extended period of time.
blood-oxygenation-level dependent (BOLD) contrast: The difference in signal on T₂*-weighted images as a function of the amount of deoxygenated hemoglobin.
bolus: A quantity of a substance that is introduced into a system and then progresses through that system over time.
Bonferroni correction: A stringent form of family-wise error rate correction for multiple comparisons in which the alpha value is decreased proportionally to the number of independent statistical tests.
brain extraction: A step during preprocessing that removes unwanted parts of the imaging volume, like bones and scalp, leaving only the desired brain tissue for subsequent analyses.
brain stem: The midbrain, pons, and medulla.
Brodmann areas: Divisions of the brain based on the influential cytoarchitectonic criteria of Korbinian Brodmann.

-C-

calcium-sensitive contrast agents: A type of contrast agent with its ability for signal enhancement triggered by binding to calcium ions (Ca²⁺).
capillaries: Small. thin-walled blood vessels. The extraction of oxygen and glucose from the blood and the removal of waste carbon dioxide occur in the capillaries.
categorical variable: A variable that can take one of several discrete values.
cathode: An attractor for positive charge or ions, and a source of free electrons.
caudal: Toward the back of the brain.
causality: The judgment that one event led to another. For fMRI data, measures of causality attempt to determine whether changes in the activation of one brain region led to changes in the activation in another region.
central autoregulation: Autonomic regulatory mechanisms that maintain a constant perfusion of the brain despite large variations in blood pressure that can occur over the course of a day.
central nervous system (CNS): The brain and spinal cord.
central sulcus: A deep fissure that separates the frontal and parietal lobes of the brain.
cerebellum: A large cortical structure at the caudal base of the brain that plays an important role in motor function.
cerebral blood volume (CBV) contrast: A type of fMRI contrast that is sensitized to the cerebral blood volume changes subsequent to brain activation.
cerebral cortex (neocortex): The thin wrapping of cells around the outer surface of the cerebral hemispheres. It has a layered structure, referred to as cortical columns or cortical layers.
cerebrospinal fluid (CSF): A colorless liquid that surrounds the brain and spinal cord and fills the ventricles within the brain.
cerebrum (cerebral hemispheres): The largest and most rostral component of the mammalian brain, composed of a left and a right hemisphere.
chemical shift imaging: A technique for measuring the concentration of particular chemicals, based on subtle differences in the resonance of the protons they contain.
circle of Willis: The interconnection between the basilar artery and the carotid arteries at the base of the cranial vault.
cluster-size thresholding: The adoption of a minimum size, in voxels, for a cluster of active voxels to be labeled as significant.
coactivation: The simultaneous activation of two or more brain regions within a single experimental task. Coactivation of brain regions does not imply that the regions are functionally connected.
collinear regressors: Model factors that are highly correlated with one another. The inclusion of collinear regressors reduces the validity of general linear model analyses.
color map: The association between numerical values of a parameter and a set of colors.
complex cell: A neuron in the visual cortex with a larger receptive field than a simple cell that responds to a stimulus with preferred orientation anywhere within its receptive field.
component: In the context of data-driven analyses, a feature of a data set that represents some aspect of its intrinsic structure.
compressed sensing: A new technique that takes sparse (i.e., underdetermined) data and, by estimating the sparseness of the data, reconstructs the original signal.
concentration gradient: A difference in the density of a substance across space. Substances diffuse along concentration gradients from areas of high concentration to areas of low concentration.
conditions (levels): Different values of an independent variable.
confounding factor: Any property that co-varies with the independent variable within the experiment but could be distinguished from the independent variable using a different experimental design.
consent form: A document that describes the procedures, risks, and benefits of a research study in clear language so that potential subjects can make an informed decision about participating.
construct: An abstract concept that explains behavior but that itself is not directly observable. Attention, for example, is a psychological construct.
continuous ASL: A type of perfusion imaging that uses a second transmitter coil to label spins within an upstream artery while collecting images.
continuous variable: A variable that can take any value within a range.
contrast: (1) The intensity difference between different quantities being measured by an imaging system. (2) The physical quantity being measured (e.g., T₁ contrast). (3) A statistical comparison of the activation evoked by two (or more) experimental conditions, in order to test a research hypothesis.
contrast agent: A substance injected into the body to increase image contrast.
contrast weights: A vector that expresses the predictions of a research hypothesis for the different regressors in a design matrix. When multiplied by the parameter weights from a fMRI regression analysis, the result can be evaluated for statistical significance.
contrast-to-noise ratio (CNR): The magnitude of the intensity difference between different quantities divided by the variability in their measurements.
control block: A time interval that contains trials of the control condition.
control condition: A condition that provides a standard to which the experimental condition(s) can be compared. Also called the baseline condition or the non-task condition.
converging operations: Employing two or more techniques to provide complementary evidence used to test an experimental hypothesis or scientific theory.
coregistration: The spatial alignment of two images or image volumes.
coronal: A frontal view of the brain (along the x–z plane in MRI).
corpus callosum: The large white-matter bundle that is the primary connection between the cerebral hemispheres. The anterior portion is known as the genu, the posterior portion as the splenium.
correlation analysis: A type of statistical test that evaluates the strength of the relation between two variables. For fMRI studies, correlation analyses typically evaluate the correspondence between a predicted hemodynamic response and the observed data.
correlation coefficient (r-value): A number between –1 and 1 that expresses the strength of the correlation between two variables.
cortex: The thin wrapping of cells around the outer surface of the brain.
cortical layers (cortical laminae): The six cellular layers of the neocortex, distinguished by differences in the types, densities, sizes, and shapes of their neurons.
cost function: A quantity that determines the amount of residual error in a comparison.
counterbalancing: A process for removing confounding factors by ensuring that they have equal influence on the different conditions of the independent variable, usually by matching values across conditions.
covariates: Regressors that can take any of a continuous range of values.
cross product: The vector product of two vectors. Its direction is perpendicular to the plane defined by those vectors, and its magnitude is given by multiplying their product times the sine of the angle between them.
cross-validation: In pattern classification analysis, an approach to evaluating the effectiveness of classification using a given feature set. It involves the iterated generation and testing of classifiers based on different parts of the same training set.
cryogens: Cooling agents used to reduce the temperature of the electromagnetic coils in an MRI scanner.
current dipole: An idealized pairing of a current source and a current sink separated by an infinitesimal distance. A current dipole is used as a simple and convenient model for the electromagnetic fields produced by an activated neuron.
current sink: An attractor of positive ions. A depolarized patch of neuronal membrane is a current sink because positively charged ions will flow toward it.
current source: A source of positive ions.
cytoarchitecture: The organization of the brain into physically distinguishable regions on the basis of cellular structure.

-D-

data-driven analysis: Drawing inferences based on examination of the intrinsic structure of data.
data matrix: A representation of the measured fMRI data in two-dimensional form (i.e., voxels by time points).
data reduction: The simplification of a data set by reducing its variability, such as by eliminating irrelevant, redundant, or nonpredictive variables.
deactivation: Decrease in BOLD activation during task blocks compared with non-task blocks.
dB/dt: The change in magnetic field strength (dB) over time (dt).
deception: The use of experimental procedures that intentionally mislead subjects.
default network: A set of brain regions whose activation tends to decrease during the performance of active, engaging tasks, but to increase during conditions of resting and reflection.
degrees of freedom (df): The number of independent observations within a data set. For many statistical tests, there are n – 1 degrees of freedom associated with n data points.
de-identification: Removal of information that may link research data or medical information to a particular individual.
dendrite: A neuronal process that receives signals from other cells. A neuron typically has multiple dendrites, which perform a primarily integrative function.
deoxygenated hemoglobin (dHb): Hemoglobin without attached oxygen; it is paramagnetic.
dependent variables (DVs): Quantities that are measured by the experimenter to evaluate the effects of the independent variables.
depolarization: A change in the cell membrane potential caused by admitting positive charge into the cell and thus reducing its negative resting potential.
descriptive statistics: Statistics that summarize the sample data but do not allow inferences about the larger population.
design matrix: In fMRI implementations of the general linear model, the specification of how the model factors change over time.
detection: Determination of whether activation within a given voxel changes in response to the experimental manipulation.
detector coil: An electromagnetic coil that measures energy emitted back to the environment after its initial absorption by the sample.
diamagnetic: A property of a substance that opposes a magnetic field (i.e., decreases the strength of the magnetic field).
diencephalon: Region of the brain lying just rostral to the midbrain and containing the hypothalamus and thalamus.
diffusion tensor imaging (DTI): The collection of images that provide information about the magnitude and direction of molecular diffusion. It is often used to create maps of fractional anisotropy.
diffusion: The random motion of molecules through a medium over time.
diffusion weighting: The application of magnetic gradients to cause changes in the MR signal that are dependent on the amplitude and/or direction of diffusion.
direct cortical stimulation: Applying small currents directly to brain tissue to excite or disrupt neural activity. Direct cortical stimulation is usually conducted in humans to localize critical brain regions in the context of neurosurgery.
dispersion derivative: A regressor that when added to a model improves the robustness of that model to small variations in the width of the hemo-dynamic response.
distribution: The pattern of variation of a variable under some conditions. For example, the normal distribution has a characteristic bell shape.
dopamine: An important neurotransmitter that is produced within cells in the substantia nigra and ventral tegmentum that project broadly to the striatum and cortex (especially the frontal lobe).
dorsal: Toward the back (spine) of the body or toward the top of the brain.
dot product: The scalar product of two vectors. It is created by summing the products along each dimension.
double dissociation: The demonstration that two experimental manipulations have different effects on two dependent variables. One manipulation affects the first variable but not the second, and the other manipulation affects the second but not the first.
dura: The outermost membrane covering the brain; its name comes from its thickness and toughness.
dynamic causal modeling (DCM): A statistical approach for testing models of the connectivity between brain regions based on hypotheses about how experimental manipulations alter activation and connectivity between regions.

-E-

echo-planar imaging (EPI): A technique that allows collection of an entire two-dimensional image by changing spatial gradients rapidly following a single excitation pulse from a transmitter coil.
echo time (TE): The time interval between an excitation pulse and data acquisition (defined as the collection of data from the center of k-space), usually expressed in milliseconds.
efficiency: The power of an experimental design to test a research hypothesis. Highly efficient designs can reject the null hypothesis even when the experimental manipulation has only a small effect.
eigenimage: Spatial maps, as generated by a principal components analysis, that reflect orthogonal components of a complex image (or time series of images).
eigenvalue: A mathematical description of the amount of variability in a data set that is accounted for by a given component.
eigenvector: Following principal components analysis, a set of values that describes a component of the intrinsic variability in a data set.
electric dipole: A point in space whose electrical properties can be approximated by assuming that it consists of physically separated positive and negative charges.
electroencephalography (EEG): The measurement of the electrical potential of the brain, usually through electrodes placed on the surface of the scalp.
electrogenesis: The generation of electrical electrophysiological phenomena by a living organism.
electromotive force (emf): A difference in electrical potential that can be used to drive a current through a circuit. The MR signal is the electromotive force caused by the changing magnetic field across the detector coil.
electron transport chain: The third step in aerobic glycolysis; it generates an additional 34 ATP molecules.
endogenous contrast: Contrast that depends on an intrinsic property of biological tissue.
epiphenomenal: A secondary consequence of a causal chain of processes, but playing no causal role in the process of interest.
epoch: A time segment extracted from a larger series of images, usually corresponding to the period in time surrounding an event of interest.
equipotentiality: The concept that a function is so widely distributed within the brain that it depends on the activity of the brain as a whole. Equipotentiality is the antithesis of localization of function.
equivalent dipole: A simplifying model that represents the electromagnetic field produced by a population of neurons as though it were produced by a single dipole.
ERP component: A stereotypic feature of an ERP waveform, such as a peak or trough at a particular latency, that has a presumed functional significance.
error matrix: That component of the fMRI data that is not fit by the design matrix (i.e., it remains unexplained after applying the statistical model).
estimation: Measurement of the pattern of change over time within an active voxel in response to the experimental manipulation.
event: A single instance of the experimental manipulation.
event-related design: The presentation of discrete, short-duration events whose timing and order may be randomized.
event-related potentials (ERPs): Small electrical changes in the brain that are associated with sensory or cognitive events.
evoked magnetic fields (EMFs): A change in the MEG signal that occurs in response to a particular stimulus. An EMF is the magnetic equivalent of an evoked potential or event-related potential in EEG.
evoked potential: A field potential that occurs in response to a sensory stimulus.
excitation: The process of sending electromagnetic energy to a sample at its resonant frequency (also called transmission). The application of an excitation pulse to a spin system causes some of the spins to change from a low-energy state to a high-energy state.
90º excitation pulse: A quantity of electromagnetic energy that, when applied to a spin system during MR excitation, results in equal numbers of nuclei in the low- and high-energy states.
180º excitation pulse: A quantity of electromagnetic energy that, when applied to a spin system during MR excitation, results in a flipping of the usual net magnetization, such that there are now more nuclei in the high-energy state than in the low-energy state.
excitatory postsynaptic potential (EPSP): A depolarization of the postsynaptic cell membrane.
excitotoxicity: Damage or death of neurons caused by excess concentrations of glutamate and other substances.
exogenous contrast: Contrast that requires the injection of a foreign substance into the body.
expected Euler characteristic: The number of clusters of significant activation expected due to chance, as estimated from the number of independent statistical tests (i.e., resels).
experiment: The controlled test of a hypothesis. Experiments manipulate one or more independent variables, measure one or more dependent variables, and evaluate those measurements using tests of statistical significance.
experimental condition: A condition that contains the stimulus or task that is most relevant to the research hypothesis. Also called the task condition.
experimental design: The organization of an experiment to allow effective testing of the research hypothesis.
experimental regressors: Model factors that are associated with specific experimental hypotheses.

-F-

F-test: A statistical test that evaluates differences among a set of distributions. For fMRI studies, F-tests can evaluate whether any of a set of contrasts exhibited a significant effect.
false discovery rate (FDR): The probability of having at least one false-positive result, given the set of reported positive results.
family-wise error rate (FWER): The probability of making at least one type I error, given the total number of statistical tests.
feature selection: An initial step in pattern classification that involves the determination of which input variables should be included in the classification algorithm.
fiber tracts: Bundles of axons that convey signals, in the form of action potentials, from one brain region to another.
field map: An image of the intensity of the magnetic field across space.
field of view (FOV): The total extent of an image along a spatial dimension.
field potentials: Changes in electrical potential over space associated with postsynaptic neuronal activity.
field strength: The magnitude of the static magnetic field generated by a scanner, typically expressed in teslas.
field uniformity: In the context of MRI, a uniform magnetic field is one that has a constant strength throughout a wide region near the center of the scanner bore.
filling k-space: The process of collecting samples from throughout k-space to collect data sufficient for image formation.
filter: Within the context of fMRI, an algorithm for removing temporal or spatial frequency components of data.
finite impulse response (FIR): A signal processing approach that treats each time unit with a separate function (i.e., an impulse); it has the major advantage of making no assumptions about the shape of the observed response function.
fixed-effects analysis: An analysis that assumes that the effect of the experimental manipulation has a constant effect, with differences between successive observations caused by random noise.
flat map: An unfolded and flattened representation of the cortical sheet to allow viewing of topographic changes over cortical space. Flat maps are most commonly used in fMRI to illustrate the organization of the visual cortex.
flip angle: The change in the precession angle of the net magnetization following excitation.
flux: A measure of the strength of a magnetic field over an area of space.
fMRI-adaptation: Reduction in the BOLD response to the repeated presentation of a set of stimuli that differ in some attribute, indicating that the brain region being studied is insensitive (as measured by fMRI) to the stimulus attribute being varied.
forward inference: Reasoning from the experimental manipulation (i.e., changes in the independent variable) to infer the effects on a dependent variable.
forward solution: The direct calculation of the electric and magnetic fields that would occur at an array of sensors based on a given distribution of dipoles with known orientations and magnitudes.
Fourier transform: A mathematical technique for converting a signal (i.e., changes in intensity over time) into its power spectrum.
fractional anisotropy (FA): The preference for molecules to diffuse in an anisotropic manner. An FA value of 1 indicates that diffusion occurs along a single preferred axis, while a value of 0 indicates that diffusion is similar in all directions.
frequency domain: The expression of a signal in terms of its power at different frequencies.
frequency-encoding gradient: A gradient that is applied during the data acquisition period so that the spin precession frequencies change over space.
frontal lobe: The most anterior lobe of the cerebrum; it is important for executive processing, motor control, memory, and many other functions.
functional connectivity: A pattern of functional relationships among regions, inferred from common changes in activation over time, that may reflect direct or indirect links between those regions.
functional contrast: A type of contrast that provides information about a physiological correlate of brain function, such as changes in blood oxygenation.
functional hyperemia: The local increase in blood flow that occurs in response to a sensory, motor, or cognitive event.
functional magnetic resonance imaging (fMRI): A neuroimaging technique that uses standard MRI scanners to investigate changes in brain function over time.
functional neuroimaging: A class of research techniques that create images of the brain’s functional properties, notably different aspects of cognition and related information processing. Common functional neuroimaging techniques include fMRI, PET, and optical imaging.
functional resolution: The ability to map measured physiological variation to underlying mental processes or behaviors.
functional ROI: A region of interest that is chosen based on functional criteria, such as the output of an independent voxel-wise analysis.
functional signal-to-noise ratio (functional SNR): The ratio between the intensity of a signal associated with changes in brain function and the variability in the data due to all sources of noise. Functional SNR is sometimes called dynamic CNR or functional CNR.

-G-

GABA (γ)-aminobutyric acid): One of the most important inhibitory neurotransmitters.
general linear model (GLM): A class of statistical tests that assume that the experimental data are composed of the linear combination of different model factors, along with uncorrelated noise.
glass-brain view: A two-dimensional projection of fMRI data, as if the brain were made transparent and only the activations were visible.
glial cells (glia): Brain cells that support the activities of neurons but are not primarily involved with information transmission.
glutamate: The most common excitatory neurotransmitter in the brain.
glycolysis: The process of breaking down glucose into other compounds to produce ATP.
gradient coils: Electromagnetic coils that create controlled spatial variation in the strength of the magnetic field.
gradient-echo (GRE) imaging: One of the two primary types of pulse sequences used in MRI; it uses gradients to generate the MR signal changes that are measured at data acquisition.
Granger causality: A form of time series analysis that quantifies the information gained by using the past history of one variable to improve predictions of future values of another variable.
gyri: Rises (ridges) in the surface of the cerebral cortex. Singular, gyrus.
gyromagnetic ratio (γ): The ratio between the charge and mass of a spin. The gyromagnetic ratio, a scaling factor, is a constant for a given type of nucleus.

-H-

Health Insurance Portability and Accountability Act (HIPAA): An act passed by the U.S. Congress that requires specific procedures for ensuring the privacy of health information.
hemifield: One-half of a visual display, usually referring to the left half or the right half relative to fixation.
hemodynamic: Having to do with changes in blood flow or other blood properties.
hemodynamic response (HDR): The change in MR signal on T₂* images following local neuronal activity. The hemodynamic response results from a decrease in the amount of deoxygenated hemoglobin present within a voxel.
heteroscedastic: Having the property that the distributions of noise are different across experimental conditions.
hindbrain: The most caudal region of the brain; includes the medulla oblongata, pons, and cerebellum.
homogeneity: Uniformity over space and time.
homoscedastic: Having the property that the distributions of noise are similar for all experimental conditions.
homotopic: The cortex in one cerebral hemisphere that corresponds to the same region in the other hemisphere.
hyperpolarization: A change in the cell membrane potential caused by admitting negative change into the cell and thus increasing its negative resting potential.
hyperscanning: The simultaneous collection of fMRI data from two or more subjects who are interacting in an experimental paradigm.
hypothalamus: A collection of brain nuclei that supports homeostatic functions, including the regulation of temperature and of food and water intake.
hypothesis-driven analysis: The evaluation of data based on statistical tests of the validity of a null hypothesis.

-I-

image: In MR imaging, a visual description of how one or more properties of the atomic nuclei within a sample vary over space.
image reconstruction: The process by which the raw MR signal, as acquired in k-space form, is converted into spatially informative images.
imaging genomics: A field that investigates the effect of genetic variation on brain structure and function.
imaging plane: The plane in which changes in the MR signal are recorded during perfusion imaging.
impulse: A single input to a system. Impulses are assumed to be of infinitely short duration.
incidental finding: The discovery of an abnormality, usually on a structural MR image, in an asymptomatic individual who was scanned for nonmedical reasons.
independent components analysis (ICA): An important class of data-driven analyses that identify stationary sets of voxels whose BOLD time courses vary together over time and are maximally distinguishable from other sets.
independent variables (IVs): Aspects of the experimental design that are intentionally manipulated by the experimenter and are hypothesized to cause changes in the dependent variables.
indicators: Regressors that have integral values to indicate a qualitative level.
individual differences: Measures of variation among individuals within a population.
inferential statistics: Statistics that make inferences about the characteristics of a population based on data obtained from a smaller sample.
inflated brain: A transformation of the cortical sheet into a balloon-like structure, removing gyral and sulcal folds so that activation can be more easily viewed.
informed consent: The process in which a potential subject voluntarily agrees to participate in a research study after learning about the procedures, risks, and benefits of the study.
inhibitory postsynaptic potential (IPSP): A hyperpolarization of the postsynaptic cell membrane.
initial dip: The short-term decrease in MR signal immediately following the onset of neuronal activity, before the main positive component of the hemodynamic response. The initial dip may result from initial oxygen extraction before the later overcompensatory response.
Institutional Review Board (IRB): An independent group of individuals who evaluate the ethical practice of research conducted at an institution. Researchers who wish to conduct research with human subjects must have the approval of their IRB.
insula: The “island” cortex hidden inside the anterior part of the Sylvian fissure; it is important for emotional processing and for the chemical senses.
integrated RF and shimming array: A new class of array coil that can simultaneously acquire MRI signal and perform local magnetic field shimming.
integrative activity: The collection of inputs from other neurons through dendritic or somatic connections.
intellectual property: The protected legal status given to an idea, product, or invention so that its owner has exclusive rights for its use, commercial or otherwise.
interleaved slice acquisition: The excitation of slices in an alternating order. Data are first acquired from the odd-numbered slices and then from the even-numbered slices, so as to minimize the influence of excitation pulses on adjacent slices.
interleaved stimulus presentation: The presentation of events of interest at different points within a TR over trials (e.g., one-forth, one-half, and three-fourths of TR in addition to TR onset), increasing the effective sampling rate of an experiment at the expense of fewer trials per condition.
interneuron: A neuron that is connected locally to other neurons. Interneurons participate in local brain circuits, but do not project to distant cortical regions.
interocular trauma test: An intuitive evaluation of data based on highly visible effects of the experimental manipulation. It states that data are significant if, when plotted, they hit you between the eyes.
interstimulus interval (ISI): The separation in time between successive stimuli. Usually refers to the time between the end of one stimulus and the onset of the next, with the term “stimulus-onset asynchrony” (SOA) used to define the time between successive onsets.
intersubject correlations: Functional MRI time courses that are shared by different individuals while performing the same experimental tasks or experiencing the same stimuli.
intersubject variability: Variability in fMRI data across a set of subjects; it includes the factors associated with intrasubject variability, along with between-subjects differences in task performance and physiology.
intrasubject variability: Variability in the fMRI data from a single subject associated with thermal, system, and physiological noise, as well as with variability in the pattern of brain activity during task performance.
inverse problem: The mathematical impossibility of determining the distribution of electrical sources within an object based on the measurement of electric or magnetic fields at the surface of the object.
inversion recovery: A technique for increasing T₁ contrast by adding a 180º inversion pulse before a standard pulse sequence.
ion: An atom or molecule that carries an electrical charge.
ion channel: A pore in the membrane of a cell that allows passage of particular ions under certain conditions.
ionizing radiation: Electromagnetic radiation with sufficient energy to break chemical bonds.
isomorphic: Having an identical form. A physiological measurement that is isomorphic with a psychological construct would vary over time consistently with the postulated changes in the construct.
isotropic: Having similar properties in all directions.
item-related processes: Changes in the brain that are assumed to be caused by the properties of individual stimuli, or items. Item-related processes are more easily measured with event-related designs than with mixed designs.

-J-

jittering: Randomizing the intervals between successive stimulus events over some range.
justice: In the context of research involving human subjects, the principle that the costs of research are distributed broadly and fairly across society.

-K-

k-space: A notation scheme used to describe MRI data acquisition. The use of k-space provides mathematical and conceptual advantages for describing the acquired MR signal in image form.
k-space trajectory: A path through k-space. Different pulse sequences adopt different k-space trajectories.

-L-

labeling plane: The plane in which initial excitation pulse(s) are applied during perfusion imaging.
laboratory frame: The normal reference frame that is aligned with the magnetic field of the scanner.
large-vessel effects: Signal changes in veins that drain a functionally active region but are distant from the neuronal activity of interest.
Larmor frequency: The resonant frequency of a spin within a magnetic field of a given strength. It defines the frequency of electromagnetic radiation needed during excitation to make spins change to a high-energy state, as well as the frequency emitted by spins when they return to the low-energy state.
latent variable: A variable whose value is not directly measured, but is inferred based on the values of other variables.
lateral: Toward the sides of the brain.
least-squares error: A commonly used cost function, the sum of the squared residuals.
ligand-gated ion channel: An ion channel that opens or closes in response to binding of chemical signals (ligands). The ligand is often a neurotransmitter molecule.
linear system: A system that obeys the principles of scaling and superposition.
localization of function: The idea that the brain may have distinct regions that support particular mental processes.
localizer task: A simple experimental paradigm designed to identify a set of voxels based on a known functional property in preparation for subsequent analyses of that region in different paradigms.
logistic regression: A subset of regression analysis that uses a set of independent variables to predict a binary outcome variable.
longitudinal: Parallel to the main magnetic field, or in the z direction, of the scanner (i.e., into the bore).
longitudinal relaxation (spin–lattice relaxation): The recovery of the net magnetization along the longitudinal direction as spins return to the parallel state.

-M-

machine learning: A subdiscipline within computer science that develops algorithmic rules for relating input data to desirable outputs.
magnetic field mapping: The collection of explicit information about the strength of the magnetic field at different spatial locations.
magnetic moment (μ): The torque (rotational force) exerted on a magnet, moving electrical charge, or current-carrying coil when it is placed in a magnetic field.
magnetic resonance: The absorption of energy from a magnetic field that oscillates at a particular frequency.
magnetic resonance angiography (MRA): The creation of images of the vascular system using MRI.
magnetic susceptibility: The intensity of magnetization of a substance when placed within a magnetic field.
magnetoencephalography (MEG): A noninvasive functional neuroimaging technique that measures very small changes in magnetic fields caused by the electrical activity of neurons, with potentially high spatial and temporal resolution.
matched filters: The principle that a filter of the same frequency as the signal of interest provides the maximal signal-to-noise ratio.
medial: Toward the center of the brain.
medulla oblongata: A continuation of the spinal cord at the base of the brain that is important for the control of basic physiological functions.
membrane potential: The difference in electrical charge between the inner and outer surfaces of a cell membrane, the result of a difference in the distribution of ions.
midbrain (mesencephalon): A section of the brain rostral to the pons; it includes a number of important nuclei.
midsagittal: A sagittal view along the midline of the y–z plane.
mind reading: The ability to construct a comprehensive description of the contents of consciousness. Currently, mind reading is far beyond the capacity of any neuroscience technique.
mixed design: A design that contains features of both blocked and event-related approaches.
mixed-effects analysis: In the context of fMRI, the common practice of modeling the effect of the experimental manipulation as stable within a participant (fixed effects) but variable across participants (random effects).
mixing matrix: A statistical description of how a set of hypothesized sources (e.g., components) combine to form the observed data.
MNI space: A commonly used space for normalization of fMRI data; its coordinates are derived from an average of MRI structural images from more than 100 individuals.
mock scanner: A device that simulates a real MRI scanner, usually by reproducing the scanner bore, the bed that the subjects lie on, and the sounds made during scanning.
model: A collection of independent variables (and the relationships between those variables) that serve to predict a dependent variable.
motion contrasts: Contrast mechanisms that are sensitive to the movement of spins through space (e.g., diffusion, perfusion).
MR signal: The current measured in a detector coil following excitation and reception.
MR signal equation: A single equation that describes the MR signal as a function of the properties of the object being imaged under a spatially varying magnetic field.
multi-band (MB) imaging (simultaneous multi-slice imaging): A class of accelerated imaging techniques that can simultaneously acquire multiple slices and separate the individual slices via postprocessing, using the sensitivity profiles of individual coils in an RF array.
multi-channel imaging (parallel imaging): The use of multiple receiver channels to acquire data following a single excitation pulse.
multiple comparison problem: The increase in the number of false-positive results (i.e., type I errors) with an increasing number of statistical tests. It is of particular consequence for voxel-wise fMRI analyses, which may have many thousands of statistical tests.
multiple regression: A family of statistical approaches that evaluate the relative contributions of several independent variables to a dependent variable.
multi-voxel pattern analysis (MVPA): An approach for pattern classification in fMRI research that uses as its input data the relative changes in activation across a set of voxels.
mutual information: In the context of MRI, the amount of information about one image that is provided by knowledge of another image.
myelin: A fatty substance that forms sheaths surrounding axons that serve to speed the transmission of action potentials.

-N-

net magnetization (M): The sum of the magnetic moments of all spins within a spin system.
network: A description of the relationships among a set of brain regions, including their connectivity and causal relationships.
neuroeconomics: The combination of neuroscience measures and behavioral modeling to understand decision making and related aspects of cognition.
neuroelectromagnetic contrast: A new generation of contrast mechanism aimed at detecting the minute electric and/or magnetic field changes as the result of neuronal firing.
neuroessentialism: The intuition that neuroscience data are isomorphic with the subjective self.
neurological convention: The practice of displaying images of the brain so that the left and right sides of the image correspond to the same sides of the brain, as if one were behind the subject.
neuromarketing: The use of neuroscience data, sometimes including fMRI, to generate recommendations about how commercial products and brands should be presented to consumers.
neurons: These cells are the basic information-processing units of the nervous system. There are several types of neurons, all of which are capable of generating and conducting electrical signals.
neurorealism: The tendency to consider a behavioral or mental phenomenon to be more real based on the presence of neuroscience data.
neurotransmitters: Chemicals released by presynaptic neurons that travel across the synaptic cleft to influence receptors on postsynaptic neurons.
neurovascular unit: A functional unit consisting of astrocytes and neurons that impinge on a local microvessel to control blood flow.
nitric oxide (NO): A rapidly diffusing soluble gas that is produced in pyramidal cells, interneurons, astrocytes, and endothelial cells; possibly a molecular modulator of blood flow.
NMR property: A label for atomic nuclei that have both a magnetic moment and angular momentum, which together allow them to exhibit nuclear magnetic resonance effects.
noise: Nonmeaningful changes in some quantity. There are many sources of noise in fMRI studies, and some changes may be classified as either noise or signal, depending on the goals of the study.
nonlinearity: The property whereby the combined response to two or more events is not equivalent to the summation of the responses to the individual events in isolation.
noradrenaline (NA): Neurotransmitter used extensively in the central and peripheral nervous systems. Within the brain, NA projections from the locus coeruleus nuclei of the brain stem plays a role in a number of psychological processes, including attention and alertness. Also known as norepinephrine (NE).
normalization: The transformation of MRI data from an individual subject to match the spatial properties of a standardized image, such as an averaged brain derived from a sample of many individuals.
nuclear induction: The initial term for nuclear magnetic resonance effects, as labeled by Bloch and colleagues.
nuclear magnetic resonance (NMR): The measurable changes in magnetic properties of atomic nuclei induced by the application of an oscillating magnetic field at the resonant frequency of the nuclei.
nuclei: Anatomically discrete and identifiable clusters of neurons within the brain that typically serve a particular function.
nuisance regressors: Model factors that are associated with known sources of variability that are not related to the experimental hypotheses.
null hypothesis: The proposition that the experimental manipulation will have no effect on the experimental data. Most statistical analyses evaluate the probability that the null hypothesis is true, i.e., that the observed data reflect chance processes.
null-task block: A control block in which there are no task requirements for the subject. Also called a baseline block or non-task block.
Nuremberg Code: A set of principles for the ethical conduct of research involving human subjects, developed following the trials of Nazi war criminals in the 1940s.
nutation: The spiraling change in the precession angle of the net magnetization during an excitation pulse.
Nyquist frequency: The highest frequency that can be identified in a digitally sampled signal; it is defined as one-half of the sampling rate.

-O-

occipital lobe: The most posterior lobe of the brain; it is primarily associated with visual processing.
ocular dominance columns: Cellular columns in the primary visual cortex that receive separate inputs from each eye. ”Ocular dominance” refers to the degree to which a given neuron responds more to stimuli presented to one eye than to stimuli presented to the other eye.
ocular dominance: The degree to which a given neuron in the visual cortex responds more to stimuli presented to one eye than to stimuli presented to the other eye.
off-resonance excitation: The presentation of an excitation pulse at a frequency other than the resonant frequency of the sample, resulting in reduced efficiency.
oligodendrocyte: A type of glial cell that constructs the myelin sheaths around axons.
on-resonance excitation: The presentation of an excitation pulse at the resonant frequency of the sample, resulting in maximum efficiency.
orientation column: Vertically organized collections of neurons in visual cortex that respond preferentially to stimuli of a particular orientation, such as lines.
orthogonal: A property of two variables (or vectors, sets of variables) such that they are completely uncorrelated with each other.
orthogonalize: To remove correlation between two variables. In the context of fMRI data analysis, orthogonalizing one regressor (with regard to one or more other regressors) changes that regressor so that it is no longer correlated with the other regressor(s).
oscillating magnetic field: A magnetic field whose intensity changes periodically over time. Most such fields used in MRI oscillate at the frequency range of radio waves (megahertz, or MHz), and as such they are often called radiofrequency fields.
oxygen extraction fraction (OEF): The proportion of available oxygen that is removed from the blood.
oxygenated hemoglobin (Hb): Hemoglobin with attached oxygen; it is diamagnetic.

-P-

parallel imaging (multi-channel imaging): The use of multiple receiver channels to acquire data following a single excitation pulse.
parallel state: The low-energy state in which an atomic spin precesses around an axis that is parallel to that of the main magnetic field.
paramagnetic: A property of some substances that concentrates magnetic field lines, thus increasing the strength of the local magnetic field.
parameter matrix: A matrix that describes the relative contributions of each model to the observed data for each voxel.
parameter weights: For most fMRI analyses, quantities that reflect the relative contributions of the different model factors to the observed data within a given voxel.
parametric effect: A manipulation of some independent variable so that it takes a number of levels to evoke regular changes (e.g., a linear increase) in the dependent variable.
parietal lobe: The lobe on the posterior and dorsal surfaces of the cerebrum; it is important for spatial processing, cognitive processing, and many other functions.
partial least squares (PLS): An approach to analyzing functional neuroimaging data that is used to identify components whose amplitude is influenced by an experimental manipulation.
partial volume effects: The combination, within a single voxel, of signal contributions from two or more distinct tissue types or functional regions.
pattern classification: An attempt to separate individual examplars into different categories by constructing a set of decision rules based on some combination of their features.
peak: The maximal amplitude of the hemodynamic response, typically occurring about 4 s to 6 s following a short-duration event.
peer review: The practice of vetting scientific research by experts in the discipline. Most journals and funding agencies use a peer review system to determine what research can be published or funded.
perfusion MRI: A type of MRI that provides information on blood flow through tissue.
pericytes: Contractile cells that wrap around the endothelial cells of capillaries and that can constrict the vessel, thus influencing local blood flow patterns.
periodic event-related design: An experimental design in which events of interest occur at regular intervals.
permutation: In the context of significance testing, approaches that involve resampling the original data to directly determine the size of an effect that might be observed with a given alpha level.
pH-dependent imaging: An imaging technique that is sensitive to the pH changes, currently based on amide-proton transfer contrast.
phantom: An object used for testing MR systems. Most phantoms are filled with liquids or gels with known properties, so that problems with the scanner system can be readily identified.
phase: Accumulated change in angle as the result of rotation over time.
phase-encoding gradient: A gradient that is applied before the data acquisition period so that spins can accumulate differential phase offsets over space.
phased array: A method for arranging multiple surface detector coils to improve spatial coverage while maintaining high sensitivity.
physiological noise: Fluctuations in MR signal intensity over space and time due to physiological activity of the human body. Sources of physiological noise include motion, respiration, cardiac activity, and metabolic reactions.
pia: The innermost membrane covering the brain; it closely adheres to the brain’s contours.
pixel: A two-dimensional picture element.
plasticity: The change in the normal functional properties of brain tissue following injury or experience.
polygraph: A device that measures multiple physiological indicators to judge whether an individual is lying. Despite their pervasiveness, polygraphs have proven to have minimal validity for detecting lies in real-world settings.
polymorphism: A common variation in a gene or segment of DNA.
pons: Part of the brain stem; it serves as a relay system for motor and sensory nerves.
positron emission tomography (PET): A functional neuroimaging technique that creates images based on the movement of injected radioactive material.
postsynaptic potential (PSP): Any postsynaptic potential, excitatory or inhibitory, that results from synaptic activity.
power spectrum: A representation of the strength of different frequency components within a signal. The Fourier transform converts a signal (i.e., changes in intensity over time) into its power spectrum.
precession: The gyroscopic motion of a spinning object, in which the axis of the spin itself rotates around a central axis, like a spinning top.
precoloring: The introduction of autocorrelations to a time series of data so that the time series will have known statistical properties; it is less commonly used than prewhitening in fMRI data analysis.
preprocessing: Computational procedures that are applied to fMRI data following image reconstruction but before statistical analysis. Preprocessing steps are intended to reduce the variability in the data that is not associated with the experimental task, and to prepare the data for statistical testing.
presurgical planning: The use of fMRI or another neuroscience technique to map particular functions in a single individual to guide clinical decisions about the potential course and consequences of neurosurgery in that individual.
prewhitening: The application of filters to remove autocorrelations in a time series of data; in fMRI, prewhitening is typically applied before data analysis to remove task-unrelated noise.
primary current: The current flow within a neuron caused by the inflow of ions through ionic channels opened by synaptic activity.
principal components analysis (PCA): A common technique for data reduction that simplifies high-dimensional data into a smaller set of components that retains most of the variability in the original data.
principle of reciprocity: The rule stating that the quality of an electromagnetic coil for transmission is equivalent to its quality for reception (i.e., if it can generate a homogeneous magnetic field at excitation, it can also receive signals uniformly).
projectile effect: The movement of an untethered ferro-magnetic object through the air toward the bore of the MRI scanner.
proton-density imaging: The creation of MR images that are sensitive to the number of protons present within each voxel.
psychophysiological interaction (PPI): A statistical approach for identifying the effect of an experimental manipulation on the functional connectivity between two brain regions.
pulse sequence: A series of changing magnetic field gradients and oscillating electromagnetic pulses that allows the MRI scanner to create images sensitive to a particular physical property.
pulsed ASL: A type of perfusion imaging that uses a single coil both to label spins in one plane and to record the MR signal in another plane, separated by a brief delay period.
pump: A transport system that moves ions across a cell membrane against their concentration gradient.
pyramidal cell: A common neuronal type of the cerebral cortex. These cells have a pyramid-shaped soma, extensive spined dendrites, and are characterized by a long, branching axon that can extend for many centimeters.

-Q-

quality assurance (QA): A set of procedures designed to identify problems with fMRI data so that they do not compromise experimental analyses.
quantitative susceptibility mapping (QSM): A relatively new MRI technique that generates imaging contrast based on the magnetic susceptibility of the tissue, which can provide exquisite details in the cortical and subcortical areas.

-R-

radiofrequency (RF) coils: Electromagnetic coils used to generate and receive energy at the sample’s resonant frequency, which for field strengths typical to MRI is in the radiofrequency range.
radiological convention: The practice of displaying images of the brain so that the left side of the image is the right side of the brain and vice versa, as if one were facing the subject.
random field theory: A branch of mathematics that deals with the properties of smooth, spatially extended data. Using random field theory, researchers can better calculate the number of independent tests within fMRI analyses.
random-effects analysis: An analysis that assumes that the effects of the experimental manipulation are randomly sampled from some larger population, as when participants are drawn from the community, so that there is a distribution of effects across possible observations.
randomization: A process for removing confounding factors by ensuring that they vary randomly with respect to the independent variable.
raster: A depiction of the firing rate of action potentials by a neuron in which time is represented along the horizontal axis and a dot indicates the occurrence of an action potential.
raw signal-to-noise ratio (raw SNR): The ratio between the MR signal intensity associated with a sample (e.g., the brain) and the thermal noise that is measured outside the sample.
reaction time: The time required for someone to make a simple motor response to the presentation of a stimulus. Note that this is distinct from response time, which applies to situations in which someone must choose between two or more possible responses.
real-time analyses: A set of computational steps designed for the rapid analysis of fMRI data so that statistical tests can be conducted immediately following the acquisition of images.
reception: The process of receiving electromagnetic energy emitted by a sample at its resonant frequency (also called detection). As spins return to a low-energy state following the cessation of the excitation pulse, they emit energy that can be measured by a receiver coil.
receptive field: The part of the visual field that, when stimulated, will result in an increase in firing of a particular neuron.
recovery of function: The improvement in a previously impaired ability over time due to functional or structural changes within the brain.
redundant safeguards: The use of multiple independent procedures that could each identify potential problems or unsafe situations.
reference volume: A target image volume to which other image volumes are to be aligned.
refocusing pulse: A 180º electromagnetic pulse that compensates for the gradual loss of phase coherence following initial excitation.
refractory effects: Changes in the amplitude and timing of a response based on the characteristics of preceding responses.
refractory period: A time period following the presentation of a stimulus during which subsequent stimuli evoke a reduced response. For BOLD fMRI, the refractory periods for many types of stimuli last approximately 6 s.
region-of-interest (ROI) analyses: Evaluations of hypotheses about the functional properties of brain regions (i.e., aggregated over a predetermined set of voxels), often chosen to reflect a priori anatomical distinctions within the brain.
registry: A patient database. A registry might include information about the locations of brain lesions in a large population of individuals who might then be asked to participate in experimental studies.
regressor: A hypothesized time course of BOLD activation caused by the manipulations of an independent variable or by another known source of variability.
relaxation: A change in net magnetization over time.
rendered image: A display of MRI data in three-dimensional perspective.
repetition enhancement: The increase in magnitude in the hemodynamic response when a stimulus is repeated.
repetition suppression: The decrease in magnitude in the hemodynamic response when a stimulus is repeated.
repetition time (TR): The time interval between successive excitation pulses, usually expressed in seconds.
repetitive TMS (rTMS): The delivery of an extended series of closely spaced TMS stimulation pulses so as to effect long-lasting changes in brain function.
research: The accumulation of data, whether by observation or experimentation, to develop general knowledge.
research hypothesis: A proposition about the nature of the world that makes predictions about the results of an experiment. For a hypothesis to be well formed, there must be some experiment whose outcome could prove it to be false.
research protocol: A document describing the procedures of a research study in a form that can be evaluated by the local Institutional Review Board.
residual: The variability in the data that remains unexplained after accounting for the model factors.
resistance vessels: Arterioles that control the flow of blood through the capillary bed.
resolution elements (resels): The independent statistical tests within an fMRI volume.
resonance: The repeated application of small amounts of energy at a particular frequency to induce large changes in a system.
resonant frequency: The frequency of oscillation that provides maximum energy transfer to the system.
respect for persons: The principle that individuals should be treated as autonomous decision makers who should be given the opportunity to make informed decisions about their participation in research studies. Individuals with an impaired capacity for autonomous decision making must be granted additional protection.
response time: The time required for someone to execute a choice between two or more possible responses. Note that this is distinct from reaction time, which applies to situations in which only one possible response is present.
resting-state connectivity: The functional connectivity of a given brain region when measured while the participant is not performing any coordinated, purposeful task.
reverse inference: Reasoning from the outcome of a dependent variable to infer the state of an independent variable (or an intervening unobservable variable).
right-hand rule: A method used to determine the direction of a magnetic moment generated by a moving charge or electrical current. If the fingers of the right hand are curled around the direction of spin, the magnetic moment will be in the direction indicated by the thumb.
rigid-body transformation: A spatial transformation that does not change the size or shape of an object; it has three translational parameters and three rotational parameters.
rostral: Toward the front of the brain (“noseward”).
rotating frame: A reference frame that rotates at the Larmor frequency of the spin of interest. The rotating frame is adopted to simplify mathematical descriptions of the effects of excitation.
rotation: The turning of an object around an axis in space (in the absence of translation).
run: An uninterrupted presentation of an experimental task, usually lasting 5 to 10 minutes for fMRI studies. It also refers to the set of functional images collected during that task presentation.

-S-

sagittal: A side view of the brain (anywhere along the y–z plane in MRI).
sample: (1) A set of observations drawn from a larger population of potential observations. (2) An object to be imaged using magnetic resonance.
sampling rate: The frequency in time with which a measurement is made.
scalar: A quantity that has magnitude but not direction. Scalars are italicized in this text.
scaling: A principle of linear systems that states that the magnitude of the system output must be proportional to the system input.
scanner drift: Slow changes in voxel intensity over time.
searchlight: An approach to feature selection in the pattern classification of fMRI data. As its name implies, a searchlight reflects a geometrically defined ROI (e.g., a sphere of 5-voxel radius) that can be moved throughout the brain.
seed voxel: A voxel chosen as a starting point for a connectivity analysis.
segmentation: The process of partitioning an image into constituent parts, typically types of tissue (e.g., gray matter, white matter) orƒ topographical divisions (e.g., different structural regions like Brodmann areas).
semirandom design: A type of event-related design in which the probability that an event will occur within a given time interval changes systematically over the course of the experiment.
session: A single visit to the scanner by a subject. For fMRI studies, each session usually includes both structural and functional scans.
shimming: A procedure to improve main magnetic field homogeneity by adjusting the electric currents within a set of electromagnetic coils in the MRI scanner.
shimming coils: Electromagnetic coils that compensate for inhomogeneities in the static magnetic field.
signal: Meaningful changes in some quantity. For fMRI, an important class of signals includes changes in intensity associated with the BOLD response across a series of T₂* images.
signal averaging: The combination of data from multiple instances of the same manipulation in order to improve functional SNR.
signal-to-noise ratio (SNR): The relative strength of a signal compared with other sources of variability in the data.
significance testing: The process of evaluating whether the null hypothesis is true. Also known as hypothesis testing.
simple cell: A neuron in the visual cortex that responds with increased firing to a stimulus with a preferred orientation in its receptive field and responds with decreased firing to a stimulus in the region surrounding its receptive field.
single dissociation: The demonstration that an experimental manipulation has an effect on one variable but not on a second variable.
single-pulse TMS: The delivery of a single TMS stimulation pulse so as to disrupt some ongoing brain process.
single-unit recording (single-cell recording): Collection of data about the electrophysiological activity (e.g., action potentials) of a single neuron.
sinuses: (1) Air-filled cavities in the skull. (2) Long venous channels that form the primary draining system for the brain.
slice: A single slab within an imaging volume. The thickness of the slice is defined by the strength of the gradient and the bandwidth of the electromagnetic pulse used to select it.
slice selection: The combined use of a spatial magnetic field gradient and a radiofrequency pulse to excite spins within a slice.
small-volume correction: The restriction of analyses to specific regions of interest, defined a priori, to reduce the total number of statistical tests and thus allow for a more liberal significance threshold.
smoothness: The degree to which the time courses of nearby voxels are temporally correlated.
sodium–potassium pump: A transport system that removes three sodium ions from within a cell while bringing two potassium ions into the cell.
soma: The body of a cell; it contains cytoplasm, the cell nucleus, and organelles.
spatial extent: The number of active voxels within a cluster of activation (i.e., the size of the active region).
spatial frequency: The frequency with which some pattern occurs over space.
spatial gradient (G): A magnetic field whose strength varies systematically over space. Note that since a given spatial location experiences only one magnetic field, which represents the sum of all fields present, spatial gradients in MRI act to change the effective strength of the main magnetic field over space.
spatial ICA: A form of independent component analysis that generates components that have minimal spatial redundancy.
spatial interpolation: The estimation of the intensity of an image at a spatial location that was not originally sampled, using data from nearby locations.
spatial resolution: The ability to distinguish changes in an image (or map) across different spatial locations.
spatial smoothing: The blurring of fMRI data across adjacent voxels to improve the validity of statistical testing and maximize the functional signal-to-noise ratio at a cost of spatial resolution.
specific absorption rate (SAR): A quantity that describes how much electromagnetic energy is absorbed by the body over time.
speed–accuracy trade-off: The improvement in the speed of a response at the expense of accuracy, or vice versa, within an experimental task.
spin system: A collection of atomic nuclei that possess the NMR property within a spatial location.
spin-echo (SE) imaging: One of the two primary types of pulse sequences used in MRI; it uses a second 180º electromagnetic pulse to generate the MR signal changes that are measured at data acquisition.
spins: Atomic nuclei that possess the NMR property; that is, they have both a magnetic moment and angular momentum.
spiral imaging: A technique for fast image acquisition that uses sinusoidally changing gradients to trace a corkscrew trajectory through k-space.
standard deviation: A commonly used measure of the variability within a sample of data points.
standard error: A commonly used estimate of the likely discrepancy between a measured value and a true value, often calculated from a measure of variability in the data (i.e., the standard deviation) and the number of data points in the sample.
state-related processes: Changes in the brain that are assumed to reflect distinct modes, or states, of function. State-related processes are more easily measured with blocked designs.
static contrasts: Contrast mechanisms that are sensitive to the type, number, relaxation properties, and local environment of spins (e.g., T₁, T₂, proton density).
static magnetic field (B₀): The strong magnetic field at the center of the MRI scanner whose strength does not change over time. The strength of the static magnetic field is expressed in teslas (T).
statistical map (statistical parameter map): In fMRI, the labeling of all voxels within the image according to the outcome of a statistical test.
statistical power: The probability of detecting an effect of the experimental manipulation.
stereotaxic space: A precise mapping system (e.g., of the brain) using three-dimensional coordinates.
structural connectivity: A pattern of structural connections between regions based on known axonal projections.
structural equation modeling (SEM): A statistical approach for testing a model of the relationships among a set of independent and dependent variables.
structural neuroimaging: A class of research and clinical techniques that create images of the brain’s physical structure, often to provide insight into the locations and distribution of different types of tissue.
subject: A participant in a research study. Some journals and scientific societies prefer the term participant, thereby emphasizing the voluntary nature of research.
subsequent memory: An approach to fMRI analyses that sorts experimental stimuli based on whether they were remembered or forgotten in a later testing session; this approach allows identification of brain regions whose activation predicts successful encoding of stimulus properties into memory.
subtraction: In experimental design, the direct comparison of two conditions that are assumed to differ only in one property, the independent variable.
sulci: Troughs (valleys) in the surface of the cerebral cortex. Singular, sulcus.
superconducting electromagnets: A set of wires made of metal alloys that have no resistance to electricity at very low temperatures. By cooling the electromagnet to near absolute zero, a strong magnetic field can be generated with minimal electrical power requirements.
superparamagnetic iron oxide (SPIO) nanoparticles: A new class of exogenous contrast agents that are super paramagnetic and can greatly enhance the imaging contrast when injected into humans.
superposition: A principle of linear systems that states that the total response to a set of inputs is equivalent to the summation of the independent responses to the inputs.
support vector machines (SVMs): A class of algorithm used in pattern classification that attempts to identify the combination of features in the original data set that can most effectively differentiate between two categories.
surface coil: A radiofrequency coil that is placed on the surface of the head, very close to the location of interest. Surface coils have excellent sensitivity to the signal from nearby regions but poor sensitivity to signal from distant regions.
susceptibility artifacts: Signal losses on T₂-dependent images due to magnetic field inhomogeneities in regions where air and tissue are adjacent.
Sylvian fissure: The deep sulcus separating the temporal lobe from the frontal and parietal lobes.
synapse: A junction between neurons where the presynaptic process of an axon is apposed to the postsynaptic process of a dendrite or cell body.
synaptic cleft: A gap between presynaptic and postsynaptic membranes.
synaptic plasticity: A change in the strength of a synapse as a consequence of functional activation.
system: A set of regions that are linked by coactivation, but for which the connectivity and causal relationships remain unknown.
system noise: Fluctuations in MR signal intensity over space or time that are caused by imperfect functioning of the scanner hardware.

-T-

t-test: A test for statistical significance based on the Student’s t-distribution. The t-test typically evaluates whether the mean values of two sets of observations are sufficiently different to preclude their being drawn from the same distribution.
T₁ (recovery): The time constant that describes the recovery of the longitudinal component of net magnetization over time.
T₁-weighted (T₁-dependent): Images that provide information about the relative T₁ values of tissue; also known as T₁ images.
T₂ (decay): The time constant that describes the decay of the transverse component (i.e., transverse relaxation) of net magnetization due to accumulated phase differences caused by spin–spin interactions.
T₂-weighted (T₂-dependent): Images that provide information about the relative T₂ values of tissue; also known simply as T₂ images.
T₂* (decay): The time constant that describes the decay of the transverse component of net magnetization due to both accumulated phase differences and local magnetic field inhomogeneities. T₂* is always shorter than T₂. BOLD-contrast fMRI relies on T₂* contrast.
T₂* blurring: Distortions in T₂* images that result from having a data acquisition window that is sufficiently long that significant T₂* decay occurs over that interval.
T₂*-weighted (T₂ *-dependent): Images that provide information about the relative T₂* values of tissue. T₂*-weighted images are commonly used for BOLD-contrast fMRI.
Talairach space: A commonly used space for normalization of fMRI data; its coordinates are based on measurements from a single postmortem human brain, as published in the atlas by Talairach and Tournoux.
task frequency: The rate of presentation of a periodic experimental task.
TCA cycle: The tricarboxylic acid cycle, the second step in aerobic glycolysis. The TCA cyle, also known as the citric acid cycle or the Krebs cycle, involves the oxidation of pyruvate.
TE: See echo time
telencephalon (forebrain): The largest and most evolutionarily advanced region of the human brain, containing the cerebral hemispheres, including the cerebral cortex and important subcortical structures such as the hippocampus, amygdala, and basal ganglia.
temporal derivative: A regressor that when added to a model improves the robustness of that model to small variations in the timing of the hemodynamic response.
temporal ICA: A form of independent component analysis that generates components that have minimal temporal redundancy.
temporal interpolation: The estimation of the value of a signal at a time point that was not originally collected, using data from nearby time points.
temporal lobe: The lobe on the ventral surface of the cerebrum; it is important for auditory and visual processing, language, memory, and many other functions.
temporal resolution: The ability to distinguish changes in a signal (or map) across time.
tensor: A collection of vector fields governed by three principal axes.
testing set: In pattern classification analysis, a novel part of the data set used to evaluate the robustness of the classification algorithm.
thalamus: A structure composed of a number of nuclei that are important for relaying many aspects of perception and cognition. The nuclei of the thalamus are highly interconnected with many regions of the cerebral cortex.
theory: An organized set of ideas that guides thinking on a topic and that can be used to generate a variety of experimental hypotheses.
thermal noise: Fluctuations in MR signal intensity over space or time that are caused by the thermal motion of electrons within the sample or scanner hardware.
time course: The change in MR signal over a series of fMRI images.
time domain: The expression of a signal in terms of its intensity at different points in time.
time-locking: Synchronization of analyses to events of interest, usually for the extraction of data from specific epochs in time around those events.
time-of-flight (TOF) MRA: A type of magnetic resonance angiograpy that generates contrast by suppressing the signal from spins within an imaging plane so that voxels with inflowing spins (i.e., those with blood vessels) have a high signal.
time series: A large number of fMRI images collected at different points in time.
torque: A force that induces rotational motion.
torsion: Rotation (twisting) of an object. Even if the motion of an object is restricted so that it cannot translate, a strong magnetic field will still exert a torque that may cause the object to rotate so that it becomes aligned with the magnetic field.
TR: See repetition time
tractography: The identification and measurement, often using diffusion tensor imaging, of white-matter tracts that connect distant brain regions.
training set: In pattern classification analysis, that part of the data set used to develop the classification algorithm.
trait: A psychological term used to define an intrinsic, and perhaps stable over time, feature of one’s nature.
transcranial direct current stimulation (tDCS): An inexpensive and safe neuroscience technique in which a weak electrical current is generated between a pair of electrodes on the scalp; as that current passes though the brain, it changes the excitability of neurons and alters brain function.
transcranial magnetic stimulation (TMS): A technique for temporarily stimulating a brain region to disrupt its function. TMS uses an electromagnetic coil placed close to the scalp; when current passes through the coil, it generates a magnetic field in the nearby brain tissue, producing localized electric currents.
translation: The movement of an object along an axis in space (in the absence of rotation).
transmissive activity: The relaying of the outcome of an integrative process from one neuron to another, typically through signals sent via axons.
transmitter coil: An electromagnetic coil that generates an oscillating magnetic field at the resonant frequency of atomic nuclei within a sample.
transverse: Perpendicular to the main magnetic field of the scanner, in the x–y plane.
transverse relaxation (spin–spin relaxation): The loss of net magnetization within the transverse plane due to the loss of phase coherence of the spins.
trial: A single instance of the experimental manipulation.
trial sorting: The post hoc assignment of events to conditions, often based on behavioral data.
tripartite synapse: A synapse formed by a presynaptic axon and a postsynaptic dendrite, with the addition of the astrocytic process that ensheathes and modulates the synapse.
type I error: Rejecting the null hypothesis when it is in fact true. Also known as a false positive.
type II error: Accepting the null hypothesis when it is in fact false. Also known as an incorrect rejection or false negative.

-U-

undershoot: The decrease in MR signal amplitude below baseline due to the combination of reduced blood flow and increased blood volume.
unknown risks: Possible negative outcomes that, although not anticipated based on the best available science, nevertheless influence research or clinical procedures. Most fMRI centers do not scan pregnant women because of potential unknown risks to the developing fetus.

-V-

variable: A measured or manipulated quantity that varies within an experiment.
vascular conducted responses: The rapid spread of vasodilation or constriction along small blood vessels that is not dependent on neural activity or a passive response to changes in blood flow.
vascular steal: The idea that increased blood flow in one region comes at the cost of decreased blood flow in a closely adjacent region
vascular tone: The degree to which a blood vessel resists blood flow.
vasoactive substances: Substances that change the diameter of blood vessels.
vector: A quantity with both magnitude and direction. Vectors are in boldface in this text.
veins: Blood vessels that carry blood from the body to the heart. Blood in the veins (except for the pulmonary vein) is partially deoxygenated.
velocity-encoded phase contrast (VENC-PC) MRA: A type of magnetic resonance angiography that uses gradient fields to induce phase differences associated with vascular flow so that the flow velocity of vessels can be measured.
ventral: Toward the front (belly) of the body, or toward the bottom of the brain.
ventricles: Fluid-filled cavities within the brain.
venules: Small veins.
voltage-dependent ion channel: An ion channel that opens or closes in response to changes in membrane potential.
volume: A single image of the brain, itself consisting of multiple slices and voxels.
volume coil: A radiofrequency coil that surrounds the entire sample, with roughly similar sensitivity throughout.
volume conductor: A continuously conductive medium. The brain, meninges, skull, and scalp constitute a volume conductor throughout which currents created by ionic flow can be measured.
volume current: The return current through the extracellular medium that balances the primary current within a neuron.
volume transmission: The transmission of an information-carrying signal molecule such as a neurotransmitter from a presynaptic cell into intercellular space. The molecule can travel some distance and have long-lasting effects.
voxel: A three-dimensional volume element.
voxel-wise analysis: Evaluation of hypotheses about the functional properties of individual voxels (or small clusters of voxels), often throughout the entire brain. The evaluation of statistical tests at the level of individual voxels.

-W-

wired transmission: The transmission of information from one neuron to a closely apposed neuron across a synaptic cleft. Often used synonymously with synaptic transmission.
within-subjects manipulation: A manipulation in which each subject participates in all experimental conditions.