Glossary

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W

180-degree 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.
90-degree 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.

A

action potential: A 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, 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.
anaerobic glycolysis: The conversion of glucose to lactate in the absence of oxygen.
anatomical ROI: Region of interest that is 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, while 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 weblike appearance.
arterial spin labeling (ASL): A family of perfusion imaging techniques that measure blood flow by labeling spins with excitation pulses and then waiting for the labeled spins to enter the imaging plane before data acquisition.
arteries: 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, so 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.
autoradiography: An invasive imaging technique that labels molecules using radioactive isotopes and then measures the concentration of those molecules by exposing slices of tissue to photographic emulsions.
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 hillock: A region of the cell body located at the emergence of the axon. Changes in its electrical potential lead to the generation of action potentials.
axon: A neuronal process that transmits an electrical impulse from the cell body to the synapse, performing a primarily signaling function.

B

b factor: The degree of diffusion weighting applied within a pulse sequence.
B: The sum of all magnetic fields experienced by a spin.
B₀: The strong static magnetic field generated by an MRI scanner.
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, to improve the flexibility of their design matrices.
between-subjects: 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.
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.
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 familywise error rate correction for multiple comparisons in which the alpha value is decreased proportionally to the number of independent statistical tests.
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 agent: A compound that, when injected into an organism, influences the MR signal differently depending on the local concentrations of calcium ions. Such agents could lead to maps of neuronal signaling.
capillaries: Small and thin-walled blood vessels. The extraction of oxygen and glucose from the blood and the removal of waste carbon dioxide occur in the capillaries.
capillary recruitment: The idea that increased blood flow through the capillary bed results in perfusion of previously unperfused 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 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.
cerebrospinal fluid (CSF): A colorless liquid that surrounds the brain and spinal cord and fills the ventricles within the brain.
cerebrum: The two hemispheres forming the major part of the brain.
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.
coactivation: The simultaneous activation of two or more brain regions within a single experimental task. Coacti-vation 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.
complex cell: A neuron in the visual cortex with a larger receptive field than a simple cell and 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.
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 (or levels): Different values of the independent variable(s).
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.
conjugate mirroring: A partial k-space imaging technique in which data collected from one half of k-space is used to estimate data from the other half.
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 which itself is not directly observable. Attention is an example of 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. It also can refer to the physical quantity being measured (e.g., T₁ contrast). (2) 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 nontask condition.
converging operations: The use of 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 and the posterior portion is known 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 (neocortex): The thin wrapping of cell bodies around the outer surface of the brain.
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: A positive and negative point charge 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 on the basis of cell structure.

D

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 non-predictive variables.
data-driven analysis: Exploration of the intrinsic structure of data.
dB/dt: The change in magnetic field strength (dB) over time (dt).
deactivations: Decreases in BOLD activation during task blocks compared with nontask blocks.
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, performing a primarily integrative function.
detection: Determination of whether activation of 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: Having the property of a weak repulsion from a magnetic field.
diffusion: The random motion of molecules through a medium over time.
diffusion tensor imaging (DTI): A 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 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 hemodynamic 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 part of the family known as biogenic amines. Dopamine is produced within cells in the brainstem that project broadly to the striatum and cortex (especially the frontal lobe).
dorsal: 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 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.
effect size: The numerical difference between means divided by the standard deviation.
effective bore size: The clearance within the bore of the MRI scanner that limits the maximum size of the sample that can be scanned.
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 dataset 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 dataset.
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 unexplained by the design matrix, when fit by the parameter matrix.
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. Also known as a trial.
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.
excitatory postsynaptic potential (EPSP): A depolarization of the postsynaptic cell membrane.
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

false discovery rate (FDR): The probability of having at least one false positive result, given the set of reported positive results.
familywise 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 units of Tesla.
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.
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); this has the major advantage of making no assumptions about the shape of the observed response function.
fixed-effects analyses: Intersubject analyses that assume that the effect of the experimental manipulation is fixed across subjects, with differences between subjects 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 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.
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.
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 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 functional organization of the brain. Common functional neuroimaging techniques include fMRI, PET, and optical imaging.
functional resolution: The ability to map measured physiological variation to underlying mental processes.
functional ROI: A region of interest that is chosen based on functional criteria, such as the output of an independent voxelwise 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

γ-aminobutyric acid (GABA): 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.
glucose: A sugar made by the human body whose stored energy is used to produce ATP.
glutamate: One of the most important excitatory neurotransmitters.
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 in the cortical surface.
gyromagnetic ratio (γ): The ratio between the charge and mass of a spin. The gyromagnetic ratio 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 or right half.
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.
hemodynamic: Having to do with changes in blood flow or other blood properties.
heteroscedastic: Having the property that the distributions of noise are different across experimental conditions.
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.
hyperscanning: The simultaneous collection of fMRI data from two or more subjects who are interacting in an experimental paradigm.
hypothalamus: A brain nucleus that supports homeostatic functions, including the regulation 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 reconstruction: The process by which the raw MR signal, as acquired in k-space form, is converted into spatially informative images.
image: A visual description of how one or more quantities vary over space.
imaging genomics: A new field that investigates the effect of genetic variation on brain structure and function.
imaging plane: The plane in which changes in 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 non-medical reasons.
independent components analysis (ICA): An important class of data-driven analyses that identify stationary sets of voxels whose activations 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 that 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 their 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.
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 collection of data in an alternating order, so that data are first acquired from the odd-numbered slices and then from the even-numbered slices, to minimize the influence of excitation pulses upon adjacent slices.
interleaved stimulus presentation: The presentation of events of interest at different points within a TR over trials (e.g., one-quarter, one-half, and three-quarters of TR in addition to TR onset), increasing the effective sampling rate of an experiment at the expense of fewer trials per condition.
interocular trauma test: An intuitive test of significance 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.
inverse problem: The mathematical impossibility of determining the distribution of electrical sources within an object based on the measurement of electrical or magnetic fields at the surface of the object.
inversion recovery: A technique for increasing T₁ contrast by adding a 180° inversion pulse before a standard pulse sequence.
ion channel: A pore in the membrane of a cell that allows passage of particular ions under certain conditions.
ion: A charged atom.
ionizing radiation: Electromagnetic radiation that has sufficient energy to separate electrons from electrically neutral atoms, turning them into ions.
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.

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

keyhole imaging: A partial k-space imaging technique in which only the center of k-space is collected following each excitation, in order to maximize raw SNR while minimizing acquisition time.
k-space trajectory: A path through k-space. Different pulse sequences adopt different k-space trajectories.
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.

L

labeling plane: The plane in which initial excitation pulses 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 side of the brain.
least-squares error: A commonly used cost function, the sum of the squared residuals.
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: An 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 relaxation (or spin–lattice relaxation): The recovery of the net magnetization along the longitudinal direction as spins return to the parallel state.
longitudinal: Parallel to the main magnetic field, or the z-direction, of the scanner (i.e., into the bore).
Lorentz effect imaging (LEI): A technique for direct visualization of ionic electrical activity using MRI.
Lorentz force: The force on a moving charge within a magnetic field. Lorentz forces cause spatial displacements in ions and conductors if they are placed in strong magnetic fields.

M

machine learning: A subdiscipline within computer science that develops algorithmic rules for relating input data to desirable outputs.
magnet diameter: The diameter of the electromagnetic coil that generates the strong static field used in MRI.
magnetic field mapping: The collection of explicit information about the strength of the magnetic field at different spatial locations.
magnetic moment (μ): The torque (i.e., turning force) exerted on a magnet, moving electrical charge, or current-carrying coil when it is placed in a magnetic field.
magnetic resonance angiography (MRA): The creation of images of the vascular system using MRI.
magnetic resonance: The absorption of energy from a magnetic field that oscillates at a particular frequency.
magnetic susceptibility: The intensity of magnetization of a substance when placed within a magnetic field.
magnetization transfer: An MR imaging technique that uses an off-resonance excitation pulse to saturate the MR signal from large molecules; the subsequent influence of that pulse upon free protons in water indicates the concentration of those large molecules.
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.
massive coil array: A method for arranging a large number of surface detector coils to improve spatial coverage while maintaining high sensitivity.
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 middle 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.
microstimulation: Applying currents through microelectrodes to stimulate activity in a small number of neurons.
midbrain: A section of the brain rostral to the pons; it includes a number of important nuclei.
mind reading: The ability to construct a comprehensive description of the contents of consciousness. This is currently far beyond the capacity of any neuroscience technique.
mixed design: A design that contains features of both blocked and event-related approaches.
MNI space: A commonly used space for normalization of fMRI data; its coordinates are derived from an average of MRI structural images from several hundred 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.
morphometric: Relating to the measurement of shape.
motion contrasts: Contrast mechanisms that are sensitive to the movement of spins through space (e.g., diffusion, perfusion).
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.
MR signal: The current measured in a detector coil following excitation and reception.
multiple comparison problem: The increase in the number of false-positive results (i.e., Type I errors) with 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 classification: 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.
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.
neuron: A cell that is the basic information-processing unit of the nervous system.
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.
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: Non-meaningful 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.
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.
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 nontask block.
Nuremberg Code: A set of principles for the ethical conduct of research involving human subjects that was 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: 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.
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 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.
outer k-space (OK) imaging: A partial k-space imaging technique in which only the periphery of k-space is collected following each excitation, in order to ensure that high-spatial-frequency components of the MR signal are present.
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 or (multiple-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.
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 k-space imaging: A technique for reducing data acquisition time (and thus increasing temporal resolution) by collecting only part of the k-space data following each excitation and filling the uncollected portions of k-space with estimated data.
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, occurring typically about 4 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: Blood flow through tissue.
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 determine the size of an effect that might be observed with a given alpha level.
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.
phased array: A method for arranging multiple surface detector coils to improve spatial coverage while maintaining high sensitivity.
phase-encoding gradient: A gradient that is applied before the data acquisition period, so that spins can accumulate differential phase offsets over space.
phrenologists: Adherents to the belief that bumps and indentations on the skull provided information about the magnitude of some trait supported by the underlying brain region.
pH-sensitive contrast agent: A compound that, when injected into an organism, influences the MR signal differently depending on the pH of the local environment.
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.
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.
power: The probability of detecting an effect of the experimental manipulation.
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; this 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.
pre-surgical planning: The use of fMRI or another neuroscience technique to map particular functions in a single individual, in order 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 ferromagnetic 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.
PSP: Any postsynaptic potential, excitatory or inhibitory, that results from synaptic activity.
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 fields 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 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 gradients.

Q

quality assurance (QA)

A set of procedures designed to identify problems with fMRI data so that they do not compromise experimental analyses.

R

radiofrequency 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

Intersubject analysis that treats the effect of the experimental manipulation as variable across subjects, so that it could have a different effect on different subjects.

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 visual 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 nuclei 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 180°-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 pre-determined 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 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, in order to effect long-lasting changes in brain function.

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.

research

The accumulation of data, whether by observation or experimentation, to develop general knowledge.
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 (or resels)

The independent statistical tests within an fMRI volume.

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 when 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, then 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.

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 (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) or topographical divisions (e.g., different structural regions like Brodmann areas).

selectivity

The tendency for a manipulation to lead to one outcome. Perfect selectivity is sometimes referred to as “specificity.”

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 coils

Electromagnetic coils that compensate for inhomogeneities in the static magnetic field.

signal averaging

The combination of data from multiple instances of the same manipulation in order to improve functional SNR.

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.

signaling activity

The transmission of the outcome of an integrative process from one neuron to another.

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 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, in order to disrupt some ongoing brain process.

single-unit recording

Collection of data about the electrophysiological activity (e.g., action potentials) of a single neuron.

sinuses

The term sinus has two primary meanings in neuroanatomy: (1) long venous channels formed by meningeal coverings that form the primary draining system for the brain, and (2) air-filled cavities in the skull.

slice

A single slab of 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 an electromagnetic 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 the cell; it contains cytoplasm, the cell nucleus, and organelles.

spatial extent

The number of active voxels within a cluster of activity (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 only experiences 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 functional SNR, 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 180° 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.

spiral-out trajectory

A corkscrew path that begins at the center of k-space and ends at the periphery. It is the most common form of spiral imaging.

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

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 Tesla (T).

statistical map (or statistical parameter map)

In fMRI, the labeling of all voxels within the image according to the outcome of a statistical test.

stereotaxic space

A precise mapping system (e.g., of the brain) using 3-D 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.

subject

An individual who participates in a research study. Some journals and scientific societies prefer the term “participant,” to emphasize 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 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 in the cortical surface.

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.

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 machine (SVM)

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.

system noise

Fluctuations in MR signal intensity over space or time that are caused by imperfect functioning of the scanner hardware.

system

A set of regions that are linked by coactivation, but for which the connectivity and causal relationships remain unknown.

T

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 of net magnetization due to accumulated phase differences caused by spin–spin interactions.

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.

T₂-weighted (T₂-dependent)

Images that provide information about the relative T₂ values of tissue; also known simply as T₂ images.

Talairach space

A commonly used space for normalization of fMRI data; its coordinates are based on measurements from a single post-mortem human brain, as published in an atlas by Talairach and Tournoux.

task frequency

The rate of presentation of a periodic experimental task.

TCA cycle

The second step in aerobic glycolysis; it involves the oxidation of pyruvate.

temperature-sensitive contrast agent

A compound that, when injected into an organism, influences the MR signal differently depending on the local tissue temperature.

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 brain nucleus that is important for many aspects of perception and cognition; it is 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 series

A large number of fMRI images collected at different points in time.

time-locking

Synchronization of analyses to events of interest, usually for the extraction of epochs.

torque

A force that induces rotational motion.

torsion

A 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 it to rotate so that it becomes aligned with the magnetic field.

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.

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).

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 (or spin–spin relaxation)

The loss of net magnetization within the transverse plane due to the loss of phase coherence of the spins.

trial sorting

The post hoc assignment of events to conditions, often based on behavioral data.
trial A single instance of the experimental manipulation.
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.

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

ultra-high-resolution MRI

The acquisition of MR images with voxel sizes in the order of tens of micrometers. Applications of ultra-high-resolution MRI to animal tissues are known as MR microscopy.

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, though 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.

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 MR 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 bottom of the brain.

ventricles

Fluid-filled cavities within the brain.

venules

Small veins.

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

A single image of the brain, itself consisting of multiple slices and voxels.

volumetric

Relating to the measurement of volume.

voxel

A three-dimensional volume element.

voxelwise analyses

Evaluations of hypotheses about the functional properties of individual voxels (or small clusters of voxels), often throughout the entire brain.

voxelwise analysis

The evaluation of statistical tests at the level of individual voxels.

W

within-subjects

A manipulation in which each subject participates in all experimental conditions.