Introduction to fMRI and MR Imaging Principles

Comprehensive vocabulary flashcards covering basic principles, physics, scanner components, contrast mechanisms, neurovascular coupling, and preprocessing steps in fMRI.

Localization of function

The idea that the brain may have distinct regions that support particular mental processes.

Static magnetic field

The strong magnetic field at the center of the MRI scanner whose strength does not change over time, typically measured in Teslas ($T$).

Pulse sequence

A series of changing magnetic field gradients and electromagnetic pulses that allows the MRI scanner to create images sensitive to a particular physical property.

Structural neuroimaging

Techniques that create images of the brain's physical structure.

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.

Positron emission tomography (PET)

A technique that creates images based on the movement of injected radioactive material to measure glucose metabolism.

Measurement techniques

Techniques that measure brain function while subjects engage in one or more behaviors (e.g., single-unit recording, EEG, MEG, PET, fMRI).

Manipulation techniques

Techniques that change the brain's structure or function and then examine the effects of those changes on behavior (e.g., lesions, TMS, stimulation).

Electroencephalography (EEG)

A technique that measures the electrical potential of the brain via electrodes on the surface of the scalp.

Magnetoencephalography (MEG)

A technique that measures very small changes in magnetic fields caused by the electrical activity of neurons.

Contrast

The intensity difference between different quantities measured by an imaging system, the physical quantity being measured, or a statistical comparison of activation between experimental conditions.

Contrast-to-noise ratio (CNR)

The magnitude of the intensity difference between different quantities divided by the variability in their measurements.

Functional contrast

A type of contrast that provides information about a physiological correlate of brain function, such as changes in blood oxygenation.

Voxel

The basic sampling unit of MRI; a 3-D volume element.

Functional resolution

The ability to map measured physiological variation to underlying mental processes or behaviors.

Magnetic resonance

The absorption of energy from a magnetic field that oscillates at a particular frequency.

Resonant frequency

The frequency of oscillation that provides maximum energy transfer to the system.

Transmitter coil

An electromagnetic coil that generates an oscillating magnetic field at the resonant frequency of atomic nuclei within a sample.

Detector coil

An electromagnetic coil that measures energy emitted back to the environment after its initial absorption by the sample.

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.

Spatial gradients ($G$)

A magnetic field whose strength varies systematically over space.

Echo-planar imaging (EPI)

A fast technique that allows collection of an entire two-dimensional image by changing spatial gradients rapidly following a single excitation pulse from a transmitter coil.

Blood-oxygenation-level-dependent (BOLD) contrast

The difference in signal on $T_2^*$ -weighted images as a function of the amount of deoxygenated hemoglobin.

Field uniformity

Having a constant magnetic field strength throughout a wide region near the center of the scanner bore.

Homogeneity

Uniformity of a magnetic field over space and time.

Superconducting electromagnets

A set of wires made of metal alloys that have no electrical resistance at very low temperatures, generating very strong magnetic fields with minimal energy requirements when cooled near absolute zero.

Cryogens

Cooling agents used to reduce the temperature of the electromagnetic coils in an MRI scanner.

Radiofrequency coils

Electromagnetic coils used to generate and receive energy at the sample's resonant frequency.

Excitation

The process of sending electromagnetic energy to a sample at its resonant frequency, causing spins to change from a low-energy state to a high-energy state.

Reception

The process of receiving electromagnetic energy emitted by a sample as nuclei return to a low-energy state following the cessation of the excitation pulse.

MR signal

The current measured in a detector coil following excitation and reception.

Surface coil

A radiofrequency coil placed on the surface of the head that provides excellent sensitivity to signal from nearby regions but poor sensitivity to distant regions.

Volume coil

A radiofrequency coil that surrounds the entire sample and provides similar sensitivity throughout.

Phased array

A method for arranging multiple surface coils to maintain sensitivity with improved spatial coverage.

Parallel/multi-channel imaging

The use of multiple receiver channels to acquire data following a single excitation pulse.

Gradient coils

Electromagnetic coils that create controlled spatial variation in the strength of the magnetic field.

Shimming coils

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

Projectile effect

The movement of an untethered ferromagnetic object through the air toward the bore of the MRI scanner.

Translation

Movement of an object along an axis in space.

Torsion

Rotation or twisting of an object.

Specific absorption rate (SAR)

A measure of how much electromagnetic energy is absorbed by the body over time.

Magnetic moment ($\mu$)

The torque exerted on a magnet, moving electrical charge, or current-carrying coil when placed in a magnetic field.

Angular momentum ($J$)

A quantity given by multiplying the mass of a spinning body by its angular velocity.

Spins

Atomic nuclei that possess both a magnetic moment and angular momentum (the NMR property).

Spin system

A collection of atomic nuclei that possess the NMR property within a spatial location.

Net magnetization ($M$)

The sum of all the magnetic moments of all spins within a spin system.

Precession

The gyroscopic motion of a spinning object, in which the axis of spin itself rotates around a central axis.

Larmor frequency

The resonant frequency of a spin within a magnetic field of a given strength ($\nu = \frac{\gamma}{2\pi} B_0$).

Parallel state

The low-energy state in which an atomic spin precesses around an axis parallel to the main magnetic field.

Antiparallel state

The high-energy state where an atomic spin precesses around an axis opposite to the main magnetic field.

Transverse relaxation (spin-spin relaxation)

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

Longitudinal relaxation (spin-lattice relaxation)

The recovery of net magnetization along the longitudinal direction as spins return to the parallel state.

$T_1$ (recovery)

The time constant for the recovery of the longitudinal component of net magnetization ($M$) over time.

$T_2$ (decay)

The time constant that describes the decay of the transverse magnetization component due to accumulated phase differences caused by spin-spin interactions.

$T_2^*$ (decay)

The time constant describing the decay of transverse magnetization due to both accumulated phase differences and local magnetic field inhomogeneities.

Slice selection

The combined use of a spatial magnetic field gradient and radiofrequency pulse to excite spins exclusively within a specific slice.

Frequency-encoding gradient

A gradient applied during the data acquisition period so that spin precession frequencies vary systematically over space.

Phase-encoding gradient

A gradient applied before the data acquisition period so that spins accumulate differential phase offsets over space.

Static contrasts

Contrast mechanisms that are sensitive to the type, number, relaxation properties, and local environment of spins (e.g., $T_1$, $T_2$, proton density).

Motion contrasts

Contrast mechanisms sensitive to the movement of spins through space (e.g., diffusion, perfusion).

Endogenous contrast

Contrast that depends on an intrinsic physical or physiological property of biological tissue.

Exogenous contrast

Contrast that requires the injection of a foreign substance into the body.

Repetition time (TR)

The time interval between successive excitation pulses.

Echo time (TE)

The time interval between an excitation pulse and data acquisition.

Gradient-echo (GRE) imaging

A primary MRI pulse sequence that uses magnetic field gradients to generate the MR signal changes measured at data acquisition.

Spin-echo (SE) imaging

A primary MRI pulse sequence that uses a second $180^\circ$ electromagnetic refocusing pulse to generate measured signal changes.

Refocusing pulse

A $180^\circ$ EM pulse that compensates for the gradual loss of phase coherence following initial excitation.

K-space

A temporary spatial-frequency data storage matrix that stores all acquired raw MR signal information prior to Fourier Transformation.

Functional hyperemia

A local increase in blood flow that occurs in response to sensory, motor, or cognitive activity.

Diamagnetic

The physical property of a substance that slightly opposes a magnetic field (e.g., oxygenated hemoglobin).

Paramagnetic

The physical property of a substance that concentrates magnetic field lines, increasing local magnetic field strength (e.g., deoxygenated hemoglobin).

Tripartite synapse

A functional synapse formed by a presynaptic axon and postsynaptic dendrite, ensheathed and modulated by an astrocytic process.

Neurovascular unit

A functional unit consisting of astrocytes, pericytes, and neurons impinging on a local microvessel to regulate blood flow.

Hemodynamic response (HDR)

The characteristic change in MR signal on $T_2^*$ -weighted images over time following local neuronal activity.

Initial dip

A short-term decrease in MR signal immediately following the onset of neuronal activity, preceding the main hyperemic peak of the HDR.

Balloon model

A model describing the dynamic interactions between changes in blood volume and blood flow associated with neuronal activity.

Partial volume effects

The combination within a single voxel of signal contributions from two or more distinct tissue types or functional regions.

Spatial smoothing

The blurring of fMRI data across adjacent voxels to improve statistical test validity and maximize functional SNR at the cost of spatial resolution.

Normalization

The spatial transformation of individual subject data to match a standardized brain image or stereotaxic space.

Region-of-Interest (ROI) analyses

Evaluations of hypotheses regarding brain functional properties aggregated over a pre-determined set of voxels.

fMRI adaptation

The reduction in BOLD response upon repeated presentation of stimuli sharing a specific attribute, indicating regional sensitivity to that attribute.

Preprocessing

Computational operations applied to raw reconstructed fMRI data before statistical analysis to reduce non-task variability and prepare data for testing.

Raw SNR

The ratio between the MR signal intensity of a sample and the thermal noise measured outside the sample.

Functional SNR (fSNR)

The ratio between the intensity of a signal associated with functional brain changes and the variability from all noise sources.

Thermal noise

Fluctuations in signal caused by thermal motion of electrons within the subject's tissue or scanner hardware.

Scanner drift

Slow, low-frequency changes in baseline voxel intensity over time during scanning.

Aliasing

The artifactual expression of high-frequency signal components at lower frequencies due to an insufficient sampling rate.

Coregistration

The spatial alignment of images or image volumes acquired across different modalities or sessions for a single subject.

Rigid-body transformation

A spatial transformation that preserves object size and shape using 3 translational and 3 rotational parameters.

Nyquist frequency

The highest frequency component that can be accurately resolved in a digitally sampled signal, equal to half the sampling rate.

Multiple comparison problem

The substantial increase in false-positive results (Type I errors) when performing simultaneous statistical tests across tens of thousands of voxels.