Week 1: MRI physics Flashcards
MRI summary
MRI is based on the magnetization properties of atomic nuclei. A powerful, uniform, external magnetic field is employed to align the protons that are normally randomly oriented within the water nuclei of the tissue being examined. This alignment (or magnetization) is next perturbed or disrupted by introduction of an external Radio Frequency (RF) energy. The nuclei return to their resting alignment through various relaxation processes and in so doing emit RF energy. After a certain period (TE) following the initial RF, the emitted signals are measured. Fourier transformation is used to convert the frequency information contained in the signal from each location in the imaged plane to corresponding intensity levels, which are then displayed as shades of gray in a matrix arrangement of pixels. By varying the sequence of RF pulses applied & collected, different types of images are created. Repetition Time (TR) is the amount of time between successive pulse sequences applied to the same slice. Time to Echo (TE) is the time between the delivery of the RF pulse and the receipt of the echo signal.
Tissue can be characterized by two different relaxation times – T1 and T2. T1 (longitudinal relaxation time) is the time constant which determines the rate at which excited protons return to equilibrium. It is a measure of the time taken for spinning protons to realign with the external magnetic field. T2 (transverse relaxation time) is the time constant which determines the rate at which excited protons go out of phase with each other. It is a measure of the time taken for spinning protons to lose phase coherence among the nuclei spinning perpendicular to the main field.
Longitudinal Relaxation (T1)
This process describes how quickly the magnetic moments of protons return to their equilibrium alignment with the main static magnetic field (B0) after being perturbed by a RF pulse. This process is characterized by an exponential growth (expressed by a constant T1) which differs for different tissues. Each tissue has a different T1 value, which represents the time (in ms) it takes for that tissue to reach 63% of the original magnetization.
Transverse Relaxation (T2)
Characterizes how quickly the magnetic moments of protons lose coherence and dephase in the transverse (xy) plane. This process is characterized by an exponential decay (expressed by a constant T2) which differs for different tissues. Each tissue has a different T2 value, which represents the time (in ms) it takes for that tissue to reach 37% of the original magnetization (and dephasing?).
Different tissues have different…
…T1 and T2 relaxation times, which is what makes them appear differently in MRI images.
Repetition time (TR)
TR is the time between successive RF pulses. It influences T1 relaxation. Longer TR allows for more complete recovery of longitudinal magnetization. This is like giving tissues more time to relax and return to their equilibrium state. Therefore, a short TR will highlight T1 tissue differences.
TE (Echo Time)
TE is the time at which the MRI machine measures the MR signal in the transverse plane after the RF pulse. It affects T2 relaxation. A shorter TE captures signals when the transverse magnetization is still coherent; hence, a longer TE will emphasize T2 effects, because we need to wait some time for the differences in dephasing in different tissues to show.
T/F: TR and TE are adjustable parameters in MRI sequences.
True: By choosing appropriate TR and TE values, we can control the contrast in MRI images.
Short TR (and short TE) emphasizes…
…T1 contrast, making differences in T1 relaxation times more prominent, resulting in T1-weighted images.
T1-weighted MRI enhances the signal of the fatty tissue
Long TE (and long TR) emphasizes…
…T2 contrast, making differences in T2 relaxation times more pronounced, leading to T2-weighted images.
T2-weighted MRI enhances the signal of the water.
Field of view (FOV)
It is a crucial parameter in MRI that defines the size of the anatomical region that is imaged or the area covered by the MRI scan. FOV is typically measured in units of length, such as millimeters or centimeters, and it determines the spatial extent of the MRI image.
Pixel
the smallest discrete unit or picture element in a digital image, representing a single point of color or brightness
Voxel
In MRI, a voxel, short for “volume element,” represents a three-dimensional pixel, serving as the smallest unit in a 3D image. It encompasses a tiny volume within the body, with specific spatial dimensions, and contains information about the tissue properties within that volume, contributing to the construction of detailed 3D MRI images.
Larmor frequency
the specific resonant frequency at which the nuclei of protons in the body precess when exposed to a strong magnetic field in MRI. It is directly proportional to the strength of the magnetic field and is fundamental for the precise manipulation and detection of MRI signals, allowing for the creation of detailed images.
Precession
refers to the circular or spiraling motion of the magnetic moments of atomic nuclei (e.g., protons) when subjected to a strong static magnetic field. This motion occurs at the Larmor frequency and is essential for the generation of MRI signals. It forms the basis for encoding spatial information and creating detailed images of the body’s internal structures in MRI.
Gradient fields
additional magnetic fields that are superimposed on the main static magnetic field (B0) in MRI. These gradient fields are applied along three orthogonal axes: X, Y, and Z. Gradient fields are used to spatially encode the MRI signal by creating variations in the magnetic field strength along these axes.
Frequency encoding
typically corresponds to the X-axis in most MRI systems. It is used to determine the left-to-right or horizontal position of structures within the imaging slice. The gradient applied along the frequency encoding axis causes protons at different positions to precess at slightly different frequencies. This frequency variation is detected and used to encode the horizontal spatial information.
Phase encoding
applied along the Y-axis or vertical direction in most MRI systems. It determines the top-to-bottom position of structures within the imaging slice. The gradient applied along the phase encoding axis introduces phase differences in the MRI signal based on vertical position, allowing the encoding of vertical spatial information.
K-space
an array of numbers representing spatial frequencies in the MR image. The cells of k-space are commonly displayed on rectangular grid with principal axes kx and ky. The kx and ky axes of k-space correspond to the horizontal (x-) and vertical (y-) axes of the image. The k-axes, however, represent spatial frequencies in the x- and y-directions rather than positions. The individual points (kx,ky) in k-space do not correspond one-to-one with individual pixels (x,y) in the image. Each k-space point contains spatial frequency and phase information about EVERY pixel in the final image. Conversely, EACH pixel in the image maps to EVERY point in k-space.
Inhomogenity
Changes in the magnetic field caused by e.g., the insertion of the body in the scanner. Most prominent near nasal and auditory structures. Shimming can be used to deal with this; at the beginning of the recording, the scanner “shims” the magnetic field. This applies minor changes in the magnetic field to compensate for the insertion of the body.
BOLD contrast allows to measure….
…the ration between oxygenated and de-oxygenated hemoglobin in the blood
BOLD uses the fact that hemoglobin…
…exists in 2 different states, each with different magnetic properties
Deoxyhaemoglobin (DEO) is …
paramagnetic; it works as suppressor of MR signal.
Oxyhaemoglobins is …
diamagnetic
explanation of BOLD signal in terms of hemoglobin
An initial increase in DEO leads to initial decrease BOLD signal. This leads to overcompensation to dilute DEO > peak in BOLD signal about 5-6 seconds following activation > after peak, the BOLD signal decreases to an amplitude below baseline (due to decrease blood flow and increased blood volume)
Properties of HRF
1) 0.1% to 5% = magnitude of signal change is quite small, hence hard to see in single scans
2) Response is delayed and quite slow; extracting temporal information is tricky but possible; even short events have rather long response
3) Shape of the response has been shown to vary across subjects and regions! > important when picking the canonical HRF to convolve the predictors
Often, BOLD signal corresponds quite well with the…
…local field electrical potential from a group of cells
T/F: The BOLD signal is often localized in areas of increased neural activity and the higher the field strength (the closer the coil to the head) the more true this is
True
Signal-to-noise (SNR) ratio
Strength of the signal / its variability; used as basic effect size (related to t-statistic!)
Contrast-to-noise ratio
Difference in intensity between two tissue types / the variability within their measurements
Temporal SNR
strength of signal over time / its variability across time
Scaling
The absolute scaling of BOLD responses is arbitrary > issue when we want to compare signal from e.g., different scanners and parameters
Saturation of BOLD response
Non-linear effect; caused by stimuli being presented too close to eachother (better to present them 5-6 seconds apart to reduce this saturation effect)
In terms of neuronal activity, BOLD most likely reflects …
integrated post-synaptic activity
The quality of the MR signal for BOLD-fMRI signal for a given voxel is best characterized by its …
temporal SNR
Which phenomena hint at the non-linearity of the BOLD-response?
1) saturation; 2) refractory effects
