w8 Flashcards
list the imaging modalities for:
structural imaging
functional imaging
multimodal imaging system
structural: Microscopy, CT, sMRI, dMRI
functional imaging: PET, SPECT, fMRI, EEG, ECG
multimodal imaging systems: PET/CT, PET/MRI, EEG/MRI, MRI/MRI
CT uses the ionizing X-rays to take images from different angles in very fine slices through the
specific part of the body. Because of the risks of ionizing radiation associated with CT scans, patients should not receive CT screening in excess of those recommended by established guidelines.
how does CT combine these x-ray images to produce the slices (tomographic images) of the body
uses a filtered back projection scheme
http://xrayphysics.com/ctsim.html
what is the most powerful and versatile approach to study neurotransmitter / receptor interactions
PET
what is the most widely used radiotracer that can assess glucose metabolism in the brain.
FDG
what are some software packages for analyzing PET
Statistical Parametric Mapping (SPM)
NEUROSTAT
what is Electroencephalography (EEG)
EEG is an electrophysiological monitoring method to record electrical activity of the brain. It is typically non-invasive, with electrodes placed along the scalp. EEG measures the voltage fluctuations resulting from the ionic current within the neurons of the brain.
the recording of the brain’s spontaneous electrical activity over a period of time, as recorded from multiple electrodes placed on the scalp.
what is Magnetoencephalography (MEG)
MEG is a functional neuroimaging technique for mapping brain activity by recording the magnetic fields produced by electrical current occurring natually in the brain, using very sensitive magnetometers.
why combine EEG and MEG
Recent advances in EEG / MEG have significantly improved localization of event-related brain activity in healthy human subjects, and of intracranial spikes in epilepsy patients.
MEG and EEG both detect activity below the surface of the cortex very poorly. However, the errors are very different between these two techniques, thus combining them allows for correction of some noise.
what other imaging technique may be used with EEG/MEG
An important opportunity lies in integrating high temporal resolution EEG (and MEG) source imaging with high spatial resolution fMRI. Significant progress has been made to leverage the complementary nature of EEG and fMRI, which can be performed simultaneously in an MRI scanner.
Describe the typical EEG/MEG pipeline
EEG / MEG pre-processing: Want to find peaks in brain activity. Filtering, artefact correction, baseline correction, ERP/ERF analysis. Power spectrum and time-frequency analysis. Potential/Field and spectrum mapping.
Source estimation: Want to find the source of found brain activities. Forward modelling, Inverse calculation, ROI analysis, Individual anatomic head model.
Connectivity analysis: Construct information pathways. Granger causality analysis, Connectivity visualization.
Is MRI safe? and why
MRI is generally a safe procedure, as it uses magnetic and radio waves to generate images, not ionizing radiation like X-ray or gamma ray.
There are no known harmful side-effects associated with temporary exposure to strong magnetic field (8 Tesla) and radio waves used by MRI scanners.
Due to the potential interactions with pacemakers and cardioverterdefibrillators (ICDs), patients with these implanted devices are selectively restricted from use of MRI examination by the US Food and Drug Administration (FDA).
what is the T1 time of a tissue (MRI)
the time it takes for the excited spins to recover and be available for the next excitation. Related to the amount of hydrogen atoms.
how do tissues with a short T1 time appear in T1-Weighted MRI
and how do tissues with a long T1 time appear in T1-Weighted MRI
short: bright because they regain most of their longitudinal magnetization during the TR interval and produce a stronger MR signal. Generally less hydrogen-rich tissue e.g. fat.
long: dark because they do not regain much longitudinal magnetization during the TR interval and produce a weaker MR signal. Generally more hydrogen-rich tissue e.g. water.
what are TR times (MRI)
repetition time
the length of time between corresponding consecutive points on a repeating series of pulses and echoes
https://mriquestions.com/tr-and-te.html
what are TE times (MRI)
echo time
represents the time from the center of the indiced RF-pulse to the center of the echo / the time of MR sampling
how is a T1-Weighted MRI produced
produced by using short TE and TR times
what is Post Gadolinium T1 Contrast Enhanced MRI
why is this used
an imaging method where the T1-weighted MRI is
acquired after injection of a contrast agent : gadolinium.
It enables analysis of blood vessels generated by brain tumors or brain lesions. The blood vessels and pathologies with high vascularity appear bright on T1 weighted post gadolinium images.
what is t2 time
The T2 time determines how quickly an MR signal fades after excitation. The T2 decay occurs as a result of energy transfer between spins.
how do tissues with a short T2 time appear in T2-Weighted MRI
and how do tissues with a long T2 time appear in T2-Weighted MRI
Tissues with a short T2 appear dark on T2-weighted images. Loses transverse magnetization more rapidly.
Tissues with a long T2 appear bright on T2-weighted images. Magnitude of transverse magnetisation is large.
Pathological process normally increase the water content in tissues. Consequently, pathological processes are usually bright on T2 weighted images
how is a T2-Weighted MRI produced
produced by using longer TE and TR times
what is proton density (PD)
the number of excitable spins per unit volume.
Proton density determines the maximum signal that can be obtained from a given tissue.
what is a Proton Density Weighted MRI
The image contrast in PD images is not dependent
on T1 or T2 relaxation. The signal we receive is completely dependent on the amount of protons in the tissue. Proton density can be enhanced by minimizing the effect of T1 and T2 contrast.
what type of tissue produces brights or dark areas in Proton Density Weighted MRI
Less protons means low signal and appear as dark areas on the image
whereas more protons produce a lot of signal and will be bright on the image.
Same as T2-weighted MRI, pathological processes normally increase the water content in tissues. The added water component results in a signal increase on FLAIR images. Consequently, pathological processes are usually bright on FLAIR images.
how is a Proton Density Weighted MRI produced
a long TR allows tissue to fully recover their longitudinal magnetisation and therefore reduces the T1 weighting
a short TE does not give tissue time to decay and therefore reduce the T2 weighting.
why is Proton Density Weighted MRI used
PD sequences are very useful for evaluating structures with low signal intensities such as the bones or connective tissue structures (ligaments and tendons)
mainly used for the imaging of the brain, spine, and musculoskeletal system.
what is Fluid-Attenuated Inversion Recovery (FLAIR)
a pulse sequence used in MRI that nulls fluids.
when is FLAIR used
This sequence is commonly used in the brain and spinal cord where the lesions are normally covered by bright cerebrospinal fluid (CSF) signals.
what is Diffusion Tensor Imaging (DTI) / Diffusion MRI (dMRI) used for and why
currently the only technique that allows us to infer the brain white matter pathways in vivo.
most applicable when the tissue of interest is dominated by isotropic water (or other molecule) movement, e.g., in brain grey matter or cerebral spinal fluid (CSF).
By probing at many different orientations, dMRI is able to estimate the orientation of axonal fibre bundles, based on the fact that water diffuses most rapidly along the length of axons. This also leads to longer scanning time as compared to sMRI.
in what settings is dMRI used
mainly used in laboratories, and has not been evaluated in clinical trials due to the differences in signal estimation models and fibre tracking algorithms, the variations in datasets, and the lack of ground truth.
still being researched for new models and methods.
have a close correspondence to the anatomy of the tracts in the post-mortem specimens, but DTI still await
confirmatory validation.
White matter is one of the two components of
central nervous system. The other main component of the brain is grey matter.
what is the % of white matter in the brain
45%
what is white matter composed of
White matter is formed by the glial cells and myelinated nerve fibers (axons)
what is grey matter composed of
neuronal somas.
what are the functions of white and gray matter
While grey matter is primarily associated with processing and cognition, white matter modulates the distribution of action potentials, acting as a relay and coordinating communication between different brain regions.
White matter is believed to be related to a range of neurological disorders, referred to collectively as disconnection syndromes, what are some examples
conduction aphasia, visual associative agnosia, apraxia, pure alexia, etc.
what is the Corpus Callosum
a broad thick bundle of dense myelinated fibers that connect the left and right hemisphere. Corpus callosum is the largest white matter structure in the
brain.
what is the Optic Chiasm
Our optic nerve receives different inputs from our two eyes. The optic chiasm corresponds to the part of
the brain where the left and right optic nerves cross.
what is the Corticospinal Tract (CST)
conducts impulses from the brain to the spinal cord. It
is made up of a lateral and anterior tract. The CST is involved in voluntary movement.
what is the Arcuate fasciculus (AF)
a bundle of axons that forms part of the superior
longitudinal fasciculus.
The arcuate bidirectionally connects the caudal temporal cortex and inferior parietal cortex to locations in the frontal lobe.
what is Brownian motion
the random translational motion of molecules
the erratic random movement of microscopic particles in a fluid, as a result of continuous bombardment from molecules of the surrounding medium.
what is the meaning of isotropic and anisotropic
If the diffusion rates along all directions are the same then we may say such diffusion is isotropic
if the diffusion rate depends on directions and some directions faster than others, then such diffusion is anisotropic
what is Fick’s first Law
J = -D (d phi/dt)
J is the diffusion flux / measures the amount of substance that will flow through a unit area during a unit time interval.
D is the diffusion coefficient or diffusivity.
phi is the concentration
what is pulsed gradient spin echo (PGSE)
a pulse sequence introduced to replace the constant magnetic field with short-duration gradient pulses to enable the measurement of diffusion by NMR and MRI.
Why measure diffusion in the body
Based on the fact that biological cells may hinder the Brownian motion of extracelluar water molecules.
The diffusion measurement can be useful for obtaining valuable information about the biological microstructure simply by observing the motion of water molecules.
MRI is the only means we have to observe diffusion in vivo noninvasively. Note that diffusion is an intrinsic physical process that is independent of the MR effect or the magnetic field.
Despite the relatively poor resolution of the actual images, DTI is powerful because it is sensitive to molecular displacement on the order of 5-10um.
how is Diffusion Weighted Image (DWI) produced
addition of (1) diffusion sensitizing gradients (MR pulse sequence designed to be sensitive to molecular diffusion), also know as motion-probing gradients (e.g. PGSE), and (2) a T2-weighted spin-echo sequence.
what is Tractography
the virtual reconstruction of the trajectory of water molecules along white matter bundles.
how does DTI segment white and grey matter
By incorporating DTI orientation information onto anisotropy maps, white matter can be parcellated into various tracts using a color-coded map or a vector map
A voxel thus contains bundles of axons and neuroglial cells. Axons are filled with neuronal filaments running along its longitudinal axis, which may contribute in superimposing anisotropy on the direction of
water diffusion
what is the meaning of the intensity of each voxel in a DWI image
reflects the best estimate of the rate of water (or other molecule) diffusion at that location
DWI is said to be more sensitive to the pathological changes than the traditional MRI measurements, why
Because the mobility of water is driven by thermal agitation and highly dependent on its cellular processes
DWI is most applicable when the tissue of interest is dominated by isotropic water (or other molecule) movement, e.g., in brain grey matter or cerebral spinal
fluid (CSF), where the diffusion rate appears to be the same when measured along any axis.
what are some applications of DWI
Pre-Surgical Planning, Connectivity Analysis, Diagnosis.
Clinical research on the early corpus callosum development in human brain using DTI. Studies aiming to understand structure-function relations of the healthy heart & understanding cardiac adaptation and remodelling.
Usually a set of diffusion-weighted images along several gradient directions are collected with a directional sampling scheme.
describe these sampling schemes
The original sampling schemes consist of 6 (or even 4)
directions, but progress has been made in scanning the space more uniformly along as many directions as possible, especially for fibre tracking (12, 42, 162, 642)
what is a diffusion tensor (D) of a voxel
a 3 x 3 symmetric matrix describing the local molecule (e.g., water) mobility along each direction and correlation between these directions.
how is the diffusion tensor visualised
can be visualized as a diffusion ellipsoid, with the eigenvectors indicating the directions of the principal axes, and the square root of the eigenvalues defining the ellipsoidal radii
what are the limitations of DTI
accuracy is limited by the information contained in the diffusion tensors and the fibre tracking methods.
Another fundamental limitation of DTI is that it cannot distinguish antegrade from retrograde along a fibre pathway, due to the antipodal symmetry inherent to the diffusion process.
what is the underlying assumption of DTI
that the orientation of the fibre is collinear with
the direction of the principal eigenvectors of the tensors.
Currently there are several approaches to reconstruct white matter tracts deterministically, which can be classified roughly into two types, what are they
The first category are based on line propagation algorithms that start from a seed point and use local tensor information for each step of the propagation.
The second type of approach, such as fast marching algorithms and simulated annealing algorithms, are based on global energy minimization to find the
energetically most favorable path between two predetermined pixels.
Probabilistic Tractography makes the following statement: “Given the model and the data, I have x%
confidence that the path of least hindrance to diffusion from seed point A passes through region B.”
why would a probabilistic model be useful, as opposed to a deterministic one
It enables tracking through regions of high uncertainty, where deterministic techniques would be forced to stop.
The goal of probabilistic tractography is, instead of simply stopping tractography in regions and along trajectories, to develop a full representation of the uncertainty associated with any eventual statement that might be made.
In DTI, If the fibres are parallel, the representation will be reasonable. However, when fibres cross inside a single voxel, diffusion tensor will look isotropic
what are some models that will solve the crossing fibre problem
Multi-Tensor: A simple generalisation of DTI which replaces the Gaussian model with a mixture of n Gaussian densities
QBall-Imaging (QBI): approximates the diffusion orientation function (dODF) that estimates using measurements from a spherical acquisition scheme. The spherical probabilistic function is represented by the spherical harmonics.
Spherical Deconvolution (CSD): The key idea is to consider the set of measurements as the sum of measurements we would get from a fibre population with each orientation weighted by the fraction of fibres with that orientation (Dirac delta function).
what is Functional MRI (fMRI)
measures brain activity by detecting changes in blood oxygen and flow that occur in response to neural activity – when a brain area is more active it consumes more oxygen and to meet this increased demand blood flow increases to the active area.
uses blood-oxygen-level dependent (BLOD) contrast, which is closely related to cerebral blood flow (CBF)
describe the spatial and temporal resolution of fMRI
It has relatively high spatial resolution (2mm isotropic) and medium temporal resolution (minutes) for a set
of successive scans.
what are the benefits of fMRI
it is able to detect the altered brain activation induced by a task,
and provide the connectivity between population of neurons based on their co-activation at resting state.
These two benefits essentially define the two categories of fMRI analyses, task-evoked fMRI and resting state fMRI.
what are some advantages of multimodal medical image computing
Improved system performance.
Improved detection, tracking and identification.
Improved situation assessment and awareness.
Improved robustness.
Extended spatial and temporal coverage.
