HC5 Structural Neuroimaging Flashcards
MRI and fMRI
- MRI: anatomy
- fMRI: brain function
- You need to take a MRI before taking a fMRI as you have to know the anatomy before being able to make a FMRI scan.
- Same machine used for both scan types, based on the same principle
Magnets produce magnetic fields
o Strong visible attraction and repulsion effects on range of materials
o MRI safety: life or death
▪ NEVER bring anything metal into a MRI room!
o Less obvious effect on human body: influence on nuclei
Less obvious effect on human body: influence on nuclei
→ nuclear magnetic resonance imaging (NMR)
▪ = MRI
▪ Nuclear because of the effect on nuclei it has
▪ ≠ Radioactivity
▪ Nausea (because of influence of magnet on the nuclei in the brain, if you get up quickly)
▪ No consequent short- or long-term illness
Most relevant element for brain imaging
Hydrogen
o Human body is made of ~ 70% water, the brain ~ 75%
o Water molecules contain hydrogen atoms
o Hydrogen atoms only contain one single proton
o Hydrogen could take another electron in its innermost shell
o Atoms with uneven number of protons act as dipoles. Dipoles have an positive and a negative side, two “poles”. Basically, they are small magnets.
Nuclei with odd number of protons/neutrons spin at the Larmor frequency
o Depends linearly upon magnetic field strength of the magnet (For 1H: 1.5T = 63.76 MHz, 3T = 127.7 MHz, 7T = 298.0 MHz)
o A stronger magnetic field causes the protons/neutrons to spin faster
Nuclear MAGNETIC resonance imaging
Part of nuclei align with direction of the magnetic field
Nuclear magnetic RESONANCE imaging
If additional magnetic field oscillates with the Larmor frequency, nuclei absorb energy from the field.
Nuclei resonate with the additional magnetic field you add
Static magnetic field
Atoms align with direction magnetic field
Oscillating magnetic field
= radio frequency (RF) pulse
o Spins individual atoms so they get in phase
o Atoms flip and take direction of oscillating field
▪ Increase in energy state
When RF pulse is no longer applied
o Dephasing of atoms
o Realigning to static magnetic field (flip back)
▪ emits energy = small signal in radio
frequency range -
▪ This energy you measure in the MRI
Small signals over all the re-aligning nuclei integrate
o The less dephasing happened, the stronger this signal is
o The time it takes to go back to equilibrium depends on the kind of tissue
Gradients of field strength
- Remember: Larmor frequency depends upon field strength
- Gradients: as linear as possible, stationary and of short duration
- Static magnetic field differs across space
Three orthogonal gradients of field strength on top of static magnetic field
Static magnetic field differs across space
o Nuclei in different locations have a different Larmor frequency
→ RF pulse only affects the nuclei with matching Larmor frequency
Three orthogonal gradients of field strength on top of static magnetic field
o Slice selection gradient (Z): applied at time of RF pulse
o Phase encoding gradient (Y): use of dephasing after RF pulse
o Frequency encoding gradient (X): applied at time of read out of signal
Slice slection gradient
Applied during RF pulse
RF pulse only affects nuclei that experience a total field strength with matching Larmor frequency
Slice: volume of excited nuclei
Every slice has a different frequency
One slice per RF pulse if 2D image
Interleaved slice acquisition: to minimize cumulative effects due to cross-slice excitation
The excited nuclei (the slice) are affected by the 2 other gradients
RF pulse only affects nuclei that experience a total field strength with matching Larmor frequency
3T (B0) & 127.7 MHz RF pulse & slice selection gradient G from
inferior to superior → RF pulse only affects nuclei in horizontal
slice where summed field strength = 3T
One slice per RF pulse if 2D image
→ scanning a full 3D image requires as many RF pulses as number of slices needed
Interleaved slice acquisition: to minimize cumulative effects due to cross-slice excitation
Less spill over, keeps the slices separate
Phase encoding gradient
- Applied after RF pulse
- Change spin resonance frequency of excited nuclei depending on their location in the gradient, causing dephasing
- When removed, resonance frequencies are the same again, but differences in phase persist
- All nuclei at a certain position in the gradient have same phase, thus phase is informative about position
Frequency encoding gradient
- Applied during data acquisition
- Frequency encoding gradient = the read-out direction
- All nuclei at a certain position in gradient have same resonance frequency, thus frequency at read-out is informative about position
.
Gradient-echo echo planar imaging
- Gradient reversals un-do effect of initial gradient
o signal consists of a series of echo’s elicited by the reversals
Sufficient echo’s: all combinations of phases and frequencies are characterized
o use Fourier analysis to reconstruct image
>< Spin-echo sequence: reverses the RF pulse to create echo
Voxels
- Unit of space = voxel
- The shorter the time in which an image has to be taken, the lower the number of slices that can be imaged
- Number of voxels per row/column in the slice relates back to number of steps of phase encoding gradient
o 128 steps per dimension with field of view of 256 mm → resolution of 2 mm
How do these physical principles give rise to an image with anatomical structure?
- Emitted signal decays over time
- Signal intensity depends upon several (biological) factors
- Factors are different in different tissues, resulting in signal contrast
- Pulse sequence and parameter choice determine which factor has most weight
Signal intensity depends upon several (biological) factors:
o Density of 1H protons
o T1-recovery: recovery of longitudinal orientation = spin-lattice relaxation (realign with static magnetic field)
▪ Speed of going back to static magnetic field, depends on the kind of tissue
o T2-decay: loss of transverse magnetization due to the loss in phase coherence = spin-spin interactions
▪ The speed of dephasing, depends on the kind of tissue
Pulse sequence and parameter choice determine which factor has most weight
→ T1-weighted vs T2-weighted imaging
o details on these pulse sequences and parameter choice: read only (e.g. page 42)
T1-recovery time
= time it takes the longitudinal magnetization to grow back to 63% of its final value
= spin-lattice relaxation time
What is T1-recovery time?
The time it takes for longitudinal magnetization to grow back to 63% of its final value.
Also known as spin-lattice relaxation time.
What happens during T1-recovery?
After being deflected, protons prefer to realign with the magnetic field (low-energy state).
As they do, they release RF energy back into their surroundings (the “lattice”).
Characteristics of a T1-weighted image
- White matter appears white (shorter relaxation time, less dephasing).
- Fast T1 = less dephasing = higher signal = brighter image.
- More dephasing = lower signal = darker image.
What is T2-decay?
Right after a 90° RF pulse, transverse magnetization is maximized.
Protons collide and begin to dephase, causing the MR signal to decrease.
What is T2-decay time?
The time it takes for transverse magnetization to decrease to 37% of its starting value.
Also known as spin-spin relaxation time.
Characteristics of a T2-weighted image
Fast T2 = more dephasing = lower signal = darker image.
MRI principles recap
- Protons have spin and align with a magnetic field (B0).
- A 90° RF pulse deflects them.
- Two relaxation processes occur:
T1 (longitudinal relaxation): How fast protons realign with B0.
T2 (transverse relaxation): How fast protons dephase and release energy.
What are the three main components of an MRI scanner?
- Magnet
- Gradient coils (create varying magnetic fields)
- Radio frequency (RF) coil (transmits and measures RF waves)
How does the magnet in an MRI scanner work?
- Electrons flow along a wire, generating a magnetic field (Faraday’s principle).
- Wires are cooled with liquid helium for superconductance.
- Magnetic field strength depends on the number of loops and current (e.g., 1.5T, 3T, 7T, 9.4T).
- Higher field strength = better signal, resolution, and contrast, but more artifacts.
CT scan vs. MRI scan
CT scan: Used in clinical settings for inflammation, infection, TBI, stroke, tumors, etc.
MRI scan: Used when no contraindications (e.g., pacemaker) exist.
Three structural MRI methods
- T1-weighted MRI (anatomical imaging)
- Diffusion tensor imaging (DTI)
- Magnetic resonance spectroscopy (MRS)
T1-weighted anatomical imaging: Quality check
- Artifacts due to: Fixed materials (e.g., braces, implants).
Removable materials (e.g., hairpins). - Purpose: Find anatomical abnormalities (clinical or incidental).
- High-field scanning = optimized local images but poor images of other brain areas.
Voxel-Based Morphometry (VBM)
- Morphometry = Quantifying brain anatomy properties.
- Compares regional tissue volumes to detect differences between subject groups.
Used for:
- Identifying correlations with age, behavior, disease.
- Studying neurodegenerative/neurovascular diseases.
Examples of neuroanatomical abnormalities
Patient HM (Corkin, 2002):
Damage to medial temporal lobe → anterograde amnesia. Patient DF (Steeves et al., 2006):
Lateral occipital lesion → visual agnosia (cannot recognize objects but can act on them).
Relevance of brain structure for behavior
- MRI studies link brain structure to IQ, personality traits (Big Five), etc.
- Effect sizes are small, but findings are statistically significant.
Connectivity in the brain
- “Nothing defines the function of a neuron better than its connections.” – M. Mesulam
- Visual system connectivity (Felleman & Van Essen, 1991):
Studied monkey visual system.
Found hierarchical organization in visual processing.
Diffusion tensor imaging (DTI)
Pattern of action potentials
o From where and to where?
o Paths = axons
Noninvasive imaging:
o Large bundles of 1000s of axons
o Axons that start and end in each other’s vicinity, stay together
→ white-matter pathways or tracts
Diffusion
movement of flow from higher concentration to lower concentration (molecules in this case)
What is Diffusion-Weighted Imaging (DWI)?
- Special pulse sequence adapted for molecular diffusion.
- Based on movement of molecules from high to low concentration.
- Cell walls & myelin affect diffusion → results in anisotropy (direction-dependent diffusion).
Types of diffusion
Isotropic diffusion → Equal in all directions (e.g., in cerebrospinal fluid).
Anisotropic diffusion → Different diffusion rates depending on direction (e.g., in white matter).
Diffusion Tensor and Visualization
Diffusion is described by a tensor:
- Isotropic diffusion → circle shape.
- Anisotropic diffusion → ellipse shape.
Used to analyze white matter integrity (e.g., in multiple sclerosis)
Mean diffusion (MD)
Overall amount of diffusion
Fractional anisotropy (FA)
From zero (isotropic diffusion) to 1 (only diffusion along main axis)
Axial and radial diffusivity (AD and RD)
amount of diffusion in certain direction: main axis (AD) or other directions (RD)
Different indices
differential sensitivity to diffusion-related phenomena
DTI in Neurological Conditions
In some neuropathological conditions specific predictions can be made about which indices are affected and how (e.g. decreased myelination: FA ↓ because RD ↑ , AD =)
o For example in people with MS
Orientation maps in DTI
- Darker areas → Lower FA (less structured pathways).
- Lighter areas → Higher FA (highly directional tracts).
corpus callosum: light red color → goes in one direction from right to left and left to right
What is Tractography?
- A method to trace white matter connections by following main diffusion direction.
- Three types of connections:
Projection fibers → Connect cortex to subcortex.
Commissural fibers → Connect left & right hemispheres.
Association fibers → Connect distant areas within one hemisphere.
DTI and Behavioral Relevance
- Used to test disconnection hypotheses (brain connectivity changes affecting mental processes).
- Hard to determine exact biological cause (e.g., less myelination? Fewer axons? Synaptic issues?).
Example DTI - Van de Putte et al. (2018):
Simultaneous interpreting training leads to changes in control
related brain networks.
▪ frontal-basal ganglia subnetwork related to domain-general and language-specific cognitive control
▪ language control related subnetwork with key role for cerebellum and SMA
▪ Interpreters (translate and at same time get new information) vs. translators
(translate text to other text), scanned before and after internship → interpreters develop stronger language control
Example tractography - Thiebaut de Schotten et al. (2015)
Reconstructing structural disconnections in famous case
studies
▪ Phineas Gage: Pole through frontal cortex
▪ louis victor leborgne: tan tan → first non-fluent aphasic patient of Broca
▪ Henry Molaison (HM): memory
