neuroimaging Flashcards
What are the physics associated with displacement of protons to project images in MRI?
Radiofrequencies to displace the protons in water molecules to form linear and structured formations. Once the RF signal leaves, the energy required to return water to original conformation is what is emitted by the molecules and recorded by the MRI.
Therefore, if water content is lower in a region, there is less signals emitting back eg. fat cannot hold water.
Types of structural imaging processes
CT - Poor detail of brain, good for larger bleed, stroke, lesions, masses
X-ray - good for fractures (fast)
MR I- gold standard
Explain T1 (recovery) imaging
Recovery of the protons back to longitudinal positioning
faster
FAT is BRIGHT and WATER is DARK
Explain T2 (dephasing) imaging
Dephasing = no signal
loss of transverse magnetisation
longer
FAT and WATER are BRIGHT
Explain T2 FLAIR (Fluid-Attenuated Inversion Recovery) imaging.
Uses longer recovery and echo times to use T1 values to null signal from CSF in T2 images. (the T1 and T2 images are overlaid and T1 is then nullified to reveal darkened CSF).
Longest.
T2 image but CSF is DARK
Explain T2 FLAIR (Fluid-Attenuated Inversion Recovery) imaging.
Uses longer recovery and echo times to use T1 values to null signal from CSF in T2 images. (the T1 and T2 images are overlaid and T1 is then nullified to reveal darkened CSF).
Longest.
T2 image but CSF is DARK
What is DTI imaging and FA
Records the organisation of white matter tracts. Determines 3D image, strength, direction of diffusion of water in brain (check to see if water is flowing in correct direction in white matter tracts)
Fractional anisotropy (FA) of the entire diffusion tensor can be color-coded for directionality.
Tractography to reconstruct fibre tracts.
What are function imaging techniques
Functional MRI (fMRI)
Blood oxygen level dependent (BOLD)
–> Measures
- higher activity requires more blood (greater metabolic demand)
- changes in deoxygenated hemoglobin
- Deoxygenated blood has paramagnetic characteristics
- ->Resting state or task-evoked fMRI
- resting-state useful for looking at broad connectivity, hubs and networks
- task-evoked allows for observing which areas of the brain are active during stages/trials in cognitive tests
How does fMRI measure functional processing?
fMRI is task evoked.
- Block design
- Event related (division of action)
- Mixed block/event related.
multiple models and approaches needed to validate fMRI findings
BOLD cannot directly measure neural reactivity –> too many statistical measures on top of removing noise etc. (Low signal to noise, with many background issues.)
Explain the idea of reversal learning in fMRI
Reversal learning generally occurs in orbitofrontal cortex,
associated with selective activation in reversal learning. Monitors change in reward value to guide reversal learning behaviour
location of activity determined by fMRI
Explain the two main modes of Nuclear Imaging
SPECT : Single Photon Emission Computed Tomography
- gamma transmitting radioisotopes
- cheaper then PET
- lower resolution and contrast
PET : Positron emitting tomography
- positron spectrometry for various amino acids
- requires small areas to measure
Describe mechanism of PET scans
Useful in Schizophrenia
Uses F-dopa (dopamine precursor) as a tag OR;
IB2M - D2 antagonist as a tag (to prevent dopamine from binding)
What is an example of a PET tag?
Raclopride (D2 antagonist) assesses dopamine release after administering amphetamine by binding to D2.
amphetamine displaces raclopride from the D2 receptor to make way for the rise in DA. Thus, the free Raclopride is tagged and associated to the
greater displacement of the tag is associated to the dopamine binding on D2 –> this high release in dopamine is characteristic of schizophrenia
What are the structural, functional, and nuclear imaging techniques?
Structural:
Xray, CT, MRI
Functional:
fMRI
Nuclear:
PET
SPECT
What are the different methods of Post-mortem neuroimaging?
CT, Ex Vivo MRI, Radiographs, Histological slices
What are the tissue changes that occur post-mortem?
Remember: THD
- Temperature changes post-death
- Hypostasis –> fluid accumulation lower extremities
- Decomposition of brain tissue (cerebral autolysis)
What is the purpose of post mortem imaging?
To determine cause of death, human identification, forensics, research, anatomical ground truth (validate in vivo findings)
Why is important to consider postmortem changes?
- lowering misdiagnosis in autopsy
- accurate determination of post-mortem interval (PMI) when time of death is unknown
Discuss ex vivo MRI advantages.
- long scans have no motion interference –> precise details of previously hard to define features in vivo
- therefore, smaller voxels (more detailed), greater resolution and sensitivity
- the exact MR image slice can be compared to histological (linking histological findings to MRI properties)
- can measure G ratio, the degree of myelination
Discuss how g ratio is determined
degree of myelination = ratio of the inner and the outer diameter of the myelin sheath relative to cross-sectional
- values can deduce the neuronal conduction velocity
Ex vivo MRI limitations
- Histology‐MRI registration is difficult =
histology prone to distortion + MRI lacks microscopy
specificity - Formalin fixation artifacts (partially fixed decreases
resolution) - PMI and TIF (time of fixation) can impact the quality of imaging (shorter PMI and longer TIF is favourable)
What are the advantages of slices/sections (Neurohistology)?
Provides detail to neuronal tissue composition
Can reveal pathology that is not seen in gross anatomical imaging/examination
reveals more macroscopic changes eg. sulcal widening in AD caused by neuronal cell death and atrophy within cortex
Remember: FES-MSI
F-fixation; E-embalming; S-sectioning; M-mounting;
S-staining ; I-imaging
What are the methods of cell imaging?
Nissl
Intercellular Dye Injection - (Horseradish Peroxide)
Golgi
H&E - Hematoxylin and Eosin
Nissl Method
CELL BODIES
- morphology and pathology of neural cell bodies
- shows the form of cell body and stains nucleus
- nissl substance –> granular ER and free polyribosomes
- patterns vary between cell types
H&E
pink/red stain = eosin staining cytoplasm and ECF
dark blue/purple = hematoxylin staining cell nuclei
thick tissue needs to be cleared to enhance image
Golgi Staining vs Intracellular Dye Injection
Golgi: RANDOMISED & BROAD LABELLING
- staining a few hundred neurons
- thick sections of neurons
- detailed view of dendritic structures through embedding of metallic salts into neural tissue as metal precipitate
- 3D view of cells
Intracellular Dye Injection: LABELLING SINGLE NEURONS
- dendrite structures
Immuno-staining: Antibody-based Approach
Sections/slices are incubated with antibodies that recognise/bind to cell specific markers
Antigen-antibody complexes are visualized within the tissue via incubation with 2’ antibodies that bind to the 1’ antibody
- 2’ antibody is fused with a fluorochrome or enzyme eg. horseradish peroxide + incubation w/ substrate and section = colour change substance
Precipitation develops in or around where the specific binding site of the primary antibody occured
How is fat and water represented in T1
FAT is bright
WATER is dark
How is fat and water represented in T2?
FAT and WATER is bright
How is fat and water represented in T2 FLAIR?
Same as T2 (both bright) but CSF is dark
Spatial Transcriptomics (ST)
ST involves the aligning of cell types using molecular phenotypes w/ those molecules phenotypes defined by morphology, electrophysiology, connectivity, and functionality.
THE SPATIAL TOPOGRAPHY OF GENE EXPRESSION FORMS STRUCTURES IN ST IMAGING;
using barcode primers to capture mRNA onto brain tissues;
then transcribed from mRNA to cDNA;
thus, cDNA now can provides sequential data to obtain spatially resolved transcriptomic data (imaging can pick up on the location of the cDNA and form an image);
High Throughput and Transcriptome Wide (entire mRNA)
smFISH: shows where the gene is expressed (fluorescence)
