MRI and fMRI Flashcards
Characteristics of the scanner
Relies on electromagnetic field, radio waves and hydrogen in the body
Contain Gradient and radio frequency coils
Contains superconducting magnets
Magnetic field is measured in Tesla - 1.5T, 3T, 4T, 7T
Does not have radiation (like PET)
What is the frequency at which protons spin?
Larmor frequency
What do gradient coils do?
3 gradient coils generate secondary magnetic field.
Allows the manipulation of the magnetic field and to aquier data in x (left-right); y(anterior-posterior) and z(superior-inferior) directions
What do radio frequency coils do?
Used for specific part of the body to get the best SNR;
they disturb the proton alignment by making them to jump up and down; when they relax they give off radio waves measured by the MRI signal
Structural Imagining
Creates a static image and gives information about tissue structure, volume, gray-white matter differences, damage, tumours, etc
Types of contrast
T1 weighted - 3D volume scans, BBB contrast for leakage, used in anatomical scanning (structural scans)
T2 weighted - lesions and strokes, microtubules. and white matter micro-structures (fMRI)
Proton density (PD) - to calculate quantative T1 and T2
Fluid attenuation by inversion recovery (FLAIR)- stroke, lesions, white matter hypertensities
MPRAGE
Regions of Interest (ROI)
Depends on the research question
Allows investigation of local region, but may be affected by selection bias, size and shape of the ROI
planimetry (drawing around something)
stereological technique - sampling a part of a region
MRI is a series of 2D images building a 3D image and therefore may be affected by the slice thickness
Protocol for ROI
what size what shape criteria for placing it how many slices choose a plane (dorsal, corononal, etc) inter-rater reliability
Types of Atlases
Talarach (1988)
Montreal Neurological Institute (MNI)
What are some issues associated with Atlas use?
Using different atlases (and softwares) may give different results. Therefore, need to be careful when comparing data across studies.
Talarach Atlas
coordinate system for the human brain based on post-mortem sections of one 60 year old woman.
Smaller than average brain, oddly shaped and can lead to error and distortion after rewrapping
corresponds to Broadmann areas
doesn’t map well of MNI
Montreal Neurological Institute (MNI) Atlas
Based on large sample of normal, young subjects of 305 people.
standard atlas used may be slightly larger than the average brain
What is a Pipeline?
The series of steps that describe what is a research doing to the data and include everything that is done to the data
What are some limitations of MRI
Can answer only certain questions
A lot of poor work done by people who do not understand the method (put garbage in, get garbage out)
cannot make changes to the scanner/software partway through the study
almost everything done to the data introduces error
smoothing increases the chance of finding positive result (type 1 error)
needs a correction for multiple comparisons
expensive as it needs helium
Benefits of MRI
Great spatial resolution, anatomical information and tissue contrast
Information about blood flow, functional region and white matter microstructures
What is Automatic Segmentation?
Quick and easy, requires relatively less experience BUT:
different results across different software
less accurate than well trained individual
each stage needs to be checked for errors
still requires knowledge of software and pipelines
What is fMRI?
Creates dynamic images and measures the changes in local oxygenation of blood, which reflects the amount of local brain activity
Blood oxygenation level dependant contrast (BOLD)
Not an absolute measure as it measures difference between two brain states (e.g. oxygenated vs deoxygenated blood);
statistical methods are used to determine the areas that are reliably different in action vs baseline (no action)
Why does fMRI has poor temporal resolution
It mesures the hemodynamic response (initial dip - decrease in oxygen in the blood; overshot - compensation for oxygen demand; undershot- back to baseline) and it takes 6sec for the signal to peak, while neural processing happens in the ms range
What are the components of fMRI analysis?
Check raw images - orientation etc distortion correction motion correction slice timing correction spatial normalisation spatial smoothing temporal noise filtering statistical modeling statistical interference visualisation
fMRI design
Requires comparison between conditions as BOLD is not an absolute measure of neural activity:
Substraction paradigm - task - baseline; 2 subtypes
event related desisgn
block design
Problems with substraction based designs?
Assumes that adding a component to a task does not affect already existing processes (e.g. pure deletion);
however no such thing as neutral state, brain is active at rest..
Block design
alternating conditions A and B ot A, control B in the same order
certain number of slices is possible per brain image
Blocks are repeated during the experiment
Having a slice several times and combining them increases SNR
higher BOLD contrast
fMRI limitations
A lot of poorly planned experiments
poorly defined hypothesis
poorly defined hypothesis relating to brain structures
attenuation and fatigue (Especially block designs)
scanner drift
learning effects and habituation
Dangers with blob spotting
poor temporal resolution
limitations with interpretations of the data
limits to choices of subjects - safety criteria, weight, height, tolerance levels, etc
