fMRI Flashcards
What does fMRI take a measure of?
regional cerebral blood flow (rCBF)
fMRI relies on the certain cognitive functions being processed in what way?
Cognitive functions are region specific, if a task
involves a certain cognitive function, the areas involved will become more active, need more oxygen and more blood.
So fMRI takes a measure of what bio-physical process?
Measures regional levels of blood oxygen by detecting magnetic changes in red blood cells when they become de-oxygenated
What is the difference to MRI?
MRI: create images of soft tissue in the body, which x-rays pass through undistorted
- Tissue = water-based, different amount of water for different tissues
- Enables 3D image of layout of these tissues
fMRI uses strong xxxx to prepare which subatomic particle? fMRI measures oxygenated blood by recording?
Use strong magnetic field to line up protons
fMRI measures oxygenated blood by recording?
the spin of protons which have a magnetic charge
After aligning protons, fMRI….
Sends a radio pulse through the lined up protons, to record how they resonate
Different tissue and matter respond differently in what way?
different proton resonance patterns
Different protons (different tissues) resonate differently (magnetic susceptibility), allowing composition of a tissue image
fMRI use the different proton resonance reactions from which two forms of a substance?
fMRI: oxygenated blood resonates differently to de-oxygenated blood, allowing composition of an (indirect) image of brain activity
What can’t you take into a scanner?
metal (pacemakers)
4 main structural MRI specs: what do you get? at what spatial acuity? what does fMRI use them for? and what T is it?
Structural (anatomical) MRI: ►Static image of brain structure ►High spatial resolution (1x1x2 mm) ►Used to overlap functional images onto ►T1 contrast (measures a different magnetic property to functional scans)
although fMRI is not as spatially resolute as MRI, it can record xxxxxxmm , and more detail with a xx scanner
3x3x3mm
7t (stronger tesla coil strength)
actually both spatial and xxxxxxx rely on tesla strength
temporal
T2 contrast (measures a different magnetic property to structural scans)
So, in structural MRI physics: the magnetic field aligns
aligns protons
but protons in what?
water molecules
have weak magnetic fields, initially randomly oriented, but some align with the external field
the radio pulse impacts this process by…
knocks orientation by 90 degrees, which leads to a change in magnetic field
after this change in magnetic field, the the protons then….
‘relax’, and procedure can be repeated for different slices of brain
- Whole brain image in appr. 2 seconds (3 mm slices)
- T1: relaxation time -> T1-images – structural scans
FUNCTIONAL MRI relies on the fact the brain uses a shit ton of xxxxx but doesn’t actually xxxx
store oxygen and only little glucose yet consumes 20% of body’s oxygen uptake
the fact the brain doesn’t store oxygen etc means it needs to be …
Needs to be supplied from local blood supply
the brain consumes energy when in use, therefore the
More active tissue uses more oxygen than less active tissue
Oxygen rich blood looses oxygen to tissue
What is the Blood Oxygenation Level Dependent (BOLD) contrast?
Compares level of oxygenated with de- oxygenated blood magnetic properties: hemoglobin is diamagnetic (only magnetic when exposed to external magnetic field) when oxygenated and paramagnetic (normally magnetic) when de-oxygenated
*** Hemoglobin molecules resonate differently in these different magnetic states **
hemodynamic response function
An indirect measure of brain activity
BOLD contrast: 3 factors?
1) CMRO2: cerebral metabolic rate of oxygen (goes up when tissue is active of real interest more oxygen when expending energy, so de-oxygen goes down)
2) CBF: cerebral blood flow
3) CBV: cerebral blood volume
so fMRI compares the differences between
magnetic spins of protons in oxygenated blood and deoxygenated
Name the 3 steps in the hemodynamic response function …
1) Initial dip (as neurons consume oxygen -> small rise in amount of deoxyhaemoglobin -> reduction of BOLD signal)
2) Overcompensation: in response to the increased consumption of oxygen, blood flow to the region increases. Increased blood flow is greater than increased consumption - > BOLD signal increased
3) Undershoot: blood flow and oxygen consumption dip before returning to original levels. This may reflect a relaxation of the venous system.
however the brain is always …
active
so ‘active’ areas in fMRI refers to….
► a physiological response that is greater relative to some other condition
► Need for baseline response, well-matched to experimental task
Example: Petersen, Fox, Posner, Mintun and Raichle (1988)
Study brain activity involved in word recognition, phonology and retrieval of word meaning – cognitive subtraction
So research design in fMRI needs to exploit thisdifference by …
finding two tasks (an experimental and a baseline task) that differ in terms of a small number of cognitive components.
what are conjunction and subtraction designs? And the 2 issues associated with both?
> Subtraction is taking a task with the cognitive component in it, and then subtracting another task with only that component taken out
Formally:
Neuronal structures underlying a single process P
=Contrast: [Task with P] – [control task without P ] = P
> Conjunction requires a set of orthogonal tasks that has a particular component in common. Look for regions of activation that are shared across several different subtractions.
A test for such activation common to several independent contrasts is called “conjunction”. It resembles a factoral design in ANOVA.
ISSUE 1: The assumption of pure insertion
is the assumption that a single cognitive process can be inserted into another set of cognitive process without effecting the functioning of the rest. For example, if you wanted to find the reading comprehension area of the brain, you might scan participants while they were presented with a word and while they were presented with a non-word (e.g. “Floob”). If you infer that the resulting difference in brain pattern represents the regions of the brain involved in reading comprehension, you have assumed that these changes are not reflective of changes in task difficulty or differential recruitment between tasks. The term pure insertion was coined by Donders as a criticism of reaction time methods.
One way to minimize the baseline/pure insertion problem is to isolate the same process by two or more separate comparisons, and inspect the resulting simple effects for commonalities
ISSUE 2: BASELINE
Brain always active. Moving Baselines. Where to take comparisons.
example of this cognitive subtraction in petersen , posner 1998 who studied …
brain activity involved in word recognition, phonology and retrieval of word meaning – cognitive subtraction
e. g. contrasts passive viewing of (words vs fixation cross)
e. g. (reda aloud word vs look at word)
e. g. generate (word associated with viewed word vs read aloud a written word)
what is issue of pure insertion / pure deletion?
adding an extra component does not affect the operation of earlier ones in the sequence.
BUT: interactions are likely to occur
► Baseline task: should be as similar to the experimental task as possible
e.g. of conjunctions and factorial designs by Frith?
Example: why can’t we tickle ourselves (Blakemore, Rees, and Frith,1998).
2 Factors:
‘touch’ (felt/not)
‘self movement’ (moved/not)
What is parametric fMRI design?
to get around baseline
continuous manipulation of factor of interest
Variable of interest is treated as a continuous dimension rather than a categorical distinction.
Associations between brain activity rather than differences between two or more conditions.
- passive listening to spoken words at six different rates
- Different brain regions show different response profiles to different rates of word presentation. Adapted from Price et al. (1992), and Friston (1997).
- no baseline necessary
when stimuli are presented completely randomly, it is called a xxxxxxx design?
Event-related
new as temporal difficulties etc
event-related design can only occur when stimuli are xxxxx and xxxxx
If stimuli are infrequent and random
If conditions defined by participant - sorting what hapened in a trial (e.g. correct/incorrect trials; bistable percept (necker cube); presence of an hallucination - see right)
what is functional specialisation?
Functional specialisation: region responds to a limited range of stimuli/conditions. This distinguishes it from the responsiveness of other neighbouring regions. (not localisation).
what is functional integration?
Functional integration: the way in which different regions communicate with each other.
Model how activity in different regions is interdependent.
‘effective connectivity’ or ‘functional connectivity’ between regions when performing a task.
Use techniques like principal component analysis
Example: word production vs repeating letters in schizophrenics and controls
block vs event related designs
Block design: stimuli in one condition grouped together
> Event-related design: different stimuli or conditions are interspersed with each other (efMRI)
> Intermingled conditions are subsequently separated out for the purpose of analysis
► Blocked design:
+ strong BOLD contrast: higher signal-to-noise ratio
simple design and analysis
- practice/fatigue effects
cannot be used when participants should not know which condition is coming next
► Event-related design:
+ no practice/fatigue effects
can be used when participants should not know which condition is coming next: randomisation
can be used when trials can only be classified after experiment
- weaker BOLD contrast: lower signal-to-noise ratio more complex design and analysis
What does an fMRI session produce in total?
Session: a scanning session, all the data collected from a participant. Usually consists of structural scan, and a number of runs of functional scans
what is an fMRI run?
Run: a continuous period of scanning, consists of a specified number of volumes
what is volume?
Volume (image): Set of slices taken in succession: a 3D spatial image, with a temporal dimension. Expressed in TR (Repetition Time): how long does it take to acquire a volume
what is an epoch?
Epoch: a period when a certain condition is presented. Conditions (epochs) can be grouped together (blocked design) or randomly intermixed (event related design)
how do you correct for head movements?
► Spatial resolution -> small spatial distortions
► Individual differences in brain size and shape –
••• stereotactic normalisation ••••• (adjust the measurement of overall dimensions to the ‘standard brain’
► Individual head aligned differently in scanner over time due to movement
Regions harder to detect
False positive result
Physically restraining head (using foam or something) and participant instructions
Correction
What is smoothing?
Spreads some of the raw activion level of a given voxel to neighbouring voxels
why smoothing?
Enhances signal-to-noise ratio
Compensates for individual differences in anatomy
what does smoothing assume?
Assumption: cognition does not occur in single voxels
Increases the spatial extent of active region -> more likely to find overlap between participants
What are the 5 main fMRI analysis steps?
► Individual differences – averaging over many participants ► Correction for head movement ► Stereotactic normalisation ► Smoothing ► Statistical comparison
what is ► Stereotactic normalisation? And the name associated with it?
► Mapping regions on each individual brain onto a standard brain (brain template is squashed or stretched until it fits).
Tailarach and Tournoux (1988). Brain Atlas (based on one brain), Tailarach coordinates
► X left/right
► Y front/back ► Z top/bottom
Alternative: Montreal Neruological Instute (average of 305 brains) ► Voxels (volume elements), 3-D coordinates (x,y,z)
issue with Statistical comparison?
► Tens of thousands of voxels – capitalisation on chance Lower significance level (Bonferroni)
Choosing statistical threshold based on spatial smoothness
(random field theory)
Analyse pre-determined region
Reported ‘corrected’ or ‘uncorrected’ statistical parameters (ROI?)
how do you start stat comparison ?
dividing up data according to design - then perform stat comparison
What are the three points of interpretation?
► Inhibition versus excitation
► Activation versus deactivation
► Necessity versus sufficeincy
What is Inhibition versus excitation?
Functional imaging signals are assumed to be related to metabolic activity of neurons, and synapses in particular
However: activity can be excitatory or inhibitory!
BOLD signal more sensitive to neuronal input into a region than the output from the region
Unclear whether functional imaging can distinguish between two neural functions
what is Activation versus deactivation ?
► Activation/deactivation
► Merely refers to difference between two conditions
► Does not say anything about the direction of the difference
What is Necessity versus sufficiency?
► Are active regions critical to the task?
► Sufficiency: functional imaging shows us active regions, but these may not be crucial
► Use methods in conjunction with other methods
summary
► Structural imaging reveals the static physical characteristics of the brain (useful in diagnosing disease), whereas functional imaging reveals dynamic changes in brain physiology (that might correlate with cognitive functioning).
► Neural activity consumes oxygen from the blood. This triggers an increase in blood flow to that region and a change in the amount of de-oxyhaemoglobin in that region.
► As the brain is always physiologically active, functional imaging needs to measure relative changes in physiological activity. The most basic experimental design in functional imaging research is to subtract the activity in each part of the brain whilst doing one task away from the activity in each part of the brain whilst doing a slightly different task. This is called cognitive subtraction.
► Other methods, including parametric and factorial designs, can minimize many of the problems associated with cognitive subtraction
summary
► There is no foolproof way of mapping a point on one brain onto the putatively same point on another brain because of individual differences in structural and functional anatomy. Current imaging methods cope with this problem by mapping individual data onto a common standard brain (stereotactic normalization) and by diffusing regions of significance (smoothing).
► A region of ‘activity’ refers to a local increase in metabolism in the experimental task compared to the baseline but it does not necessarily mean that the region is essential for performing the task. Lesion studies might provide evidence concerning the necessity of a region for a task.
► Functional imaging can be used to make crude discriminations about what someone is thinking and feeling and could potentially outperform the traditional lie detectors. However, it is highly unlikely that they will ever be able to produce detailed accounts of another person’s thoughts or memories.
