neuroimaging

Question 1

fMRI terminology :
session
run
block
experiment

Answer 1

session: single participant time into the fMRI in a day without leaving the machine
can have multiple runs

run : single fMRi recording ( 5-12 min )
can have multiple blocks

block : fMRI recording to a specific continuous condition

Question 2

Advantages of fMRI

Answer 2

higher spatial resolution compared to other -_> allow for new types of analysis
non invasive –> high benefit low risk
easier to train people compared to other neuroimaging

Question 3

anatomical voxel

Answer 3

smaller than the fucntion

Question 4

spatial resolution, structural and functional voxels

Answer 4

spatial resolution : ability to detect differences, both structural and functional, across different location fo the map

for structural MRI
- spatial resolution means distinguishing afferent brainn areas ( the smallest structural change it can detect )
- voxel is smaller (0.05 to 1.5mm3)
pros: higher precision for restricted hypothesis
cons : low signal to noise ration, require more time for acquisition

functional MRI
- spatial resolution means the precision it can pinpoint activity on a map
- bigger voxel ( 2-3mm3)
pros: lower time , bigger noise to ration
cons: partial volume effect

Question 5

partial volume effect

Answer 5

in fMRI bigger voxel can cause the machine to record acticity of voxels form different structural tissues, functional regions and slices os belonging to the same voxels
solution: use smaller voxels nd slices, use slower frequency

Question 6

fictional resolution

Answer 6

the smallest detectable difference in two different bold activation

Question 7

signal to noise ratio

Answer 7

the ration between activity in target area divided by external noise ( ex: physical motion)

Question 8

contrast to noise ratio

Answer 8

the difference between two activated area divided by the (external ) noise

different within of firm have different contrats to noise ratios

Question 9

dynamic Contrast to noise ratio OR functional signal to noise ratio

Answer 9

difference within the same voxel in activation across time or different condition

Question 10

what to take into account for betewtr functional signal to noise ratio

Answer 10

since it is a measure depend experimental manipulation , make sure the manipulation is effective with the right stimulus –> ex: hone checking for the activation for FFA do not use the rest as control condition but use another visual stimulus

consider that different areas of the brain have different natural amount fo noise over time

Question 11

thermal noise

Answer 11

variation detection of single due to fluctuation of electrons either in the field or in the machine

increases with temperature and field strength

truly random ( so can be decreased with averaging

Question 12

mass motion ( mostly head )

Answer 12

if motion is larger than one voxel it is critical

motion artefact can be decomposed into 3 coordinates ( x,z,y with respect to anterior commissure ) and 3 movement components (and roll, jaw , pitch ) that can be used ars regressor of no interest to correct for the artifact

instructing the participant is fundamental ( can also have sham session to train) , also can be aided with some physical measure like padding

can also correct during preprocessing using realignment

Question 13

inter subject variability source of noise

Answer 13

people differ in RT and also BOLD signal ( especially in some more evolutionarily new areas that present more connectivity difference across subject s)

Question 14

validity problems as source of noise

Answer 14

RT is just a proxy
also different people might implement different strategies

Question 15

general solution of increase signal to noise ratio

Answer 15

use PCA And ICA
use filtering ( careful it can cut out important frequency )
increase field strength ‘??????
averaging by the number of trials

Question 16

problems with avaraging

Answer 16

• assumes noise is random , but if not wea re ignoring potential relevant info
• we make activation cluster appear bigger
• since variability is actually divide by the square root of n of trial ( not just by pure n of trial ) at one point the difference betwween sir root of different numbers will not be detectable anymore , so advantage of averaging is lost

Question 17

temporal resolution

Answer 17

ability to detect changes over time

Question 18

problems with fMRI time resolutions

Answer 18

MEnon 1998 : some area might have fixed delayed onset times independently of the task type and duration

variability between subject –> averaging

variability between task in the same subject : make sure the difference in RT for different task is not due to confounding like duration of the task , difficulty , etc..

bold single is sluggish , it does not perfectly reflect neuronal activation times

dependency on sampling rate

Question 19

how can sampling rate (repetition time ) affect time resolution

Answer 19

aliasing problems = different repetition time can give different bold signal –> ex , too large RT can make the initial dip go undetected

possible solution = jittering : starting the RT at different latencies in the Bold signal timeline

Question 20

what is the linearity system framework and what does really happen to bold signal of repeated stimuli ?

Answer 20

linearity systems assume
scaling : amplitude of single is proportional to the input magnitude
superimposition : the result of two successive stimuli is the summation of the two single output

BUT
we have refractory effects : the successive stimulus is influenced by the first one, t hey are not independent -> amplitude is lower and peak is later the closer they are
aka successive stimuli are under additive

Question 21

how do refractory effects become useful in adaptation studies ?

Answer 21

ina adaptation studies , if adaptation is present the two stimuli are perceived as a single one , so there is only one response , and therefore no refractory effect
if adaptation ins not present ,we have two successive percieve stimuli , which will show refractory effects

Question 22

ideal TR

Answer 22

for event related : 1.5-2 ms
for block design : 3-4 ms

Question 23

preprocessing steps

Answer 23

visual inspection of scans and movies to detect mass motion
check

remove dummy scans

adjust distortion: use the map fo the magnetic field to adjust distorted images

realignment : superimpose images of same modalities from same participant , by using the 6 parameters values to apply rigid body transformation ( if leftover unpatching in activated areas , sue the parameter as noise parameters , so as regressor of no interest ))

sparse scanning : alternate scanning session with non scanning session –> damp the motion artefact by avoiding recording gin unrelevant period for activation

slice timing correction: interpolate interleaved recording as if happening at the same time ,

coregistration: different modalities scans form same participant are superimposed to increase spatial resolution

normalisation: estimate the normalisation parameters form the tame plate and then apply them to the normalised scans

smoothing : a sort of wighted averaging of each voxel signal with their neighbouring ones, depending on how much each voxel influence each other
pros: better superimposition ( even more than normalisation ), less number of comparisons since we are now comparing cluster of voxels not single ones, increase signal to noise ratio
cons: bad spatial resolution, bad for ROi analysis

Question 24

General linear model components and general goal

Answer 24

Y= outcome aka activation of a voxel
x= predictors we take into account
b= how much of each parameters could be causing y
e= error

goal :
estimate for each voxel a pattern of predictors and estimate the value for their parameters such as the same pattern ( GLM ) can predict with different parameters, the activation of different voxels using different set of parameters for each voxel

How we do that ? just reminder Granziol : contrast matrix where we compare different time points ( rows) with different conditions ( columns ) to estimate the beta , then run test to first asses the model significancy and then the single parameters significancy

Question 25

problems with GLM

Answer 25

• assume errors are normally distributed in each voxel and has the same distribution in all voxels ( which sit not )

-does not take into account the fact that activation is not all or none –> usually we convolute an actual HRF activation with the one obtained by the model

• does not take into account physiological artefacts
• assumes orthogonality in parameters–> in real life they are usually not

Question 26

problem with multiple comparison

Answer 26

the more test we run the higher the probability of false positive solely because we have more test

so we have to correct for the number of comparison AKA diminish the single parameter p value so that when taking multiple test the whole model p value is still reliable

Question 27

main corrections for multiple comparisons

Answer 27

Bonferrroni :
divide the the individual parameter p value by the number of test ( problem if you do voxel by voxel comparison so with 50 to 100 thousands fo comparison

Family Wise Error Correction with gaussian field theory :
estimate a priori the probability of fall expositive for each voxel assuming they have a normal distribution of activation ( so kinda considers clusters )

False discovery rate : estimate , from the significant results, the probability of them being false positives

ROI
we estimate significant areas in that are signifiant and run a different set of test on that area specifically , reducing the number of voxel to compare
or
just take predefined areas and run test within them reducing automatically the number of voxels to compare
or we just compare rois

Question 28

first order analysis
and second orders analysis

Answer 28

first ( fixed effects ) : assume inter subject differences are noise and that effect are the same for all subjects

secodmn ( random effects). take into account inter individual difference by using the map of individual activation to estimate a single map of activation

Question 29

block design

Answer 29

pros:
no task switching effect
easier analysis
easier fro participants and tester

cons:
can make the subject predict the stimuli
some task cannot be bloked
cannot differentiate individual responses to specific stimuli

Question 30

event related design

Answer 30

pros
allow for post hoc analysis ( go back and pin point the activity correspondent to a specific stimulus )
make up for blocked design cons

cons :
some processes happen online 8 ex gestalt ) and can’t be predefined in a n event related design
some processed make it difficult to switch an cannot be made into a strip t pattern
longer experiment

Question 31

history of neurostimulation

Answer 31

galvani : found that muscles moved with electrical impulse, hypothesised myelin and ion channels

aldini : used electrical stimulation,ulation to treat melancholia

ferrier : stimulation of cortex revealed cortical maps ( effect in one cortex area showed result in a specific body part 9

MEDUNA : discovered elctroconvulsive therapie to treat some disorders like depression

penfield: homunculus and induced memories via electrical stimulation

Magnusson & Stevens . found that magnetic field applied by coil had no reaction when continuously used, but di when stopped or restarted

Bickford & Freeming : elicited muscles contraction with magnetic stimulation for peripheral nerve

Question 32

advantages of ems

Answer 32

causal elation possible
located manipualtion
possibility to change control site and task
minimise the effect of plasticity any having shorter and non longitudinal l studies ???
can manipulate networks????
neural chronometry

disadvantage : those damn cortical areas

Question 33

how does tms work

Answer 33

electric field in coil, elicit magnetic field that on skull elicit electric current on cortex

Question 34

what to take into account

Answer 34

orientation of neuron can determine whether effect is hyper or de polarisation???
orientation of the coil
direction of the current

Question 35

monophasic vs bifasic

Answer 35

monophonic ( current in one direction??)
is less powerful ( requires more intensity to reach same result as bifasic
easier to see effect of summation since affecting more specific neural population=????

bifasic ( current is a sinus )
can recover more fastly so more suited for high frequency pulse s

Question 36

how to find the right areas to stimulate

Answer 36

stimulate an area and derive which one it is forms he effect fprovoked
uset he eeg 10/20 system
navigate form a know area if you know their relative position
use a neuonavigation map

Question 37

how does fMRI work

Answer 37

protons that have moth a magnetic momentum and an angular momentum are said to have nuclear magnetic resonance (NMR) property

laos we need molecules that have an odd number of protons or they cancel each other out

hydrogen is one of those

we align the portions magnetic momentum by applying a constant magnetic field

then we tip the portions out of alignment using radiofrequencies at a specific frequency at which protons spin ( larmor frequency , calculated with angular and magnetic momentum values , protons of different molecules have different larmor frequencies)–> this make he potion go to a higher energy state
when they go back to alignement and to a lower energy state , they release the excess energy in the form of a oscillation , free induction decay , recorded by the rf coils

Question 38

how hydrogen and deoxygenated and oxyhemoglobin relation on fMRI recording

Answer 38

even if we record hydrogen portions , the deoxygenated haemoglobin is a paramagnetic properties, modified the magnetic field, the oxyhemoglobin does not

so fMRi signal increase is dictated by oxygen -deoxy , with more oxygen increasing the signal

we know that blood flow is faster than oxygen consumption
so what happen when neural activity starts is that we have a higher need and thus supply of oxy, making the single increase ( we woudl expect a decrease in signal due to increase of oxeye consumption and thus increase of deoxygenated BUT NOPE)

Hemodynamic Response function has a canonical shape :
hypo oxygen stage : initial dip due to oxygen consumption before blood flow supply
hyper oxy stage : increase in signal due to arrival of oxy
peak
overshoot : oxygen consumption rate is catching up with oxygen flow , thus the ratio with deoxygenated is coming to a balance a making the signal decrease ( undershoot )

Question 39

contrast agent ss pros and cons

Answer 39

they have higher paramagnetic properties than deoxygenated , so more sensitive
also the signal would now be based on blood volume not oxygen-deoxy ration

cons :
worse time course signal due to time requirements for the contrast agent to diffuse
participant can have side effects
injection of substances birth be discouraging