neuroimaging Flashcards
(119 cards)
fMRI terminology :
session
run
block
experiment
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
Advantages of fMRI
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
anatomical voxel
smaller than the fucntion
spatial resolution, structural and functional voxels
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
partial volume effect
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
fictional resolution
the smallest detectable difference in two different bold activation
signal to noise ratio
the ration between activity in target area divided by external noise ( ex: physical motion)
contrast to noise ratio
the difference between two activated area divided by the (external ) noise
different within of firm have different contrats to noise ratios
dynamic Contrast to noise ratio OR functional signal to noise ratio
the difference within the same voxel in activation across different condition
task related variability / non task related variability
higher in sensory area rather than associative areas
SNR range
– Total range: 0.1 to 4.0 – Typical: 0.2 – 0.5
what to take into account for betewtr functional signal to noise ratio
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
thermal noise
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
mass motion ( mostly head )
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
inter subject variability source of noise
people differ in RT and also BOLD signal ( especially in some more evolutionarily new areas that present more connectivity difference across subject s)
validity problems as source of noise
RT is just a proxy
also different people might implement different strategies
general solution of increase signal to noise ratio
use PCA And ICA
use filtering ( careful it can cut out important frequency )
increase field strength ‘??????
averaging by the number of trials
problems with avaraging
- assumes noise is random - not correlated with other proccesses , 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
temporal resolution
ability to detect changes over time
problems with fMRI time resolutions
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
how can sampling rate (repetition time ) affect time resolution
aliasing problems = different repetition time can give different bold signal
too short rt cudl take long time or have a small ccoverage
woudl noy giev the time to the flip angle to reach the peak –> smaller signal
too large RT can make the initial dip go undetected
possible solution = jittering : starting the RT at different latencies in the Bold signal timeline
what is the linearity system framework and what does really happen to bold signal of repeated stimuli ?
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
how do refractory effects become useful in adaptation studies ?
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
ideal TR
for event related : 1.5-2 ms
for block design : 3-4 ms
preprocessing steps
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
General linear model components and general goal
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