Pipelines for different techniques Flashcards
at a basic level, how is fMRI showing brain function
seeing which brain regions ‘light-up’ during a particular task e.g. visual cortex lights up during visual task
draw the flow chart from stimulus to BOLD response
see diagram
who first experimentally indicated relationship between blood flow and brain function?
Angelo Mossi (balance board 19th century)
overall fMRI set up
person lying in MRI magnet with RF head coil, headphones, mirror to see screen, holding response box for output
is the BOLD signal directly measuring blood flow?
no
if BOLD signal is not directly measuring blood flow, what is it measuring?
it is sensitive to the magnetic properties of oxygenated and deoxygenated RBCs
outline the oxygenated properties of RBCs
diamagnetic- slightly (indistinguishably) reduces magnetic field
outline deoxygenated properties of RBCs
paramagnetic- slightly increases magnetic field (distinguishable)
if magnetic field increases, precession…
increases
so if magnetic field increases where deoxygenated RBCs are present, what happens
it cause a magnetic field gradient causing adjacent water molecules to precess at different frequencies then dephase (spread out to x and y planes) causing signal loss - results in a distinguishable signal loss around deoxygenated blood, in comparison to oxygenated blood
outline activation contrast occurring in BOLD (comparing rest to activation)
at rest: oxygenated blood travels through arteries. exchanges oxygen in capillary bed and deoxygenated blood leaves via veins. Deoxygenated blood increases dephasing, hence increases T2 signal.
When active: excess oxygenated blood flows into activated region, washing out deoxygenated blood, this reduces dephasing, hence reduces T2 signal
The slight change in T2 signal between rest and activity can be expressed mathematically to give an optimum echo time
draw diagrams to represent the different techniques used for structural MRI data acquisition in K-space vs fMRI (echo planar)
see notes
why does fMRI use echo planar imaging
it’s much faster- can acquire a single slice in less than 100ms
what pattern does fMRI echo planar use
interleaved
what’s the disadvantage of interleaved echo planar
it can lead to stripes on the image due to the artefact of signal changes during acquisition or subject motion
in fMRI how is signal intensity time course looked at?
looked at along rest/task/rest/task etc. voxel by voxel- to see which voxels show difference in signal between rest and activation
what is the method of fMRI data analysis focussed on?
model based linear regression
outline the development of models to fit voxel signal activity- with images
we have our voxel signal activity going up and down between rest and task- see notes
a simple model is a poor fit for the data as the data is shifted in time due to delayed response to stimulus
improved model is time shifted to better fit this
then we take physiology into account- the sloped haemodynamic response with delay then decay
this is convoluted with the simple time shifted model
then due to signal drift over time is combined with linear ramp- best fit
outline how a study like the 10 year f/u on hippocampal volume using MRI in early dementia and cognitive decline would be run
MRI baseline of volume and repeat at defined intervals for each participant
hippocampal segmentation from a regulizer and probabilistic atlas- from registered brains
normalise volume overtime compared to see hippocampal volume changes and whether it aligns with dementia/cognitive decline
(overall- raw volume calculation -> normalisation -> percentage loss overtime calculated-)
what is the downside of ROI analysis?
you need to know what you want to look at (ROI)- an a-priori hypothesis
what do you do if you don’t have a ROI or an a-priori hypothesis
an exploratory study where you don’t have to work within pre-defined areas- this is usually Voxel Based Morphometry (VBM)
what is VBM?
a global volumetric brain analysis where a single experiment allows identification of GM changes and other associations across brain
does VBM use the same or different tools of image analysis as ROI studies?
the same
what are the steps/tools used in VBM image processing?
Brain extraction, GM tissue segmentation, templates, registration, smoothing, stats testing