Samenvatting
Brain Imaging - Summary Slides
- Instelling
- Vrije Universiteit Amsterdam (VU)
A summary of all the slides for the course Brain Imaging, MSc AI.
[Meer zien]Voorbeeld 4 van de 82 pagina's
Voorbeeld 4 van de 82 pagina's
In winkelwagengesponsord bericht van onze partner
Verkoper
Volgen
Voorbeeld van de inhoud
Module 1Lecture - Introduction
What is fMRI, really?
● Brain imaging has exploded over the last ~30 years.
● Any hospital has an MRI scanner that’s also usable for
cognitive neuroscience research.
● Brain imaging is changing how people think about
themselves; it’s placed our psyches firmly in our heads
Functional Brain Imaging
● fMRI is so popular because it is considered
non-invasive, and provides an appealing balance
between temporal and spatial resolution
● fMRI is evolving: it’s becoming faster and higher
resolution
functional MRI: What is our view on the brain like?
● The signals we measure with fMRI are primarily
dependent on the oxygen level in the blood, they
are BOLD, for Blood Oxygenation Level Dependent
● Since neural activity consumes oxygen, the level of oxygen in the blood will vary as
neurons activate.
● Thus, BOLD is a metabolic measurement.
● Keep in mind: we are measuring not neural activity itself, but a derivative of it. This
means BOLD provides only an indirect view on neural activity!
Blood response: Haemodynamic response
● Slow response to neural activation, takes over
20s to unfold
● Is dependent on a complex cascade of biological,
metabolic responses, among which Cerebral
Blood Flow, and Oxygenation
● Has a (more or less) stereotypical shape:
MRI scanner: A “standard” clinical device, repurposed for cognitive science
● Won the 2003 Nobel prize
● Used to create many different types of images of the living brain for diagnosis, both
different types of anatomical images and different types of functional images
● Different images are created by running different programs, called sequences
1
, ● Different field strengths, measured in Tesla (Earth magnetic field: 3.2 × 10-5 T)
● MR Physics lecture Feb 22nd Nikos Priovoulos
1.5 T 7T 11 T
MRI data: What does MRI data look like?
● It’s 3D: values at {x, y, z} represents the
anatomy
● Elements are called voxels, for volume
element, like picture element for pixels
● Standard anatomy has a resolution of
1mm
● At 7T, the resolution goes to ~0.3mm (27 times smaller,
because cubic relation between voxel size and volume!)
Other MRI data: What a versatile machine!
● Examples of 4D or higher-D images - store not a time-course for each voxel, but more
complex information
fMRI data: What does fMRI data look like?
2
,fMRI data: Data quality
● We are focused on 1. Signal, and 2. Noise - we want more signal, and less noise
● Measure for Scan Quality:
○ tSNR (temporal Signal to Noise Ratio)
μ
○ σ
, where μ is the mean image, and σ is the standard deviation over time
○ Normal values:
■ ~ 0, air, (μ close to 0)
■ > 40, noisy gray matter (more noise, higher σ)
■ > 80, high-signal gray matter (less noise, lower σ)
■ > 100, white matter (almost no noise, very low σ)
fMRI data: fMRI images as data
● Values in a normal fMRI dataset are not expressed in any SI unit, such as meter,
second, Tesla, etc.
● We cannot really compare across scanners, subjects, etc.
● Our workaround measure for BOLD signal strength:
○ Percentage signal change (%sc)
○ , where Ii is the image at timepoint i
○ Normal values:
■ 0.2%-1% (normal fMRI experiment @ 3T),
■ 1%-3% (finger-tapping in primary motor cortex @ 3T)
■ 1%-7% (finger-tapping in primary motor cortex @ 7T)
■ 7%-20% (voxel in a large vein in primary cortex @ 7T, where μ is very
low)
3
, fMRI analysis: How do you get to
results?
● Much more than just a single step
● Experimental design is
paramount:
● What is your goal?
● Many ways of going wrong
Replication Crisis: Many ways of going
wrong?
● With such complex analyses,
room for 1. ’Tinkering’, or 2.
Sloppiness
● We will teach you the newest approaches to reproducible neuroscience:
○ How to save your data
○ How to preprocess your data
○ How to program your data analyses
○ How to report your results
○ How to open-source your data and analyses
“Modern” fMRI: What’s the state of the art? - Naselaris et al, 2021 paper on Perusall
● With higher field strengths, more is possible. For instance, higher resolution means
“laminar” resolution
● Large, open science projects:
○ Human Connectome Project (HCP, 1200 sjs, >5 hours, 3T & 7T)
4
Voordelen van het kopen van samenvattingen bij Stuvia op een rij:
Verzekerd van kwaliteit door reviews
Stuvia-klanten hebben meer dan 700.000 samenvattingen beoordeeld. Zo weet je zeker dat je de beste documenten koopt!
Snel en makkelijk kopen
Je betaalt supersnel en eenmalig met iDeal, creditcard of Stuvia-tegoed voor de samenvatting. Zonder lidmaatschap.
Focus op de essentie
Samenvattingen worden geschreven voor en door anderen. Daarom zijn de samenvattingen altijd betrouwbaar en actueel. Zo kom je snel tot de kern!
Veelgestelde vragen
Wat krijg ik als ik dit document koop?
Je krijgt een PDF, die direct beschikbaar is na je aankoop. Het gekochte document is altijd, overal en oneindig toegankelijk via je profiel.
Tevredenheidsgarantie: hoe werkt dat?
Onze tevredenheidsgarantie zorgt ervoor dat je altijd een studiedocument vindt dat goed bij je past. Je vult een formulier in en onze klantenservice regelt de rest.
Van wie koop ik deze samenvatting?
Stuvia is een marktplaats, je koop dit document dus niet van ons, maar van verkoper tararoopram. Stuvia faciliteert de betaling aan de verkoper.
Zit ik meteen vast aan een abonnement?
Nee, je koopt alleen deze samenvatting voor €16,99. Je zit daarna nergens aan vast.
Is Stuvia te vertrouwen?
4,6 sterren op Google & Trustpilot (+1000 reviews)
Afgelopen 30 dagen zijn er 48298 samenvattingen verkocht
Opgericht in 2010, al 15 jaar dé plek om samenvattingen te kopen