Introduction to brain Magnetic Resonance Imaging (MRI) · 2020. 6. 3. · ILCB cours en ligne - IRM cérébrale partie 1 - 27/04/2020 1 Introduction to brain Magnetic Resonance Imaging

ILCB cours en ligne - IRM cérébrale partie 1 - 27/04/2020 1

Introduction to brain Magnetic Resonance Imaging (MRI)

Presented by Valérie Chanoine

Siemens Prisma 3T - CERIMED-INT Marseille


Brain MRI

• Non-invasive technique

• One of the most used to explore the

human brain

• Excellent spatial resolution (of the

order of mm for a 3 Tesla scanner)

• Temporal resolution in the order of

the second

• Useful in clinical and fundamental

research

INTRODUCTION

Siemens Prisma 3T - CERIMED-INT Marseille

Earth’s magnetic field

1 T ~ x 20,000


MRI SCANNER COMPOSITION

To obtain images, MRI combines 3 types of magnetic fields:

• a very powerful static (B0 via the magnet)

• a variable, field gradient (via gradient coils)

• one variable, radio frequency (RF, via antennas)

Aimant

Antenne

@CEA, www.cea.fr

http://www.cea.fr/


MRI PRINCIPLE – NUCLEAR MAGNETIC RESONANCE (NMR)

MRI is based on the NMR phenomenon.

• Hydrogen protons (1H) present in very large quantities

in the human body. They enter into resonance in MRI.

• A 1H proton acts like a magnetic needle.

spin

H2O

youtu.be/tcGG5njW890


MRI PRINCIPLE – SPINS AND MAGNETIC FIELD B0

In the presence of a strong magnetic field, the spins are oriented in the direction of the magnetic field.

@CEA 2006 / Les défis du CEA N°119


MRI PRINCIPLE – RF PULSE

@CEA 2006 / Les défis du CEA N°119

The RF pulse at the region to be imaged disturbs the orientation of the spins.


MRI PRINCIPLE – RF PULSE STOP

At the end of each RF pulse, the spin returns to its initial position, emitting a wave of the samefrequency (Larmor frequency) as the one that disoriented it.


MRI PRINCIPLE – SPATIAL ENCODING

The signal emitted by the spin is localized by 3D spatial encoding to allow the reconstruction of a3D MRI image..

9

X

Y

Z

MZ

X

Y

Z

MZ

The return to equilibrium. Curve T1

describes the restoration of magnetization

along the longitudinal axis Mz

B0

MRI - T1 RELAXATION

ILCB cours en ligne - IRM cérébrale partie 1 - 27/04/2020

T1: time needed to restore 2/3 of the Mz magnetisation

time

Mz

T1

T1 Relaxation


X

Y

Z

Mxy

X

Y

Z

Mxy

MRI – T2 RELAXATION

B0

T2 describes the decay of

magnetization in the transverse

plane XY

T2 Relaxation

T2time

Mxy

T2: time required for the Mxy magnetization to return to 1/3 of its initial value.


ANATOMICAL IMAGE - T1 WEIGHTED

www.youtube.com/watch?v=TQegSF4ZiIQ

In a T1w image, the white substance (SB, blue curve) appears as hypersignal (white) on the

image and the cerebrospinal fluid (CSF, green curve) as hyposignal (black).


www.youtube.com/watch?v=TQegSF4ZiIQ

ANATOMICAL IMAGE - T2 WEIGHTED

In a T2w image, the CSF (green curve) appears in white .


ANATOMICAL MRI (T1W) - SAGITTAL SLICE

http://www.astrosurf.com/



Coronal SagittalAxial

VOXEL(Volumetric Pixel)

0.8 mm

0.8 mm

0.8 mm

Spatiae rsolution

ANATOMICAL IMAGES (T1W) AND SLICES


MRI – ANATOMICAL IMAGES (A FEW EXAMPLES)

1. Grey Matter- T1w

2. White Matter- tractography

(e.g. diffusion tensor imaging)

3. Vascularisation - angiography

4. Blood distribution- perfusion

www.healthline.comwww.astrosurf.com www.cea.fr

www.imagilys.com/perfusion-imaging-MRI

1 2 3

4

https://www.healthline.com/


http://www.cea.fr/

http://www.imagilys.com/perfusion-imaging-MRI/


timeT2* weighed

FUNCTIONAL MRI - IMAGES

• Study brain activity (cognitive or perceptual processes)

• Linked to a task performed by the subject during MRI recording

T2*= “observed” T2, reflecting true T2 as well as magnetic field homogeneities

@CEA, www.cea.fr

http://www.cea.fr/


In fMRI, we don’t’ measure directly the

neuronal activity but a BOLD signal. Ogawa

and its collaborators (1990) have exploited

the fact that Desoxygenated hemoglobin

alters the NMR signal.

When neural activity increases, the demand

for oxygen increases locally in the blood cells

located near the neuron.Hannah Déclin, 2018https://psychcentral.com/lib/what-is-functional-magnetic-resonance-imaging-fmri/

Cerebral Activation: ↗ cerebral Blood Flux ↗ cerebral Blood Volume ↘ Desoxygenated hemoglobin rate ↗ Increase BOLD signal

S. Ogawa

fMRI – BLOOD OXYGENATION LEVEL DEPENDANT (BOLD) SIGNAL


time

A A A AB B B

BOLD signal timeserie

UNIVARIATE MEASURE - BOLD SIGNAL TIMESERIES PER VOXEL

~ 100 000 voxels in brain


The function of the BOLD response to a stimulus (at time

t=0) is called the HRF.

We will now assume that it is comparable across subjects

and regions.

HRF to a neural stimulation at time 0

HEMODYNAMIC RESPONSE FUNCTION (HRF)


With HRF, the response to stimulation can be

predicted by a convolution between neural

stimulation and HRF.

Direct inference. We assume that a mental

process can be isolated by a suitable

experimental design.

Neural Stimulation HRF Predicted Response

INFERENCE DIRECTE


EXPERIMENTAL DESIGN - EXAMPLE

Projet ILCB en cours : Bases Neurales destraitements morphologique et sémantique chezle lecteur adulte expert et dyslexique (maininvestigator, Johannes Ziegler)

time

A A A AB B B

BOLD signal timeseries

A = condition ‘Word’B = condition ‘Hash markers’


GENERAL LINEAR MODEL (GLM) AND DESIGN MATRIX

Observed Data = Predictors * Parameters + Error

Design matrix

=

β1

β2

+

y A B Ɛ

time Beta maps


Contrast: ‘Word - Hash markers’ on 20 subjects

STATISTICAL MAPS (T-MAPS)

p<.001 (no correction for multiple comparison) - 5 voxels cluster extent

Projet ILCB en cours : Bases Neurales destraitements morphologique et sémantiquechez le lecteur adulte expert et dyslexique(main Investigator, Johannes Ziegler)


UNIVARIATE ANALYSES – A FEW EXAMPLES

Univariate :• Whole Brain(BOLD signal timeseries)

• Region of interest(average of BOLD signal timeseries)

• Functional connectivity(ROI-to-ROI correlation)

Projet ILCB en cours : Self-monitoring of language inproduction (main investigator, E.

Runnqvist)


Univariate analysissummarizes theactivity on a group ofsubjects.

RSA is interested ofthe distribution of theactivity patterns(geometrical distance)within each individualrather than their meanvalue…

What’s the difference betweenRSA and traditional

fMRI Analysis?

Sub

ject

1Su

bje

ct 3

Sub

ject

2

distance1

0

Univariate analysis.Comparison of the activity of each voxel

Multivariate analysis (RSA).Multivoxel pattern analysis

t-value6

0

# 1 million of voxels in a 3T scanner

REPRESENTATIONAL SIMILARITY ANALYSIS (RSA) - MULTIVARIATE

Projet ILCB en cours : Bases Neurales des traitementsmorphologique et sémantique chez le lecteur adulteexpert et dyslexique (main investigator, Johannes Ziegler)


THANK YOU FOR YOUR ATTENTION

Documents

Introduction to brain Magnetic Resonance Imaging (MRI) · 2020. 6. 3. · ILCB cours en ligne - IRM cérébrale partie 1 - 27/04/2020 1 Introduction to brain Magnetic Resonance Imaging