Magnetic Resonance ImagingLecture 1

Nicolás F. Lori

IBILI, Faculty of Medicine, Coimbra University

Magnetic Resonance Imaging

Magnetic Resonance Imaging

• The magnetic field in MRI interferes with the nucleus, not the electron.

• In water (H2O), the nucleus of oxygen has an even number of protons, and an even number of protons. The spin of the nucleus of oxygen is zero, and therefore the MRI signal will come from the hydrogen alone.

• The nucleus of hydrogen is made of a single proton, which makes it simple.

• The spin of the hydrogen proton will rotate with a frequency proportional to the applied magnetic field.

• By applying a spatially dependent magnetic field, we can make different parts of the anatomy generate signals with different frequency. This enables the spatial localization of the MRI signal.

Magnetic Resonance ImagingRelation between applied magnetic field B and angular velocity ω for proton is: ω= γB

where γ is the proton’s gyro-magnetic ratio (which is a constant).

MRI Signal Measures in Humans• After the magnetic moment (created by the summing of the Hydrogen proton spins)

originally pointing in the Z direction is rotated 90º. The magnetic moment then starts going back to the Z direction as spins of the protons again start becoming aligned with the Z direction.

• The magnetic moment in the Z direction grows to approximately its original value during a time T1.

• The magnetic moment perpendicular to the Z direction goes to approximately zero during a time T2 (for a spin-echo pulse sequence) [Image Shown] and T2* (for a gradient-echo pulse sequence) [Not Shown].

•

MRI Signal Measures in Humans

• There are three types of MRI used in my projects: Anatomical, Diffusion, and Functional.

• Anatomical MRI: measures water density and average magnetic interaction between molecules in time scale of the tens to hundreds of milliseconds.

• Functional MRI: measures alteration of average magnetic interaction caused by increase in oxygenated Hemoglobin induced by increased energy consumption at a certain brain region.

• Diffusion MRI: measures diffusion of water molecules in a certain orientation by use of linear variation across that orientation of the magnetic field in the foot-to-head (a.k.a. Z) direction. Direction of favored diffusion determine directions of the white matter axonal fiber bundles. Most common approach is diffusion tensor imaging (DTI), more elaborate approaches are q-ball imaging (QBI) and diffusion spectrum imaging (DSI).

Signal intensity in the Spin-echo Pulse Sequence

90˚ pulse 180˚ pulse

TE/2 TE/2

I(0)

Echo

211

0

T

ETR

eeIT

T−

−−

−= ρ

ρ is proton density TR is repeat timeTE is echo-time

Anatomical MRIMukherjee et al, Radiology 215 (2000), 211

Diffusion MRI

Diffusion MRI

• Each diffusion-weighted volume has an intensity-reduction indicating the amount of water diffusion in a certain orientation.

• That orientation is the orientation of diffusion-sensitizinggradient, g.

• To obtain the diffusion tensor at a certain voxel only 6 non-co-linear orientations are needed.

• In single bundle WM the diffusion tensor biggest axis points in parallel to axons.

Signal intensity in the Stejskal-Tanner Pulse Sequence

δδδδ

∆∆∆∆

180˚ pulse90˚ pulse

( ) [ ] 1

21

3

1,,−

⋅⋅

−∆

−−−

−=∆ qq DT

T

T

TT

ER

eeegI

δ

ρδ gq γδ=, with

.

Diffusion MRIMukherjee et al, Radiology 215 (2000), 211

Diffusion Tensor

)

D =

Dxx Dxy Dxz

Dyx Dyy Dyz

Dzx Dzy Dzz

• Laboratory Coordinates:

• Pathway-oriented Coordinates:

=

3

2

1

00

00

00

λ

λ

λ

D)

Anisotropic Water Diffusion• Single orientation fiber bundle

• Diffusion is anisotropic

• Diffusion is represented by 3x3 tensor

Anisotropy definitions

Basser, et al., J Magn. Reson. B 111 (1996), 209

Pierpaoli et al., Radiology 201 (1996), 637

Conturo et al., Magn. Reson. Med., 35 (1996), 399

2

3

2

2

2

1

2

3

2

2

2

1

321

)()()(

2

3

33

λλλ

λλλ

λλλ

++

−+−+−≡

++=

++≡

DDDFA

DDDD

zzyyxx

What is Meaning of Anisotropy• The existence of fibers makes diffusion easier on the orientation

parallel to the fibers, and more difficult in the perpendicular orientation. This anisotropy of water diffusion makes the diffusion surface look like a Rugby ball, with the biggest axis pointing in the orientation of white matter fibers.

• The two relevant experimental parameters are the diffusion along the fiber and the relative anisotropy.

• Reduction of the diffusion anisotropy can be caused by three different occurrences:

– 1. Neuronal cell membrane disruption

– 2. Neuronal cell death (necrosis)

– 3. Existence of Crossing fibers

• Diffusion tensor imaging cannot distinguish between the three, but QBI (and other high angular resolution techniques) can distinguish 3 from the other two.

Probability from DTI

• Probability of displacement ∂r of water molecule during time t is:

• Probability-based fiber tracking can be based on probability distributions (as above), in phase variation approaches, or in space-curvature approaches.

• Probability fiber tracking considers most the pathways with higher probability.

( ) DteDt

tP 4

2

4

1,

r

r

∂−

=∂π

Tracking from a seed point

X axisGenu of the corpus callosum

83.5 84 84.5 85 85.5 86 86.5 87 87.5127.5

128

128.5

129

129.5

130

130.5

131

131.5

Y axis

Seed point

Diffusion ellipsoid

Voxel

Track

x

Sub-threshold anisotropy

HARDI Diffusion MRI

Relation between position and displacement

• Position-dependent density encoding:

• Position dependent displacement encoding:

• Diffusion MRI signal coming from Scanner:

( ) ( ) slice

i

Slice

edslice gkrrkrk γερρ == ⋅

∫ with with with with,,,, ,

Relation between position and displacement

( ) ( ) gqrrgrq γδ=∂∂= ∫

∞

∞

∂⋅ with with with with,,,,

----

iePdE

( ) ( ) ( )grgr EI ρ=,

High angular resolution anisotropy imaging

• Motivated to resolve/recover complex fiber anatomy (partial volume effects, crossing fibers, etc.)

• 43 and 256 diffusion-encoding directions

• Anisotropy calculated as variation in the 43/256 ADC measurements

single tensor FA 43 dir Anisotropy

L. Frank, Mag. Reson. Med. 45 (2001), 935

DTI WM fiber tracking with 256 directions: N. Lori et al. (support data)

Functional MRI

Functional MRI• It was explained how in diffusion MRI the MR signal intensity is reduced by

the variability of the felt magnetic filed, with that variability being caused by the magnetic field gradient in combination with the random movement of the water molecule.

• In BOLD Functional MRI the variability of the magnetic field is caused by the random movement of deoxygenated hemoglobin cells which are paramagnetic, meaning those cells create a small magnetic field.

• Functional MRI uses gradient echoes, and so the base image is a T2* image.

• Occurrence of action potentials in dendritic tree causes massive outflow of ions across the neuron’s membrane. For the neuron to recover its capacity of transmitting neuronal signal those ions have to be moved back across the membrane to recover the proper concentrations.

Functional MRI• This movement of ions constitutes the major energetic consumption of

neurons that fire an action potential, this energy consumption converts ATP to ADP.

• Because of the Krebs cycle’s creation of ATP from ADP requires oxygen, there will a reduction on the amount of oxygen in the neuronal medium.

• Reduction of oxygen in the neuronal medium activates neurons controlling the width of the vessels flowing blood into and out of the brain. Increase of blood flow increases fraction of oxygenated hemoglobin.

Functional MRI

• The bigger the fraction of deoxygenated hemoglobin, the bigger the intensity of the magnetic field oscillating. When the vessels dilate, the fraction of oxygenated hemoglobin increases, and thus the magnetic field oscillating decreases causing an increase in T2*.

• The bigger the value of T2* the bigger is the T2*-weighted MR signal intensity, so the BOLD functional MRI signal grows with the amount of neuronal energy consumption.

Example of a model

explaining the different

components to the BOLD

signal:

Compartmental ballon and

BOLD model. K. Uludag and

R. B. Buxton. Proceedings of

ISMRM 2005, P. 24.

• Image modified from: http://www.bmb.psu.edu/courses/bisci004a/cardio/capbed.jpg

Functional MRI• The difference between the BOLD signal during an event and the

BOLD signal in the resting state is typically represented by a color spectrum; with yellow representing a high positive value [increase in energy consumption] and blue representing a high negative value [decrease in energy consumption].

• There is a time lag of a few seconds between the alteration in neuronal activation and the alteration in the BOLD signal.

From BVQXGettingStartedGuide_v2.5

Present Work

WM Fiber Tracking

Experimental Setting

• Diffusion MRI data acquired for 64 different gradient orientations using a 3T Siemens Trio.

• Q-ball fiber and Diffusion Tensor WM fiber tracking was done using Trackvis, and selected fibers were those passing in regions of high BOLD activity.

• Tracks have coloration dependent on their orientation: red are medial-lateral; blue are inferior-superior, and green are anterior-posterior.

• The b-value used was 4000.

DTI WM fiber tracking with 64 directions: N. Lori et al.

QBI WM fiber tracking with 64 directions: N. Lori et al.

QBI WM fiber tracking with 64 directions: N. Lori et al.

QBI WM fiber tracking with 64 directions: N. Lori et al.

BOLD and Fiber TrackingIntegration

Experimental Setting• BOLD activations obtained every 2 seconds while subject was

tapping finger.

• Diffusion MRI data acquired for 207 and 256 different gradient orientations using a 3T Siemens Trio. The b-value used was 4000.

• Q-ball fiber tracking was done using Trackvis, and selected fibers were those passing in regions of high BOLD activity.

• Fiber tracks for sensory (cyan and blue) and motor input (yellowand green) were obtained, and were then used to identify different sections of posterior internal capsule.

• Tracks have reddish tone (left figure) when passing in voxels where BOLD activation is high (lower-right figure).

• Q-ball WM fiber tracking was successfully used in separating motorvs. sensory cortex BOLD activation. Internal capsule fiber-passage locations were anatomically reasonable (2) (upper-right figure).

Q-ball Fiber Tracking With BOLD FMRIN. Lori et al.

Conclusion

• MRI is a technique with multiple applications in neuroscience and in medicine.

• Anatomical, diffusion and functional MRI each have their usefulness.

• Advantage of MRI over X-Ray is that it can give different types of anatomical information; plus it can white matter connection and functional information.

• Advantage of MRI over the PET functional measurement approach is that it requires no ingestion of radioactive material.

• The advantage of MRI over CT scans is that it does not have the large radiation deposition that CT scans has.

Request• We are installing this weeks as we speak the first MRI

research scanner in Portugal.

• We will be running tests starting on the 24th of October, and we are looking for volunteers.

• E-mail: nflori@fmed.uc.pt

• Volunteers will undergo anatomical, diffusion, and/or BOLD functional MRI scans.

• It is my opinion that this will be good for your increased knowledge of MRI.

• This will also give you the chance to know the rest of the MRI research group at IBILI that is directly working in the MRI scanner installation.