t2* revision

T2* revision

Vector coherence

Schering

TimeTime

Spins will precess at slightly different frequencies due to variations in the local magnetic field

TimeTime

It is often easier to understand this dephasing is a frame of reference that is rotating at the average frequency of spins

Dephasing

T2* artefacts

Phantom with coin near it

Good(ish) shim

Bad shim

Resting cortex

Blood cells containing deoxy- and oxy- haemoglobin

Arteriole VenuleCapillary Bed

Glucose and O2

Glucose and O2

Active cortexBlood flow

Blood volume

Blood oxygenation

Arteriole VenuleCapillary Bed

Glucose and O2

Glucose and O2

Time after pulse

Mxy

Mo

ActiveRest

Assumed monoexponential:Decay rate is R2

*

z

x

-0.5

0.5

BOLD effect due to T2* effects around blood vessels

1 March 2009 NatureHow do people maintain an active representation of what they have just seen moments ago? The visual areas of the cerebral cortex that are the first to receive visual information are exquisitely tuned to process incoming visual signals, but not to store them.On the other hand brain areas responsible for memory lack visual sensitivity, but somehow people are able to remember a visual pattern with remarkable precision for many seconds, actually, for as long as they keep thinking about that pattern.

1 March 2009 NatureOur question was, where is this precise information being stored in the brain?"Using a new technique to analyze fMRI data, we've found that the fine-scale activity patterns in early visual areas reveal a trace or something like an echo of the stimulus that the person is actively retaining, even though the overall activity in these areas is really weak after the stimulus is removed,”.

Phospholipid structures

Blood brain barrier

departments.weber.edu/chfam/2570/Neurology.html

Central sulcus

Sensory areas of the brain

From FMRIB, Oxford

Susceptibility0

Fer

rom

agne

tic

Par

amag

netic

Dia

mag

netic

-1

Positive susceptibility: object attracted

Magnetic forces

Negative: repelled Positive: attracted

dz

dBBF BmT

Susceptibility0

Fer

rom

agne

tic

Par

amag

netic

Dia

mag

netic

-1

Negative susceptibility: object repelled or levitated

Magnetic forces

Negative: repelled Positive: attracted

Susceptibility0Negative: repelled Positive: attracted

Fer

rom

agne

tic

Par

amag

netic

Dia

mag

netic

-1

Water-910-6

Air (oxygen)+0.36 10-6

Deoxyg. Blood-6.52 10-6

Permanent magnets106

Superconductors-1

Magnetic forces

Red blood cells

Special dissociation curves

CO stop haemoglobin giving up oxygen

Fetal blood preferentially takes up oxygen in placenta

Effect of [dHb] on relaxation times

Time after pulse

Mxy

Mo

Low dHbHigh dHb

Assumed monoexponential:Decay rate is R2

*

z

x

-0.5

0.5

a b

a

d

b c

e f

1/T2* against % dHb for blood at 7T

Resting cortex

Blood cells containing deoxy- and oxy- haemoglobin

Arteriole VenuleCapillary Bed

Glucose and O2

Glucose and O2

Active cortexBlood flow

Blood volume

Blood oxygenation

Arteriole VenuleCapillary Bed

Glucose and O2

Glucose and O2

TimeTime

Spins will precess at slightly different frequencies due to variations in the local magnetic field

TimeTime

It is often easier to understand this dephasing is a frame of reference that is rotating at the average frequency of spins

Lightson

Lightson

Lightsonaa

bb

Time (s)

00 3030 6060

Boldsignal

8 s

Time (s)

Stim

ulus

Initial dipPost stimulus undershoot

Boldsignal

Heamodynamic response function

Heamodynamic response function (effect of adding CA)

EPI pulse sequence

RF

Gslice

Gphase

Gread

Time

Repeat 128 times

A B C

A

B C

kx

ky

EPI k-space trajectory

18

25

34

43

7 TTE

Effect of echo time

0.98

1

1.02

1.04

1.06

1.08

0 50 100 150time (s)

norm

alise

d s

ign

al i

nte

nsi

ty

7 T

3 T

1.5 T

B

0.98

1

1.02

1.04

1.06

1.08

1.1

0 5 10 15 20 25 30

time (s)

norm

alis

ed s

ignal

inte

nsi

ty

7 T3 T1.5T

C

stimulus

Time course of signal change at optimum TE for each field strength averaged over subjects

Cycle average for each field strength.

Rising edge of response intersects base-line earlier at higher field.

BOLD timecourses

Minimize the sum of squared differences between images

Image registration (From Welcome Functional Imaging Lab)

1 0 0 Xtrans

0 1 0 Ytrans

0 0 1 Ztrans

0 0 0 1

1 0 0 0

0 cos() sin() 0

0 sin() cos() 0

0 0 0 1

cos() 0 sin() 0

0 1 0 0

sin() 0 cos() 0

0 0 0 1

cos() sin() 0 0

sin() cos() 0 0

0 0 1 0

0 0 0 1

Translations Pitch Roll Yaw

Rigid body transformations parameterised by:

Squared Error

• Minimising mean-squared difference works Minimising mean-squared difference works for intra-modal registration (realignment)for intra-modal registration (realignment)

• Simple relationship between Simple relationship between intensitiesintensities in one in one image, versus those in the otherimage, versus those in the other– Assumes normally distributed differencesAssumes normally distributed differences

Image registration (From Welcome Functional Imaging Lab)

Image registration (From Welcome Functional Imaging Lab)

Statistical analysis(From Welcome Functional Imaging Lab)

Convolution of paradigm with HRF

From MNI

Cross Correlation

DONT FORGET TO FILL IN THE NATIONAL STUDENT SURVEY

Somatotopic mapping

Centre of activation separation

Normals(6) 11 2 mm

Dystonics (5) 4.4 0.9 mm

p=0.00048

Post Central Gyrus

Area 1Dystonia

Both Fingers

Little Finger

Index Finger

Normals

Recovery from stroke

Motor task in relation to a small lesion

BBC ‘In search of Perfection’- Heston Blumentahl

Response to fat

Correlation of BOLD response with all attributes of oral fat delivery’

Areas with a positive correlation of BOLD response with fat concentration

Different fat levels

Supertaster effect

Fetuses response to auditory stimulus(Motion correction quite a challenge)

Cochlear implant & Cochlear StimulationCochlear implant & Cochlear Stimulation

fMRI & Cochlear StimulationfMRI & Cochlear Stimulation

LLRR

Collaboration with C. Ludman (Radiology), S. Mason (Medical Physics), G. O’Donoghue (Otolaryngology)Collaboration with C. Ludman (Radiology), S. Mason (Medical Physics), G. O’Donoghue (Otolaryngology)

250 Hz, biphasic right cochlear stimulation (9V)250 Hz, biphasic right cochlear stimulation (9V)

ARTERIAL SPIN LABELLING

Possible labelling scheme

• Could measure perfusion like this:

Blood flow

INVERSION PULSE

Magnetization transfer• Could measure perfusion like this:

• The inversion pulse is off-resonance to slice– Might expect it to have no effect on slice– It does because of magnetization transfer

• Exchange between bound and free protons

Blood flow

INVERSION PULSE

INVERSION PULSETAG

EPISTAR

Blood flow

Compare TAG and CONTROL conditionsTAG: tag arterial blood that will exchange with tissueCONTROL: tag venous blood

INVERSION PULSECONTROL

Perfusion• Brain signal comes from mixture of tissue and

blood• Water assumed to be freely diffusible tracer

exchanging between capillary and tissue– Exchange time assumed to be zero

• Not quite true

IN OUT

Blood brain partition coefficient• There are

– 80.5 g water /100g blood– 84.0 g tissue /100g grey matter

• Blood flowing in has more magnetization per unit volume than tissue

• Blood brain partition coefficient = water content of brain = ~ 0.98

water content of blood

Transit time• It takes the labelled blood a finite time to

reach the voxel– And the even longer to reach the capillary

• This must be taken account of in models

Blood flow

TransitTime

Kinetic model

• IF Mz is equal at start of tag and control conditions is same

• Then different signal is given convolution:

DifferenceMz

TagControl

Kinetic model

Arterial input functionDepends on tagging scheme

Timeafter tag applied

Transit time

Transit time

Kinetic model

Residue FunctionAmount of contrast remaining after a time t

r(t)

Inputfunction

Time

Kinetic model

r(t)

Time

Time

r(t)

Magnetization decay functionDescribes T1 relaxation of tag

Labelling schemesFAIR (flow alternating inversion recovery)

Blood in slice follows inversion recoveryBlood outside slice alternates between

• following inversion recovery and • being at equilibrium (Mo)

Blood flow

Kidney ASLDr Francis