1. Richard Wise FMRI Director wiserg@cardiff.ac.uk +44(0)20 2087 0358
FMRI acquisition
Richard Wise
FMRI Director
+44(0)

5. I am going to introduce you to the methods with the help of
… John and Rami … say hello

6. Why do we need the magnet?

7. Inside an MRI Scanner z gradient coil r.f. transmit/receive
x gradient coil
Why do we need a magnet and what are all these complicated coils inside?
super conducting magnet
subject
gradient coils

8. Common NMR Active Nuclei
Isotope Spin % g
I abundance MHz/T
1H 1/ 2H
13C 1/
14N
15N 1/
17O 5/
19F 1/
23Na 3/
31P 1/

9. Nuclear Spin M
magnetic moment
M=0
spin
If a nucleus has an unpaired proton it will have spin
and it will have a net magnetic moment or field

10. Resonance
If a system that has an intrinsic frequency (such as a bell or a swing) can draw energy from another system which is oscillating at the same frequency, the 2 systems are said to resonate

11. Spin Transitions
High energy
Low energy
Show RF coil

12. ω = γ B The Larmor Frequency Frequency  Field strength
Demo FID
Modify B0 to show change in frequency
128 MHz at 3 Tesla

13. Tissue magnetization B0 M 90º RF excitation pulse
Field strength - the stronger the field the bigger is M
More signal - more blobs

14. Tissue magnetization B0 M
90º RF excitation pulse
MR signal ω = γ B

15. Tissue magnetization B0 M
90º RF excitation pulse .
MR signal ω = γ B

16. Tissue magnetization B0 90º RF excitation pulse MR signal ω = γ B
Demo FID
signal
Signal decay: time constant T2
time

17. Tissue contrast: TE &T2 decay
Echo Amplitude
Long T2 (CSF)
Medium T2 (grey matter)
Explain that we really acquire an echo rather than a single FID
Echo is needed to get more complete artifact free data
Also allows us to add interesting contrast such as BOLD and diffusion.
Contrast
Short T2 (white matter) TE

18. T2 Weighted Image

19. T2 Weighted Image T2/ms CSF 500 grey matter 8090 white matter 7080
SE, TR=4000ms, TE=100ms
SE, TR=4000ms, TE=100ms

20. Tissue magnetization B0 M M Magnetization recovery: time constant T1
Explain TR - repeat time determines T1 contrast M
Magnetization recovery: time constant T1
time

21. Tissue magnetization B0 M M Magnetization recovery: time constant T1

22. Tissue contrast: TR & T1 recovery
Short T1 (white matter) Mz
Medium T1 (grey matter)
Long T1 (CSF)
Contrast TR

23. T1 Weighted Image SPGR, TR=14ms, TE=5ms, flip=20º
Normally acquired for your FMRI structural scan
SPGR, TR=14ms, TE=5ms, flip=20º

24. T1 Weighted Image T1/s R1/s-1 white matter 0.7 1.43 grey matter 1 1
CSF 4
0.25
1.5T
SPGR, TR=14ms, TE=5ms, flip=20º
SPGR, TR=14ms, TE=5ms, flip=20º

25. Short TR Long TR Short TE Long TE T1 PD T2
Signal comes principally from water
Depends on tissue properties
Amount of water
Physical and chemical structure
Contrast comes from ‘relaxation’ processes

26. From Frequencies to Images
Vary the field by position
Decode the frequencies to give spatial information

27. Gradient coils z gradient coil r.f. transmit/receive x gradient coil
Why do we need a magnet and what are all these complicated coils inside?
super conducting magnet
subject
gradient coils

28. Image formation
Fourier
Transform
time
frequency
Signal
Spectrum

29. The Fourier Transform FFT n 2 x 2
Matrix size (2 to the power n) for the convenience of the fast fourier transform
2 x 2 n

30. Slice selection
RF excitation
ω = γ B
time
frequency 0 G

31. (Gradient echo) Pulse sequence
Pulse sequence allows us to spatially encode in 2 or 3 dimensions

32. The Pulse Sequence Controls
Slice location
Slice orientation
Slice thickness
Number of slices
Image resolution
Field of view (FOV)
Image matrix
Echo-planar imaging
Image contrast
TE, TR, flip angle, diffusion etc
Image artifact correction
Saturation, flow compensation, fat suppresion etc

33. T2* : pleasure …..

34. T2* : ….. and pain

35. T2* contrast

36. T2* contrast Field variation across the sample
Decay of summed NMR signal

37. GE-EPI is T2* weighted

38. Wilson et al Neuroimage 2003
CONTRAST
T1 spin lattice relaxation time
Thermal processes
How quickly the system gets back to equilibrium
T2 spin spin relaxation
Loss of coherence in transverse magnetisation
Random fluctuation in magnetic field felt by nucleus
T2* macroscopic field gradients
Loss of coherence across sample
Optimum TE = T2*
Wilson et al Neuroimage 2003

39. Neural activity to FMRI signal
Signalling
Vascular response
Vascular tone (reactivity)
Autoregulation
Metabolic signalling
BOLD signal
glia
arteriole
venule
B0 field
Synaptic signalling
Blood flow,
oxygenation
and volume

40. FMRI and electrophysiology
Logothetis et al, Nature 2001

41. Haemodynamic response
balloon model
Functional contrast (and what each is good for)
BOLD (blood oxygenation level dependent)
T2 and T2*
Perfusion (arterial spin labelling) - more quantitative but lower SNR
Cerebral blood volume
VASO, vascular space occupancy
Functional Spectroscopy % -1
initial dip
undershoot
Buxton R et al. Neuroimage 2004

42. Field inhomogeneity disrupts magnetic field and reduces image quality.

43. Blood oxygenation
Bandettini and Wong. Int. J. Imaging Systems and Technology. 6:133 (1995)
Bandettini and Wong. Int. J. Imaging Systems and Technology. 6:133 (1995)

44. Active: 40% increase in CBF, 20% increase in CMRO2
Rest
O2 Sat 100% 80% 60% O2 O2 O2
Active: 40% increase in CBF, 20% increase in CMRO2
BOLD signal comes mainly from the venous side
O2 Sat 100% 86% 72%
CMRO2 = OEF  CBF

45. CMRO2: CBF ratio Hoge R et al
Ant insula was most significantly modulated – consistent with previous imaging reports.
Hoge R et al

46. Signal evolution R2*  (1-Y) CBV S = Smax . e-TE/R2*
Deoxy-Hb contribution to relaxation
R2*  (1-Y) CBV
Y=O2 saturation
b~1.5
Gradient echo
S = Smax . e-TE/R2*
Longer TE, more BOLD contrast but less signal and more dropout/distortion. TE=T2*

47. Harrison RV et al. Cerebral cortex. 2002
Vessel density
500 m
100 m
Harrison RV et al. Cerebral cortex. 2002

48. Resolution Issues Spatial Resolution Temporal Resolution
How close is the blood flow response to the activation site (CBF better?)
Most BOLD signal is on the venous side
EPI is “low res”
Dropout and distortion
Slice orientation
Slice thickness
Temporal Resolution

49. Factors affecting BOLD signal?
Physiology
Cerebral blood flow (baseline and change)
Metabolic oxygen consumption
Cerebral blood volume
Equipment
Static field strength
Field homogeneity (e.g. shim dependent T2*)
Pulse sequence
Gradient vs spin echo
Echo time, repeat time
Resolution
BOLD signal is inherently messy being a mixture of physiological changes.
It is not directly comparable between brain regions as it depends on vessel architecture but we see later on that this may be a benefit in yielding information about cerebrovasculature.

50. Physiological baseline
Baseline CBF,
But CBF CMRO2 unchanged (Brown et al JCBFM 2003)
BOLD response 
Implications for disease and phsyiological state, I.e. breathing and sedation, anxiety
Vasoactive medications
Cohen et al JCBFM 2002

51. Noise sources What is noise in a BOLD experiment?
Unmodelled variation in the time-series
Intrinsic MRI noise
Independent of field strength, TE
Thermal noise from subject and RF coil
Physiological noise
Increases with field strength, depends on TE
At 3T physiological noise > intrinsic
Cardiac pulsations
Respiratory motion and B0 shift
Vasomotion, 0.1Hz
Blood gas fluctuations
“Resting state” networks
Also
Scanner drift (heating up)
Noise is why we are here

52. BOLD Noise structure 1/f dependence BOLD noise
BOLD is bad for detecting long time-scale activation
frequency

53. Spatial distribution of noise
Motion at intensity boundaries
Head motion
Respiratory B0 shift
Physiological noise in blood vessels and grey matter

55. Thanks to …
John Evans
Rami Niazy
Martin Stuart
Spiro Stathakis