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FMRI acquisition Richard Wise FMRI Director +44(0)20 2087 0358.

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Presentation on theme: "FMRI acquisition Richard Wise FMRI Director +44(0)20 2087 0358."— Presentation transcript:

1 FMRI acquisition Richard Wise FMRI Director +44(0)

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6 Why do we need the magnet? d

7 Inside an MRI Scanner subject super conducting magnet x gradient coil z gradient coil r.f. transmit/receive gradient coils

8 Common NMR Active Nuclei IsotopeSpin % g IabundanceMHz/T 1 H 1/ H C 1/ N N 1/ O 5/ F 1/ Na 3/ P 1/

9 Nuclear Spin spin magnetic moment M M=0 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 Low energy High energy

12 The Larmor Frequency ω = γ B Frequency  Field strength 128 MHz at 3 Tesla

13 Tissue magnetization B0B0 M 90º RF excitation pulse

14 Tissue magnetization B0B0 M 90º RF excitation pulse MR signal ω = γ B

15 Tissue magnetization B0B0 90º RF excitation pulse MR signal ω = γ B M.

16 Tissue magnetization B0B0 90º RF excitation pulse MR signal ω = γ B Signal decay: time constant T2 signal time

17 Tissue contrast: TE &T 2 decay TE Echo Amplitude Long T 2 (CSF) Medium T 2 (grey matter) Short T 2 (white matter) Contrast

18 T 2 Weighted Image

19 SE, TR=4000ms, TE=100ms grey matter CSF T 2 /ms  90 SE, TR=4000ms, TE=100ms 1.5T white matter 70  80

20 Tissue magnetization B0B0 M Magnetization recovery: time constant T1 M time

21 Tissue magnetization B0B0 M Magnetization recovery: time constant T1 M time

22 Tissue contrast: TR & T 1 recovery TR Medium T 1 (grey matter) Long T 1 (CSF) Short T 1 (white matter) MzMz Contrast

23 T 1 Weighted Image SPGR, TR=14ms, TE=5ms, flip=20º

24 T 1 Weighted Image SPGR, TR=14ms, TE=5ms, flip=20º white matter grey matter CSF T 1 /s R 1 /s T

25 Short TR Short TE Long TE Long TR T1 T2 PD

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

27 Gradient coils subject super conducting magnet x gradient coil z gradient coil r.f. transmit/receive gradient coils

28 Image formation Fourier Transform frequency time SignalSpectrum

29 The Fourier Transform FFT 2 x 2 n n

30 Slice selection 00 timefrequency G RF excitation ω = γ B

31 (Gradient echo) Pulse sequence

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 T 2 * : pleasure …..

34 T 2 * : ….. and pain

35 T2* contrast

36 Field variation across the sample Decay of summed NMR signal

37 GE-EPI is T2* weighted

38 Wilson et al Neuroimage 2003

39 Neural activity to FMRI signal Neural activitySignallingVascular response Vascular tone (reactivity) Autoregulation Metabolic signalling BOLD signal glia arteriole venule B 0 field Synaptic signalling Blood flow, oxygenation and volume

40 FMRI and electrophysiology Logothetis et al, Nature 2001

41 Haemodynamic response Buxton R et al. Neuroimage 2004 balloon model % initial dip undershoot

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

44 Rest Active: 40% increase in CBF, 20% increase in CMRO2 O2 Sat100%80%60% O2 Sat100%86%72% CMRO 2 = OEF  CBF O2O2 O2O2 O2O2

45  CMRO 2 :  CBF ratio Hoge R et al

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

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

48 Resolution Issues Spatial 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

50 Physiological baseline Baseline CBF , But  CBF  CMRO 2 unchanged (Brown et al JCBFM 2003) BOLD response  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)

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

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

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


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