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FMRI acquisition Richard Wise FMRI Director [email protected] +44(0)20 2087 0358 Why do we need the magnet? d Inside an MRI Scanner z gradient coil r.f. transmit/receive x gradient coil super conducting magnet subject gradient coils Common NMR Active Nuclei Isotope Spin I % abundance g MHz/T 1H 1/2 1 1/2 1 1/2 5/2 1/2 3/2 1/2 99.985 0.015 1.108 99.63 0.37 0.037 100 100 100 42.575 6.53 10.71 3.078 4.32 5.77 40.08 11.27 17.25 2H 13C 14N 15N 17O 19F 23Na 31P 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 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 Spin Transitions High energy Low energy The Larmor Frequency ω=γB Frequency Field strength 128 MHz at 3 Tesla Tissue magnetization B0 M 90º RF excitation pulse Tissue magnetization B0 M 90º RF excitation pulse MR signal ω =γB Tissue magnetization B0 M 90º RF excitation pulse . MR signal ω =γB Tissue magnetization B0 90º RF excitation pulse MR signal ω =γB signal Signal decay: time constant T2 time Tissue contrast: TE &T2 decay Echo Amplitude Long T2 (CSF) Medium T2 (grey matter) Contrast Short T2 (white matter) TE T2 Weighted Image T2 Weighted Image T2/ms CSF grey matter 500 8090 white matter 7080 1.5T SE, TR=4000ms, TE=100ms SE, TR=4000ms, TE=100ms Tissue magnetization B0 M M Magnetization recovery: time constant T1 time Tissue magnetization B0 M M Magnetization recovery: time constant T1 time Tissue contrast: TR & T1 recovery Short T1 (white matter) Mz Medium T1 (grey matter) Contrast Long T1 (CSF) TR T1 Weighted Image SPGR, TR=14ms, TE=5ms, flip=20º T1 Weighted Image white matter grey matter CSF T1/s R1/s-1 0.7 1 1.43 1 4 0.25 1.5T SPGR, SPGR,TR=14ms, TR=14ms,TE=5ms, TE=5ms,flip=20º flip=20º Long TR Short TR T1 PD Short TE T2 Long TE From Frequencies to Images • Vary the field by position • Decode the frequencies to give spatial information Gradient coils z gradient coil r.f. transmit/receive x gradient coil super conducting magnet subject gradient coils Image formation Fourier Transform time frequency Signal Spectrum The Fourier Transform FFT n n 2x2 Slice selection RF excitation ω=γB time G 0 frequency (Gradient echo) Pulse sequence 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 T2* : pleasure ….. T2* : ….. and pain T2* contrast T2* contrast • Field variation across the sample • Decay of summed NMR signal GE-EPI is T2* weighted Wilson et al Neuroimage 2003 Neural activity to FMRI signal Neural activity Signalling Vascular response Vascular tone (reactivity) Autoregulation Synaptic signalling BOLD signal Blood flow, oxygenation and volume arteriole B0 field glia Metabolic signalling venule FMRI and electrophysiology Logothetis et al, Nature 2001 Haemodynamic response balloon model % -1 initial dip undershoot Buxton R et al. Neuroimage 2004 Blood oxygenation Bandettini Bandettini andand Wong. Wong. Int.Int. J. Imaging J. Imaging Systems Systems andand Technology. Technology. 6:133 6:133 (1995) (1995) Rest O2 Sat 100% 80% O2 O2 60% O2 Active: 40% increase in CBF, 20% increase in CMRO2 O2 Sat 100% 86% CMRO2 = OEF CBF 72% CMRO2: CBF ratio Hoge R et al Signal evolution • 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* Vessel density 500 m 100 m Harrison RV et al. Cerebral cortex. 2002 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 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 Physiological baseline • Baseline CBF, • But CBF CMRO2 unchanged (Brown et al JCBFM 2003) • BOLD response Cohen et al JCBFM 2002 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) BOLD Noise structure • 1/f dependence BOLD noise – BOLD is bad for detecting long timescale activation frequency Spatial distribution of noise • Motion at intensity boundaries – Head motion – Respiratory B0 shift • Physiological noise in blood vessels and grey matter Thanks to … John Evans Rami Niazy Martin Stuart Spiro Stathakis