Statistical Parametric Mapping Lecture 5 - Chapter 6 Selection of the optimal pulse sequence for fMRI Textbook: Functional MRI an introduction to methods, Peter Jezzard, Paul Matthews, and Stephen Smith Many thanks to those that share their MRI slides online

Advantages Disadvantages BOLD Highest activation contrast 2x-4x over perfusion complicated non-quantitative signal easiest to implement no baseline information multislice trivial susceptibility artifacts can use very short TR Perfusion unique and quantitative information low activation contrast baseline information longer TR required easy control over observed vasculature multislice is difficult non-invasive slow mapping of baseline information no susceptibility artifacts Table 6.1a. Summary of practical advantages and disadvantages of pulse sequences (derived from textbook)

Advantages Disadvantages Volume unique information invasive baseline information susceptibility artifacts multislice trivial requires separate run for each task rapid mapping of baseline information CMRO2 unique and quantitative information semi-invasive extremely low activation contrast processing intensive multislice is difficult longer TR required Table 6.1b. Continued summary of practical advantages and disadvantages of pulse sequences (derived from textbook)

Time/secs 1 2 4 3 Perfusion TI ASL 3 Perfusion Venous outflow Venous outflow No Velocity Nulling Velocity Nulling Arteries Arterioles Capillaries Venules Veins TI ASL Figure 6.1a Signal is detected from water spins in the arterial-capillary region of the vasculature and from water in tissues surrounding the capillaries. Relative sensitivity controlled by adjusting TI and by incorporating velocity nulling gradients (also known as diffusion weighting). Nulling and TI~1 sec makes ASL sensitive to capillaries and surrounds.

Time/secs 1 2 4 3 Arterial inflow (BOLD TR < 500 ms) GE-BOLD No Velocity Nulling Velocity Nulling Arteries Arterioles Capillaries Venules Veins Figure 6.1b Gradient Echo BOLD is sensitive to susceptibility perturbers of all sizes, and are therefore sensitive to all intravasculature and extravascular effects in the capillary-venous portions of the vasculature. If a very short TR is used may show signal from arterial inflow, which can be removed by using a longer TR and/or outer volume saturation.

Time/secs 1 2 4 3 Arterial inflow (BOLD TR < 500 ms) SE-BOLD No Velocity Nulling Velocity Nulling Arteries Arterioles Capillaries Venules Veins Figure 6.1c Spin Echo BOLD is sensitive to susceptibility perturbers about the size of a red blood cell or capillary, making it predominantly sensitive to intravascular water spins in vessels of all sizes and to extravascular (tissue) water surrounding capillaries. Velocity nulling reduces the signals from larger vessesl.

Gradient-echo RF Gx Gz Gy 90° TE ASL pulse TI Spin-echo 180° TE RF Gx Gz Gy ASL pulse TI 90° spin-echo 180° TE RF Gx Gz Gy 90° t t/2 Figure 6.2 Pulse sequence diagrams of (a) gradient echo, (b) spin echo, and (c) asymmetric spin echo EPI. The TE is shown at the center of 9-line k-space (typically 64 or more lines).  is the offset from center of k-space to echo. Additional pulses needed for ASL are indicated schematically.

Approximate GM Relaxation And Activation Induced Rexalation Rate Changes 100 ms 80 ms T2* 60 ms 50 ms T2’ 150 ms 133.3 ms DR2 = D(1/T2) -0.2 s-1 -0.4 s-1 DR2* = D(1/T2*) -0.8 s-1 -1.6 s-1 DR2’ = D(1/T2’) -0.6 s-1 -1.2 s-1 T2, T2* and T2’ (from ASE) of GM decrease with increasing field strength During activation relaxation rates decrease (T2 increase) slightly Activation induced changes in relaxation rates (R2s) indicate potential for signal production

Asymmetric Gradient - echo spin - echo 3 T 1.5 T MRI signal TE (ms) t 0.2 0.4 0.6 0.8 1 -80 -40 40 80 MRI signal (ms) 70 90 110 130 Spin-echo time (ms) t 3 T 1.5 T -20 20 60 100 TE (ms) Gradient - echo Asymmetric spin - echo Figure 6.3a Signal intensity for GE, SE, and ASE for approximate relaxation rates of grey matter at 1.5T and 3T. SE sequence corresponds to ASE at  = 0. Signal decays more rapidly since T2 and T2* is shorter at 3T.

Asymmetric Gradient - echo spin - echo Per cent change (ms) t 3 T 2 4 6 8 10 12 14 16 -80 -40 40 80 Per cent change (ms) 130 110 90 70 Spin-echo time (ms) t 3 T 1.5 T 20 60 100 TE (ms) Gradient - echo Asymmetric spin - echo Figure 6.3b Percent signal change for approximated activation-induced relaxation rate changes (using Table 6.2). Note linear increase for GE and for ASE with |  |>0. Also, 3T shows larger change than 1.5T for all three.

Asymmetric Gradient - echo spin - echo Difference (ms) t 3 T 1.5 T 0.01 0.02 0.03 0.04 0.05 -80 -40 40 80 Difference (ms) 70 90 110 130 Spin-echo time (ms) t 3 T 1.5 T 20 60 100 TE (ms) Gradient - echo Asymmetric spin - echo Figure 6.3c Signal difference or contrast with brain activation. Peak contrast for GE when TE~T2* and ASE when  ~T2*. SE has lowest contrast.

Maximizing Signal Field Strength and sequence parameters RF coils Higher B means higher SNR but more susceptibility issues TE ~ T2* (30-40 msec @ 3T) for best activation contrast TR large enough to cover volume of interest, sampling time consistent with experiment, >500 msec recommended, T1 increases with increasing B RF coils Larger coil for transmit Smaller coil for receive RF inhomogeneity increases with B Voxel size Match to volume of smallest desired functional area 1.5x1.5x1.5 suggested as optimal (Hyde et al., 2000) T2* increase and activation signal increase with small voxels if shim is poor

Maximizing Signal Reducing physiological fluctuations Cardiac and breathing artifacts (sampling issues) Filtering to remove artifactual frequencies from time signal, breathing easier to manage by filtering Pulse sequence strategies Snap shot (EPI) each image in 30-40 msec reduces impact of artifacts Multi-shot ghosting (spiral imaging, navigator pulses, retrospective correction) Gating Acquiring image at consistent phase of cardiac cycle or respiration Problems (changing heart rate, wasted time)

Minimizing Temporal Artifacts Brain activation paradigm timing On-off cycles usually > 8 seconds Maximum number of cycles and maximum contrast between Cycling activations no longer than 3-4 minutes Post processing Motion correction Real time fMRI Monitoring immediately and repeat if artifacts are excessive Tuning of slice location

Minimizing Temporal Artifacts Physical restraint Limited success Cooperative subject helps Pulse sequence strategies Clustered acquisition (auditory stimulation 4-6 seconds before acquisition) Set phase encode direction to minimize overlap with brain areas of interest Select image plane with most motion to minimize between plane motion artifacts Crusher gradients to minimize inflow artifacts

Issues of Resolution and Speed Acquisition speed Echo planar sequence preferred for fMRI Multi-shot imaging used for anatomy Image resolution Higher resolution takes more time and T2* leads to low signal for later k-space lines multi-shot EPI Partial k-space acquisition Brain Coverage Full brain coverage desirable Uniform response throughout brain also needed

Structural and Functional Image Quality Functional time series image quality Warping Signal dropout High resolution structural image quality 3D sub-millimeter possible Matching functional to structural