Statistical Parametric Mapping

1. 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

2. Table 6.1a. Summary of practical advantages and disadvantages of pulse sequences (derived from textbook)

3. Table 6.1b. Continued summary of practical advantages and disadvantages of pulse sequences (derived from textbook)

4. Time/secs 0 1 2 3 4 No Velocity Nulling Velocity Nulling Perfusion Venous outflow Venous outflow 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.

5. Time/secs 0 1 2 3 4 No Velocity Nulling Velocity Nulling Arterial inflow (BOLD TR < 500 ms) GE-BOLD 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.

6. Time/secs 0 1 2 3 4 No Velocity Nulling Velocity Nulling Arterial inflow (BOLD TR < 500 ms) SE-BOLD 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.

7. TI TI Gradient-echo spin-echo Spin-echo TE TE 180° 180° ASL pulse ASL pulse TE t/2 t 90° 90° 90° RF RF RF Gx Gx Gx Gy Gy Gy Gz Gz Gz 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.

8. Approximate GM Relaxation And Activation Induced Rexalation Rate Changes • 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

9. Asymmetric spin - echo Gradient - echo 1 1 Spin-echo time (ms) 0.8 0.8 3 T 0.6 1.5 T 0.6 70 MRI signal 90 MRI signal 0.4 110 0.4 3 T 130 1.5 T 0.2 0.2 0 0 -20 0 20 40 60 80 100 -80 -40 0 40 80 TE (ms) t (ms) 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.

10. Asymmetric spin - echo Gradient - echo Spin-echo time (ms) 16 16 14 14 3 T 3 T 12 12 130 1.5 T 1.5 T 110 10 10 Per cent change 90 Per cent change 8 8 70 6 6 4 4 2 2 0 0 0 20 40 60 80 100 -80 -40 0 40 80 t TE (ms) (ms) 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.

11. Asymmetric spin - echo Gradient - echo Spin-echo time (ms) 0.05 0.05 70 3 T 0.04 3 T 90 0.04 110 1.5 T 1.5 T 130 0.03 0.03 Difference Difference 0.02 0.02 0.01 0.01 0 0 -80 -40 0 40 80 0 20 40 60 80 100 t (ms) TE (ms) 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.

12. Maximizing Signal Field Strength and sequence parameters 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

13. 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)

14. 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

15. 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

16. 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

17. 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