Statistical Parametric Mapping

Statistical Parametric MappingStatistical Parametric Mapping

Lecture 5 - Chapter 6Selection 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

susceptibility artifacts

processing intensive

multislice is difficult

longer TR required

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

Venous outflow

Perfusion

NoVelocityNulling

VelocityNulling

ASLTI

Time/secs 1 2 40 3

Venous outflow

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.

Arteries Arterioles Capillaries Venules Veins

GE-BOLD

NoVelocityNulling

VelocityNulling

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.

Arteries Arterioles Capillaries Venules Veins

Arterial inflow(BOLD TR < 500 ms)

Time/secs 1 2 40 3

SE-BOLD

NoVelocityNulling

VelocityNulling

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.

Arteries Arterioles Capillaries Venules Veins

Arterial inflow(BOLD TR < 500 ms)

Time/secs 1 2 40 3

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.

Gradient-echo

RF

Gx

Gz

Gy

90°

TEASLpulse

TISpin-echo

180° TE

RF

Gx

Gz

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ASLpulse

TI

90°

spin-echo

180° TE

RF

Gx

Gz

Gy

Approximate GM Relaxation And Activation Induced Rexalation Rate Changes

1.5T 3T

T2 100 ms 80 ms

T2* 60 ms 50 ms

T2’ 150 ms 133.3 ms

R2 = (1/T2) -0.2 s-1 -0.4 s-1

R2* = (1/T2*) -0.8 s-1 -1.6 s-1

R2’ = (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

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MRI signal

(ms)

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MRI signal

TE (ms)

3 T1.5 T

Gradient - echo Asymmetricspin - 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.

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Spin-echo time (ms)

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Per cent change

TE (ms)

3 T1.5 T

Gradient - echo Asymmetricspin - 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.

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Difference

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Spin-echo time (ms)

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Difference

TE (ms)

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Gradient - echo Asymmetricspin - 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

– 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