Statistical Parametric MappingStatistical Parametric Mapping

Lecture 4a - Chapter 7

Spatial and temporal resolution of 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

Spatial and Temporal Resolution Issues

• Spatial Resolution– Spatial sampling and alaising– Partial volume averaging alters strength of response

based on voxel size and size of responding region

• Temporal Resolution– Temporal sampling and averaging– Would like to sample electrical activity which happens

earlier than BOLD– Order and timing of events would improve modeling

capabilities

Spatial Resolution Issues

• Excitatory and Inhibitory neural activity are both energy consuming, but upstream inhibited neurons produce less neuronal activity.

• Need to cover all regions of brain involved in the tested brain tasks (whole brain preferred).– Activity could be weaker due to partial volume effects

at smaller nodes in a system level activated brain network.

– Need to improve task induced change and reduce partial volume averaging.

• Position errors due to veins, macroscopic susceptibility, etc.

Impact of Spatial Resolution• Extent of BOLD response (rb) is related to the extent of neuro-

vascular response (rv) and the imaging spatial resolution extent (rs).

• General relationship• rb2 = rv2 + rs2

• BOLD signal is variable due to partial volume averaging

• When rv < rs (voxel larger than signal region)• rb ~ rs• Bold signal is reduced by partial volume averaging

• When rv > rs (voxel smaller than signal region)• rb ~ rv• BOLD signal minimally affected by rs

Based on classical linear system where output(x,y,z) = input(x,y,z) PSF(x,y,z)

But?

• fMRI response ratio drops off with stimulus duration

• Dilution of signal into larger extent seems to be dominant effect

1.6

2.0

2.4

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0 4 8 12 16 20Stimulus duration (s)

fMR

I re

spon

se r

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Figure 7.3 from textbook.

time

BO

LD

res

pons

e, %

initialdip

positiveBOLD response

post stimulusundershootovershoot

1

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stimulus

• Initial dip – localized response (low signal)• Overshoot next in extent (high signal)• Plateau has greatest extent (high signal)

Response extent

Figure 8.1. from textbook.

Two Main Focus Points• Responding well to changing hemodynamics

– Initial dip in BOLD response more spatially specific to activated brain area than later rise in response, but later phase response is larger and needed for fMRI.

– Hyperoxic response more broadly distributed spatially.

• Techniques to eliminate unwanted contributions to signal (increase CNR).– Short duration stimuli seem to be more narrowly distributed spatially

than long duration stimuli in BOLD studies.– Higher B0 appears to improve microvascular signals more than

interfering signals– Better RF coils improve SNR– Improved motion correction improves CNR– Multi-shot EPI to reduce T2* blurring supports smaller voxels

Statistical Parametric MappingStatistical Parametric Mapping

Lecture 4b - 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 (SPMs less noisy)

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 (need more temporal averaging)

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 is 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

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

Statistical Parametric MappingStatistical Parametric Mapping

Lecture 4c - Chapter 4

More 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

Effects of Field Homogeneity

R2* = R2 + R2mi +R2ma

• R2 = transverse relaxation rate due to spin-spin interactions and diffusion through microscopic gradients

• R2mi = transverse relaxation rate due to microscopic changes, i.e. deoxyhemoglobin

• R2ma = transverse relaxation rate due to macroscopic field inhomogeneity

R2*a is relaxation rate during activationR2*r is relaxation rate at rest

Note: macroscopic components subtract off

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

Fig. 4.1 BOLD response as a function of TE for different values of T2*r. Note that TEopt ~ T2* and that BOLD response increases with increasing T2*r.

0.025

0.020

0.015

0.010

0.005

0.0000 50 100 150

TE, ms

Sig

nal,

arb

T2*r=80ms

70ms

60ms

50ms

40ms

30ms20ms

10ms

TEopt = optimal TE for BOLD contrast lies between T2*a and T2*r

T2*a = 1/R2*a T2*r = 1/R2*r

Echo Time Optimization

Subscripts a and r indicate during activationand rest.

Fig. 4.2 Change in histogram of T2* for thick slab through brain with changing slice thickness. Note broadening of distribution with increasing thickness with shift away from T2*a toward shorter T2*r.

0 50 100 150T2*, ms

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oxel

s 1.9mm3.8mm5.9mm

Effects of Field Homogeneity

Fig. 4.3 EPI obtained with TE= 60 and TR=3000 msec and 63 and 95 ky lines. Note recovery of signal loss in d vs c and ghosting in c.

Spin Echo

4x4x4 mm3

Gradient Echo EPI

2x2x2 mm3

Fig. 4.4 Phase fluctuations at center of k-space over 42 seconds. Spikes are due to cardiac cycles and slower periodic signal due to respiratory cycles.

0 500 1000 1500navigator index

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Intra-scan Motion Signal

Why would phase advance and retard?

Statistical Parametric MappingStatistical Parametric Mapping

Lecture 4d

The big Picture of Brain

Many thanks to those that share their MRI slides online

Brain Lobes +

Occipital Lobe

Cerebellum

Temporal Lobe

Frontal Lobe

Brainstem

Cerebrum Lobes

• Frontal

• Parietal

• Temporal

• Occipital

Brodmann’s Functional Map

Mango and Anatomy

• Talairach Daemon (TD)– Anatomical/functional labels– 5 hierarchical levels

• Hemispheres• Lobes• Gyri• Tissue• Cellular

• Spatial Normalization– Supports x-y-z coordinate lookup of

anatomical/functional labels using the TD