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
2.8
3.2
3.6
0 4 8 12 16 20Stimulus duration (s)
fMR
I re
spon
se r
atio
Figure 7.3 from textbook.
time
BO
LD
res
pons
e, %
initialdip
positiveBOLD response
post stimulusundershootovershoot
1
2
3
0
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
4000
3000
2000
1000
0
num
ber
of v
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
0.1
0.0
-0.1
-0.2
-0.3
navi
gato
r ph
ase,
deg
rees
0.2
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