1. Statistical Parametric Mapping
Lecture 6 - Chapter 4
Ultra-Fast 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. Echo Time Optimization
0.025
0.020
0.015
0.010
0.005
0.000 50
100
150
TE, ms
Signal, arb
T2*r=80ms
70ms
60ms
50ms
40ms
30ms
20ms
10ms
TEopt = optimal TE for BOLD contrast lies between T2*a and T2*r
R2*a = R2* relaxation rate during activation (1/T2*a)
R2*r = R2* relaxation rate during rest (1/T2*r)
Fig 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.

3. 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 activation
R2*r is relaxation rate at rest

4. Effects of Field Homogeneity50
100
150
T2*, ms
4000
3000
2000
1000
number of voxels
1.9mm
3.8mm
5.9mm
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 toward shorter T2*.

5. 4x4x4 mm3
2x2x2 mm3
Spin Echo
Gradient Echo EPI
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.

6. Intra-scan Motion Signal
500
1000
1500
navigator index
0.1
0.0
-0.1
-0.2
-0.3
navigator phase, degrees
0.2
Fig Phase fluctuations at center of k-space over 42 seconds. Spikes are due to cardiac cycles and slower periodic signal due to respiratory cycles.
Why would phase advance and retard?

7. For EPI where is the readout signal largest?
gradient
echo
readout window
r.f.
read gradient TE
dephase
rephase
Fig. 4.5 Gradient echo (GE) echo forms at center of readout window where area under rephasing gradient = area of dephasing gradient. Unlike spin echo dephasing is due to spatial difference in Larmor frequencies during application of gradients. First half of readout window is rephasing and second half is dephasing again. This process repeats at the center of readout window for each ky line in k-space for EPI.
For EPI where is the readout signal largest?

8. 0.00
0.02
0.04
0.06
0.08
0.10 15 30 45 60 75 90
White matter
Grey matter
Signal (fraction of M0)
Flip angle (degrees)
Fig Graphical determination of optimal TE for GM and WM signals for multishot GE pulse sequence such as FLASH. Useful for 3D high-resolution images.

9. RF
Slice
Read
Phase a)
Read
Phase b) n
n-1 1
n-1 2 n 2 1
Fig GE EPI pulse sequence and k-space organization of samples.
What flip angle is used for EPI?

10. SE
GE EPI
GE (FLASH)
SE EPI
TE=60 msec
TE=120 msec
Fig. 4.8 Half Fourier (k-space) images. Central 20 percent of ky portion of k-space used for estimating phase correction during conjugation (replacing missing + ky data with acquired -ky data). Note ghosting in B in phase encode direction.

11. Effect of system parameters on EPI images for fixed field of view.
Echo Spacing
Resolution
SNR
Geometric distortion
Increase gradient slew rate
Reduced
---
Increase sampling bandwidth (kx)
Increase number of shots (interleaving ky)
Increased
Use of ramp sampling (similar to slew rate effect)
Increase read matrix (kx)
Increase phase matrix (ky)
Increased*
Increase field strength
Table 4.1 from text.
* actual resolution increase less than expected due to smoothing effect of signal decay.

12. fMRI methods for reduced k-space coverage
Keyhole
acquire full k-space as reference
acquire reduced low-frequency k-space fMRI study
fill in missing k-space from reference
Half-Fourier
acquire 50-60% of k-space starting at highest ky
theoretical symmetry used to fill in missing ky

13. fMRI methods for reduced k-space coverage
Sensitivity encoding (SENSE)
Multiple RF coils with independent signal for each (parallel imaging)
Calibration maps from full k-space
each coil part of k-space
2X improvement EPI, 4X for GE
UNFOLD
Acquire k-space in sequential time segments
time 1 acquire lines 1, 5, 9,
time 2 acquire lines 2, 6, 10,
time 3 acquire lines 3, 7, 11,
time 4 acquire lines 4, 8, 12,
reorder into k-space
4x faster per segment reduces inter echo distortions