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Steady-state free precession and other 3D methods for high-resolution FMRI
Steady-state free precession and other 3D methods for high-resolution FMRI
Karla L. Miller FMRIB Centre, Oxford University
Karla L. Miller FMRIB Centre, Oxford University
Why is high-resolution FMRI so difficult?
• Signal-to-noise ratio:
– For example, 2x2x2 mm has 8x SNR of 1x1x1 mm (would require 64 times longer scan)
• For single-shot, distortion increases with matrix size
• Isotropic resolution (thin slices) is hard in 2D
€
SNR∝ΔxΔyΔz Tacq
2D High-resolution FMRI
Segmented EPI[McKinnon MRM 1993]
7T, 2D segmented EPI0.5 x 0.5 x 3 mm3
[Yacoub et al MRM 2003]
Acquire EPI in multiple shots (“segmented” or “interleaved”)
Allows increased resolution without increased distortion
High-resolution in-plane, but limit on slice thickness!
2D Multi-slice MRI
excited slice
Each slice excited & acquired separately
TR: time between repeated excitation of same slice (typically 1–3 seconds)
Slices no thinner than ~1 mm
t1
t2
t3
t4
t5
t6
“True” 3D imaging
Excite entire slab, readout in 3D k-space
TR: time between repeated slab excitations (5-50 ms)
Can achieve thin slices (isotropic resolution, like structurals)!
excited volume
excited volume
SNR Benefit of 3D Trajectories
SNR is higher for 3D since same magnetization is sampled more frequently
Calculated for 3D stack-of-spirals
[Yanle Hu and Gary Glover, Stanford]
3D Functional MRI
• Advantages:– SNR benefits, provided short TR can be used– Can achieve thinner slices (e.g., for “isotropic” voxels)– 3D multi-shot low distortion
• Disadvantages:– Can require long volume scan times (may be fixable!)– Acquisition time (e.g., “slice timing”) is difficult to define– Slices must be contiguous (no inter-slice gap)
3D stack-of-EPI
[Irarrazabal et al, MRM 1995]
Adapting echo planar imaging (EPI) to 3D
2D segmented EPI
3D EPI GRE at 3T
0.8 x 0.8 x 0.8 mm3 = 0.5 mm3
TR=69 ms, 7 s/vol, 24 minutes scan time
3D EPI GRE at 3T (0.8 x 0.8 x 0.8 mm3 )
Single image7 s scan time
Mean timecourse image4 min scan time
Adapting spiral to 3D
3D stack-of-spiral
2D interleaved spiral
[Yang et al, MRM 1996]
Comparison of 2D vs 3D spiral FMRI
[Hu and Glover, MRM 2006]
• 20% higher functional SNR in 3D compared to 2D
• Significantly more activated voxels (2x at chosen threshold)
3D spiral GRE with partial k-space
full k-space
partial k-space
• Faster imaging: 64 slices in 6.4 s (full) vs. 4.0 s (partial)
[Hu and Glover, MRM 2006]
• Higher statistical power due to reduced physiological noise
High-resolution retinotopy at 7T
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
2D single-shot EPI 3D segmented EPI
• 1x1x1 mm3 resolution• Identification of retinotopically-distinct regions• Reduced distortion in 3D segmented EPI
Itamar Kahn and Randy Buckner, MGH
3D GRE BOLD at 7T
0.67 x 0.67 x 0.67 mm3 = 0.3 mm3
12 minutes scan time
Karla Miller and Chris Wiggins, MGH
3D GRE BOLD at 7T
0.58 x 0.58 x 0.58 mm3 = 0.2 mm3
18 minutes scan time
Karla Miller and Chris Wiggins, MGH
3D Imaging: GRE vs. SSFP
• 3D imaging generally requires short TR• SSFP tends to out-perform GRE in this regime
Balanced Steady-state Free Precession (SSFP)
• SSFP signal dependence on off-resonance
Field mapSSFP image
• Transition band SSFP: image in signal transitions– Contrast: deoxyHb frequency shift
Scheffler 2001
Miller 2003
Bowen 2005
• Passband SSFP: image in flat part of signal profile– Contrast: T2 at short TR
Transition-band SSFP
Functional contrast occurs in “bands”• Changing center frequency shifts region of
high signal (and functional contrast)
Multi-frequency experiments• Repeat stimulus at multiple center
frequencies to extend coverage• Combine data into single activation map
3D Spiral transition-band SSFP at 1.5T
1 x 1 x 2 mm3, 3D spiral, standard head coil
QuickTime™ and a decompressor
are needed to see this picture.
Courtesy Jongho Lee, Stanford University
3D EPI tbSSFP at 3T
0.8 x 0.8 x 0.8 mm3 = 0.5 mm3
TR=35 ms, 8.3 s/vol, 24 minutes scan time
3D EPI tbSSFP FMRI at 7T
0.75 x 0.75 x 0.75 mm3 = 0.4 mm3
22 minutes scan time
Collaboration with Chris Wiggins, MGH
Physiological noise: transition-band SSFP
Compared to GRE, higher physiological noise in tbSSFP
Poor fit with standard physiological noise model
Real-timecomputerFID
Δ
ImageData
0+Δ
Respiration modulates frequency = shift in SSFP bands
Real-time feedback to compensate for frequency drift
[Jongho Lee et al, MRM 2006]
Reducing physiological noise in SSFP
Dynamic frequency tracking
compensation off compensation on
[Jongho Lee et al, MRM 2006]
Passband SSFP vs. GRE (3T)
TE=
3 m
sT
E=
25
ms
GRE pbSSFP
xo
GRESSFP
Physiological noise: passband SSFP
Compared to GRE, lower physiological noise in pbSSFP
Short TR (6-12 ms)
Conclusions
• Why 3D for high-resolution FMRI?
– High-res multi-shot short TR 3D
– Lower distortion with short, 3D readouts
– Can achieve isotropic resolution (thin slices)
• Challenges and advances
– Efficient 3D versions of both EPI and spiral trajectories
– Volume acquisition times: Speed up with partial k-space (or parallel imaging)
• SSFP FMRI
– New method for FMRI contrast
– Highly suitable to 3D due to short TR
Acknowledgements
Martinos Centre, MGHChristopher WigginsGraham WigginsItamar Kahn
FMRIB, OxfordStephen SmithPeter Jezzard
StanfordJohn PaulyJongho LeeYanle HuGary Glover
Funding: NIH, GlaxoSmithKline, EPSRC, Royal Academy of Engineering
Related work: #357 SSFP analysis (Th-AM), #272 SSFP modeling (Th-PM)
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