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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
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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
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2D High-resolution FMRI Segmented EPI [McKinnon MRM 1993] 7T, 2D segmented EPI 0.5 x 0.5 x 3 mm 3 [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!
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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 t1t1 t2t2 t3t3 t4t4 t5t5 t6t6
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“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
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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]
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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)
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3D stack-of-EPI [Irarrazabal et al, MRM 1995] Adapting echo planar imaging (EPI) to 3D 2D segmented EPI
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3D EPI GRE at 3T 0.8 x 0.8 x 0.8 mm 3 = 0.5 mm 3 T R =69 ms, 7 s/vol, 24 minutes scan time
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3D EPI GRE at 3T (0.8 x 0.8 x 0.8 mm 3 ) Single image 7 s scan time Mean timecourse image 4 min scan time
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Adapting spiral to 3D 3D stack-of-spiral 2D interleaved spiral [Yang et al, MRM 1996]
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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)
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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
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High-resolution retinotopy at 7T 2D single-shot EPI3D segmented EPI 1x1x1 mm 3 resolution Identification of retinotopically-distinct regions Reduced distortion in 3D segmented EPI Itamar Kahn and Randy Buckner, MGH
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3D GRE BOLD at 7T 0.67 x 0.67 x 0.67 mm 3 = 0.3 mm 3 12 minutes scan time Karla Miller and Chris Wiggins, MGH
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3D GRE BOLD at 7T 0.58 x 0.58 x 0.58 mm 3 = 0.2 mm 3 18 minutes scan time Karla Miller and Chris Wiggins, MGH
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3D Imaging: GRE vs. SSFP 3D imaging generally requires short TR SSFP tends to out-perform GRE in this regime
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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 2003Bowen 2005 Passband SSFP: image in flat part of signal profile – Contrast: T 2 at short T R
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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
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3D Spiral transition-band SSFP at 1.5T 1 x 1 x 2 mm 3, 3D spiral, standard head coil Courtesy Jongho Lee, Stanford University
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3D EPI tbSSFP at 3T 0.8 x 0.8 x 0.8 mm 3 = 0.5 mm 3 T R =35 ms, 8.3 s/vol, 24 minutes scan time
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3D EPI tbSSFP FMRI at 7T 0.75 x 0.75 x 0.75 mm 3 = 0.4 mm 3 22 minutes scan time Collaboration with Chris Wiggins, MGH
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Physiological noise: transition-band SSFP Compared to GRE, higher physiological noise in tbSSFP Poor fit with standard physiological noise model
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Real-time computer FID Image Data 0 + 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
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Dynamic frequency tracking compensation offcompensation on [Jongho Lee et al, MRM 2006]
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Passband SSFP vs. GRE (3T) T E = 3 ms T E = 25 ms GREpbSSFP x o GRE SSFP
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Physiological noise: passband SSFP Compared to GRE, lower physiological noise in pbSSFP Short T R (6-12 ms)
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Conclusions Why 3D for high-resolution FMRI? –High-res multi-shot short T R 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 T R
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Acknowledgements Martinos Centre, MGH Christopher Wiggins Graham Wiggins Itamar Kahn FMRIB, Oxford Stephen Smith Peter Jezzard Stanford John Pauly Jongho Lee Yanle Hu Gary 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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