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)