Avery JL Berman1,2, William A Grissom3, Thomas Witzel1,2, Daniel J Park1, Olivia Viessmann1,2, Kawin Setsompop1,2,4, and Jonathan R Polimeni1,2,4
1Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, United States, 2Department of Radiology, Harvard Medical School, Boston, MA, United States, 3Vanderbilt University Institute of Imaging Science, Nashville, TN, United States, 4Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
Synopsis
Spin-echo (SE) EPI has long been desired for fMRI acquisitions
with reduced macrovascular sensitivity; however, to achieve a purely T2-weighted
signal, requires sampling a short window around the spin-echo—generally achieved
by a segmented readout. Segmented EPI is well-known to be temporally unstable due
to sensitivity to subject motion between segments. Here we propose a reordering
of the EPI segments, known as FLEET, combined with a variable flip angle
excitation to maximize the image signal level and a recursive RF pulse design
to maintain consistent slice profiles at the spin-echo. We demonstrate the
feasibility of this approach at 3T.
Introduction
Blood oxygenation level-dependent (BOLD) functional MRI (fMRI)
using a spin-echo (SE) acquisition has long been pursued due to its reduced
macrovascular sensitivity as compared to gradient-echo (GE) BOLD,1–3 making SE-BOLD more spatially
specific to neuronal activation at ultra-high field.4,5 In practice, however, SE BOLD fMRI
uses an EPI readout, which has R2' decay away from the spin-echo time,
resulting in substantial macrovascular sensitivity.6,7 Undersampling along the phase-encode
direction will shorten the readout window, however impractical levels of acceleration are required to achieve high imaging resolution. Using a segmented
EPI readout can reduce the R2'-weighting 7 but this makes the acquisition
vulnerable to subject motion between segments (~2s inter-segment TR), resulting
in intermittent ghosting artifacts and reduced image quality. It was recently
shown that the temporal stability of segmented GE EPI can be markedly improved
with a FLEET (Fast Low Excitation-angle Echo-planar Train) readout that acquires
all shots for a given slice prior to acquiring the next slice’s data.8 To ensure optimal SNR and consistent
signal levels across shots, a variable flip angle (VFA) acquisition with recursively
designed Shinnar-Le Roux (SLR) RF pulses 9 that ensured consistent slice
profiles across shots was used. Here, we have combined the recursive pulse
design with a spin-echo VFA-FLEET acquisition to produce a segmented-accelerated
SE-EPI acquisition (SE-VFA-FLEET) with reduced motion-vulnerability.Theory
Target flip angles in the SE-VFA-FLEET scheme were determined
recursively as in standard GE-VFA:10 $$\alpha_{i-1}=\tan^{-1}(\sin(\alpha_i)).$$
To maximize magnetization, the final excitation was set to 90°, giving $$$\alpha_i$$$={45°,90°}
or {35°,45°,90°} for 2- or 3-shots, respectively (with no dummies). The
recursive SLR pulse design generates a standard excitation-refocusing pulse pair
for the first shot then accounts for attenuation of $$$M_z$$$ to design the
subsequent excitation pulses while matching the $$$M_{xy}$$$ profile from the
first shot. Scaling a standard Hann-windowed sinc RF pulse to the desired flip angles results
in non-uniform slice profiles from shot-to-shot since the $$$M_z$$$ profile
changes prior to each excitation (Figure 1). To facilitate consistent excitation
slice profiles across shots, the refocusing pulse was designed to be 1.4x wider
than the excitation profile. Due to the accelerated relaxation experienced
after inversion to the –z-axis, and the
non-negligible time between shots (~100 ms) expected for SE-VFA-FLEET, the ratio of T1 to the segment
TR ($$$TR_{seg}$$$) was factored into the pulse design (Figure 2).Methods
All experiments were conducted at 3T. To examine the impact of T1
relaxation on shot-to-shot signal consistency, a homogeneous agar phantom with
a short T1 (550 ms) was scanned using a 12-channel receive head coil
at low-resolution with a large field-of-view to resolve the ghosts. Acquisition
parameters were: 2 shots, 96×96 matrix, 4.4-mm in-plane resolution, 3.1-mm
slice thickness, 15 slices, 50% slice gap, TE=60ms, $$$TR_{seg}$$$=100ms,
volume TR ($$$TR_{vol}$$$)=3s. Scans were repeated using sets of pulses that
were designed with $$$T_1/TR_{seg}=\{\infty,10,5.5,3\}$$$ with the expectation
that the $$$T_1/TR_{seg}$$$=5.5 pulses would provide the best results given the $$$TR_{seg}$$$ and T1 of the phantom.
A healthy volunteer was scanned at 3T using a 32-channel receive
coil. A range of $$$T_1/TR_{seg}$$$ was used in the pulse design and testing to
account for the wide range of T1 in brain tissue. Unaccelerated and
combined segmented-accelerated acquisitions were acquired—in each case performing 10 repetitions to assess image quality, including stable and unstable ghosts.
Images were reconstructed offline using the FID navigators to
perform within segment Nyquist ghost
correction. To account for differences in shot-to-shot signal, a scaling factor
that minimized the mean-square error between navigators was applied across
segments. Scaling factors were determined from a separately acquired
calibration scan identical to the imaging scan but with no phase-encoding
gradients. GRAPPA reconstruction with FLEET-ACS 11 was applied to the combined
accelerated segments.Results
Figures 2
and 3 demonstrate the non-negligible impact of T1 relaxation in the RF pulse
design. As predicted, in the agar phantom, the $$$T_1/TR_{seg}$$$=5.5 pulses
resulted in the lowest level of ghosting in the phantom. Remarkably, ghosting
levels were reduced to near comparable levels by the inter-segment
normalization in all sets of pulses.
In the in
vivo scan, the image quality from the pulses designed with $$$T_1/TR_{seg}$$$=7
and 10 were qualitatively best—ghosting signal typically originated from the
periphery. Figure 4 shows an example single repetition using 3-shots and the
impact of inter-segment normalization on ghost reduction. Figure 5 shows a
high-resolution 1.5-mm isotropic acquisition achieved with 2-shots R=3 and
averaged across 9 repetitions (first repetition discarded as a dummy).Discussion and Conclusions
We have presented a novel pulse sequence to acquire segmented SE-EPI
with reduced vulnerability to subject motion. Using the recursive RF
pulse design, we could achieve a SE-VFA-FLEET acquisition that incorporates
inversion of $$$M_z$$$ during refocusing and relaxation across segments while
achieving consistent slice profiles across shots. Due to the multiple pulses
used, significant gradient spoiling and crushing were required, however, further
optimization of these gradient moments will be investigated to improve signal
stability and reduce ghosting. Ghosting from tissues whose T1 did not match the
T1 used in pulse design was problematic but could be addressed, possibly, by
using more segments, each of shorter duration. In future work, we aim to implement
the sequence at 7T where SE-EPI will have greater value for high-resolution
fMRI.Acknowledgements
This work was supported in part by the
CIHR (MFE–154755), the NIH NIBIB (grants P41-EB015896, R01-EB019437,
and R01-EB016695), by the BRAIN Initiative (NIH NIMH grant
R01-MH111419 and NIBIB grant U01-EB025162), and by the MGH/HST Athinoula A.
Martinos Center for Biomedical Imaging; and was made possible by the resources
provided by NIH Shared Instrumentation Grants S10-RR023043 and S10-RR019371.References
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