Synopsis
In this work, we combined 3D multi-slab imaging (optimal SNR efficiency for spin-echo sequence) and 7T (higher SNR) to enhance diffusion imaging. With the newly developed Slice-FLEET technique and NPEN correction, we successfully achieved robust high resolution diffusion MRI at 7T with high SNR.Purpose
To demonstrate high-resolution, high SNR
diffusion imaging using 3D multi-slab EPI at 7T, with improved slab-boundary
correction and auto-calibration acquisition.
Background
Optimal
SNR efficiency for spin-echo diffusion imaging is associated with very short
repetition times (TR=1-2s), which even the state-of-the-art simultaneous
multi-slice methods struggle to achieve. By comparison, 3D multi-slab imaging
is highly compatible with this regime
1,2, and can also achieve
thin slices. These properties make it an attractive method for high-resolution
diffusion imaging. Nevertheless, 3D multi-slab imaging does have unique
challenges, several of which are the focus of recent developments by our group
and others
3,4. Signal variations at
slab boundaries can lead to incorrect quantification of diffusion parameters, for
which we developed a non-linear correction method
5. Further, at this
meeting we present a multi-slab adaptation of FLEET
6, which reduces
sensitivity of auto-calibration scans (ACS) to subject’s motion and respiration.
Using these advances, we now aim to explore the potential for 3D multi-slab
imaging to achieve high-resolution, high-SNR diffusion imaging. In particular,
we demonstrate the benefits of 7T for 3D multi-slab imaging, to our knowledge
the first time these highly compatible technologies have been combined.
Methods
Three
healthy subjects were scanned on a Siemens 7T scanner. Scan parameters: FOV 210×210×117
mm
3, matrix size 204×204, 14 slabs, 10 slices/slab, slice thickness
1.03 mm, 20% slab overlap, in-plane GRAPPA 3, partial Fourier 6/8, echo spacing
0.82ms, BW 1442 Hz/pixel, TE/TR=71/2700ms, b=0, 1500 s/mm
2, 64
diffusion directions and 8 b=0 (phase encoding: 6 A-P, 2 P-A). One set of
Slice-FLEET ACS data was acquired. Briefly, ACS scans are acquired
with a 2D GRE-EPI sequence, with slice excitations matched to the reconstructed
slices of the final diffusion imaging volumes. ACS data for each slice is
segmented to match the in-plane acceleration factor (here, three segments) and
all segments are acquired for one slice before moving on to the next, minimizing
motion sensitivity. In NPEN, the slab boundary artefacts correction is formulated as a
nonlinear inversion problem, and slab aliasing and saturation artefacts are
corrected by iterative reconstruction. For initial estimation of slab profile (required
by NPEN), one set of b0 data was oversampled by a factor of 2 along kz.
The total scan time is around 35mins. Image distortions and eddy-current
effects were removed using topup
7,8 and eddy, respectively. Diffusion tensor
was calculated using FSL’s FDT toolbox. BedpostX was used for multi-fibre
estimation within imaging voxels
9.
Results
Figure
1 shows isotropic-resolution b=0 and DWI images acquired at 7T, demonstrating
high SNR under a challenging protocol with both high spatial resolution (~1mm
isotropic) and b-value (1500 s/mm
2) in 27s scan time. However, there
are clearly some residual artefacts at the slab boundary (green circle in the b=0
image), which the same NPEN reconstruction was able to robustly correct at 3T. The
location of these artefacts suggests that they relate to severe B0/B1
inhomogeneity (which may interfere with the NPEN assumption that slab
boundaries are periodic along z direction). It should be also noted that the low signal
intensity at temporal lobes (yellow circles) is due to B1 inhomogeneity, which could be improved
with parallel transmit technology. Despite these artefacts, we are able to
reconstruct high quality visualizations of the underlying fibre architecture
from this data. Figure 2 demonstrates fibre reconstructions in the pons, where the
corticospinal tracts (running superior-inferior) interdigitate with the decussation
of the pons (crossing right-left). On
the top, a single-fibre reconstruction is dominated by the corticospinal tract
(blue), indicating that the spatial resolution is insufficient to resolve this
interdigitation. However, the multi-fibre reconstructions on the bottom are
able to robustly estimate both populations within a voxel, demonstrating high
contrast and SNR in the data. Figure 3 demonstrates high-resolution depiction of
cortical anisotropy, which is highly consistent across three subjects. Figure 4
shows directionally-coded colour map of a sagittal slice, in
which thin tracts can be consistently captured from the high-resolution data (red arrow) from all three subjects.
Discussion and conclusion
In this work, we combined two powerful
techniques to improve diffusion MRI: 3D multi-slab acquisition (optimal SNR
efficiency) and 7T (high SNR). With several technical developments, including
Slice-FLEET to improve robustness of GRAPPA and NPEN to correct slab boundary
artefacts, we were able to acquire ~1mm isotropic resolution diffusion data
with high SNR and high b-value. Analysis of the high resolution data
demonstrates its ability to resolve crossing fibers and capture thin fibre tracts.
Acknowledgements
This work was supported by the Initial Training Network, HiMR, funded by the FP7 Marie Curie Actions of the European Commission (FP7-PEOPLE-2012-ITN-316716) and the Wellcome TrustReferences
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