High-resolution diffusion imaging at 7T using 3D multi-slab EPI
Wenchuan Wu1, Peter J Koopmans1, Robert Frost1, Myung-Ho In2, Oliver Speck3, and Karla L Miller1

1FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom, 2Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States, 3Department of Biomedical Magnetic Resonance, Otto-von-Guericke University, Magdeburg, Germany

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 regime1,2, 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 others3,4. Signal variations at slab boundaries can lead to incorrect quantification of diffusion parameters, for which we developed a non-linear correction method5. Further, at this meeting we present a multi-slab adaptation of FLEET6, 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 mm3, 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/mm2, 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 topup7,8 and eddy, respectively. Diffusion tensor was calculated using FSL’s FDT toolbox. BedpostX was used for multi-fibre estimation within imaging voxels9.

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/mm2) 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 Trust

References

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Figures

Fig. 1. High resolution b=0 images and diffusion-weighted images (b = 1500 s/mm2) acquired at 7T.

Fig. 2. Crossing fibers from high-resolution diffusion data. Top row: color-coded maps of principle eigenvectors. Bottom row: Zoomed region of the pons, demonstrating the ability of high-resolution data to resolve crossing fibers.

Fig. 3. Cortical anisotropy depicted by high-resolution diffusion data. For all subjects, the high resolution consistently supported visualisation of fibre architecture within gyri. Here, the pre-central gyrus is depicted in an axial plane just above the superior-most arch of the cingulum bundle. In all subjects, fibres can be seen entering the gyrus, turning slightly and entering cortex, with particularly clear delineation of cortical anisotropy on the anterior bank of the central sulcus.

Fig. 4. Directionally-coded color map of a sagittal slice in all three subjects. Excellent data quality is evident, for example, in the cingulum bundle (red arrows) as it descends into the temporal lobe toward hippocampal projections, a thin tract which is here several voxels thick.



Proc. Intl. Soc. Mag. Reson. Med. 24 (2016)
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