Elsevier

NeuroImage

Volume 80, 15 October 2013, Pages 220-233
NeuroImage

Pushing the limits of in vivo diffusion MRI for the Human Connectome Project

https://doi.org/10.1016/j.neuroimage.2013.05.078Get rights and content

Highlights

  • Approach for advancing the sensitivity of the diffusion connectivity measurement.

  • Optimization of Gmax = 300 mT/m gradient, RF coil and sequence.

  • Improved sensitivity and diffusion contrast in high quality DSI/Q Ball.

Abstract

Perhaps more than any other “-omics” endeavor, the accuracy and level of detail obtained from mapping the major connection pathways in the living human brain with diffusion MRI depend on the capabilities of the imaging technology used. The current tools are remarkable; allowing the formation of an “image” of the water diffusion probability distribution in regions of complex crossing fibers at each of half a million voxels in the brain. Nonetheless our ability to map the connection pathways is limited by the image sensitivity and resolution, and also the contrast and resolution in encoding of the diffusion probability distribution.

The goal of our Human Connectome Project (HCP) is to address these limiting factors by re-engineering the scanner from the ground up to optimize the high b-value, high angular resolution diffusion imaging needed for sensitive and accurate mapping of the brain's structural connections. Our efforts were directed based on the relative contributions of each scanner component. The gradient subsection was a major focus since gradient amplitude is central to determining the diffusion contrast, the amount of T2 signal loss, and the blurring of the water PDF over the course of the diffusion time. By implementing a novel 4-port drive geometry and optimizing size and linearity for the brain, we demonstrate a whole-body sized scanner with Gmax = 300 mT/m on each axis capable of the sustained duty cycle needed for diffusion imaging. The system is capable of slewing the gradient at a rate of 200 T/m/s as needed for the EPI image encoding. In order to enhance the efficiency of the diffusion sequence we implemented a FOV shifting approach to Simultaneous MultiSlice (SMS) EPI capable of unaliasing 3 slices excited simultaneously with a modest g-factor penalty allowing us to diffusion encode whole brain volumes with low TR and TE. Finally we combine the multi-slice approach with a compressive sampling reconstruction to sufficiently undersample q-space to achieve a DSI scan in less than 5 min. To augment this accelerated imaging approach we developed a 64-channel, tight-fitting brain array coil and show its performance benefit compared to a commercial 32-channel coil at all locations in the brain for these accelerated acquisitions.

The technical challenges of developing the over-all system are discussed as well as results from SNR comparisons, ODF metrics and fiber tracking comparisons. The ultra-high gradients yielded substantial and immediate gains in the sensitivity through reduction of TE and improved signal detection and increased efficiency of the DSI or HARDI acquisition, accuracy and resolution of diffusion tractography, as defined by identification of known structure and fiber crossing.

Introduction

Following years of steady growth, diffusion MRI and fMRI have reached technological turning points in their respective mappings of human structural and functional connectivity, as have the computational tools to organize and share the resulting data. As part of the US National Institutes of Health's Blueprint Initiative for Neuroscience Research; Human Connectome Project (HCP), the MGH-UCLA collaboration was charged with pushing the frontier of extant acquisition technology with the goal of building dramatically more comprehensive and complete models of the structural Connectome than currently available. To achieve this we set out with a blank sheet of paper and asked; “what would an MR scanner optimized specifically for connectomics look like and what are the potential imaging improvements?” The result required developing and validating advances in every domain of MR technology except the magnet. First and foremost, we attempted to construct the highest performance gradient set ever attempted for human imaging. The resulting gradients utilize a peak gradient strength of 300 mT/m and are capable of slewing at 200 T/m/s. Although peripheral nerve stimulation (PNS) prevents the application of waveforms combining both high strength and high slew rate, the diffusion sequence requires primarily high strength alone during the diffusion encode and high slew rate at moderate Gmax (~ 40–50 mT/m) during the EPI readout. The goal was twofold; to shorten the TE of the spin echo diffusion, reducing signal losses from T2 processes, and to decrease the diffusion time Δ. Shortening TE has a simply characterized exponential effect on image sensitivity. The effect of the shortened diffusion time is less easily characterized but is expected to sharpen features in the water probability distribution function. Because the goal is efficient human diffusion imaging, the gradients need to perform at high duty-cycle for hours at a time without inefficient cool-down periods.

The sequence was re-examined with a goal of improving the notoriously in-efficient 2D spin echo diffusion sequence. Such 2D sequences become inefficient when TR becomes higher than the theoretical optimum; TR  1.2 T1 (about 1 s for white matter at 3 T), due to the number of slices needed to cover the head with 2D EPI. Thus typical diffusion acquisitions, with a TR of up to 10 s for a 2 mm isotropic acquisition, are enormously inefficient. The nuclear magnetization spends most of its time at equilibrium waiting to be sampled. The speed up was achieved by enabling a method of exciting and reading-out multiple slices simultaneously and separating them with parallel imaging methods. Although implemented a decade ago (Larkman et al., 2001), the method was not suitable for diffusion imaging since its g-factor penalty outweighs the envisioned efficiency benefit. Nonetheless, this technique was successfulness employed to significantly accelerate fMRI acquisition at 7T, where physiological fluctuation dominates the noise time-series (Moeller et al., 2008, Moeller et al., 2010). A significant reduction of the g-factor penalty in EPI was achieved by implementing a blipped CAIPIRHINA FOV shifting scheme, (Setsompop et al., 2012) thereby allowing a net gain in efficiency as well as an increase in the number of diffusion directions obtainable in a given scan time. Finally, the RF detection was augmented with a 64-channel brain array coil designed to increase parallel imaging performance (Keil et al., 2012). Taken together, the expected efficiency gain is nearly an order of magnitude for high b-value diffusion (3.5 × from shorter TE, 1.7 × from the Rslice = 3 SMS, and 1.4 fold from the RF coil).

In this paper, we describe the strategy and implementation of the MGH-UCLA Connectome scanner, our initial validation of its performance in SNR, sequence and diffusion ODF metrics, as well as a characterization of some of the concomitant problems of the methodology; such as peripheral and central nervous system stimulation, increased eddy current fields and gradient Maxwell terms.

Section snippets

Choice of B0 field strength

The first choice for the proposed scanner involved selecting the B0 field strength. Excellent quality EPI encoding, including high resolution single-shot, has been achieved at 7 T using highly parallel arrays coils by many groups, including ours. This immediately suggests that EPI-based methods such as diffusion imaging could potentially benefit from the 2 × increase in image (thermal) SNR observed in going from 3 T to 7 T (Triantafyllou et al., 2005, Vaughan et al., 2001). However, several issues

Gradient design and implementation

Many previous approaches to high strength gradients have relied on asymmetric head gradient designs. These designs are appealing since the small size creates an intrinsically efficient design (high Gmax per Ampere of current) as well as reduced PNS stimulation since the shoulders and torso are outside of the main gradient field. However, the asymmetric head gradient also has several negative features. The small size exacerbates the heating problem by reducing the mass and the volume available

Nerve stimulation thresholds

After successful fabrication, the gradient coil was tested for PNS at the factory using a standard threshold detection protocol in 35 healthy adult subjects (20 males 15 females). The gradient coil was energized in a laboratory setting (outside of the magnet) with the subjects supine with their head at isocenter. The PNS study was conducted according to the requirements defined by IEC 60601-2-33. chapter “51.105.1 Direct determination of the limits of the Gradient Output”. The gradients were

Eddy current effects and Concomitant terms (Maxwell's terms)

Both eddy current fields and concomitant fields are increased in stronger gradients. Although careful attention was paid to the shield coil design to successfully lower the eddy current fields as expressed as a percentage of the total gradient fields, the 7.5 fold higher gradient strength yielded eddy currents that were between 2 and 3 fold higher in absolute terms. Usually the first line of defense is to use a twice refocused spin echo sequence designed to eliminate the principle eddy current

Acoustic noise and vibrations

While a 7 fold increased gradient strength might potentially be accompanied by a similar increase in acoustic noise and vibrations, it appears that the effect of the thicker, heavier gradient, as well as increased torque and force balancing afforded by the larger volume, offset this problem. The gradient running at 300 mT/m produces a lower acoustic noise than the conventional 40 mT/m 3 T and qualitative assessment of the vibration suggests it is also reduced.

Achieved TE and diffusion time (Δ) reductions and SNR gains

Fig. 5 shows the minimum TE obtained for a standard Stejskal–Tanner spin echo diffusion sequence as a function of b value for a 2 mm isotropic EPI readout (200 FOV, 3/4 partial Fourier, and R = 2 acceleration) as a function of maximum gradient strength. The TEmin is shown for a gradient strength of 40 mT/m, 80 mT/m, 100 mT/m and 300 mT/m. The largest reduction in TE and Δ occurs for the higher b values. For Gmax = 40, 80, 100 and 300 mT/m and b = 10,000 s/mm2, the diffusion time (Δ) was; 56.4, 38.4, 33.9,

RF design and implementation

Since parallel image reconstruction (both conventional in-plane and in the slice directions) was central to our acquisition strategy, we set out to create a state-of-the-art highly parallel RF brain coil. (Keil et al., 2012) The resulting 64 channel brain array is shown in Fig. 7. The array former splits into two halves and yet retains the critical overlap of the circular elements (~ 55–65 mm dia). The array adheres to the head shape to a degree previously not attempted. It is also mounted

Simultaneous multi-Slice with blipped-CAIPI FOV shift

The diffusion encoding pulses encode the water displacement in the whole brain, but are followed by the readout of only a single slice. This wastes a significant fraction of the imaging time. An alternative view is that a given spin is only sampled for a small fraction of the TR period; an inefficiency which grows with the number of 2D slices. The ultra high strength gradients allow for a significant shortening of the diffusion encoding time, while the use of parallel imaging to reduce the

Susceptibility distortion mitigation

The geometric image distortion induced by susceptibility gradients in the phase encode direction of EPI remains a significant problem for single shot SE-EPI based diffusion acquisitions. While the hardware advances described do not fully mitigate this problem, they reduce these distortions in two ways. Firstly, the stronger gradients allow a faster EPI readout than conventional gradients even though PNS prevents the use of the full gradient strength during the EPI readout. Nonetheless the

Diffusion imaging evaluation

While the higher q-space encoding, in principle, will encode higher detail in the PDF and therefore the Orientation Distribution Function (ODF), it does so at reduced SNR due to the high b-value. We assess the benefit of the higher gradient strengths in Fig. 13 by comparing the first and second fiber uncertainty metrics in b = 10,000 s/mm2 q-ball acquisitions acquired on the Connectome scanner using Gmax = 40 mT/m, 100 mT/m and 300 mT/m. The acquisition used the single refocused spin echo sequences, TR =

Conclusion

Gradient strength, acquisition efficiency and detection sensitivity are critical determinants of sensitivity in diffusion imaging, especially for high b-value high angular resolution acquisitions. Encouraged by the knowledge that small bore scanners with high gradient strength appeared to produce a richer structural Connectome in fixed tissue than is possible in living humans, we set out to re-engineer a clinical scanner to match the small bore capabilities. Owing to synergistic effects of

Acknowledgments

This work acknowledges funding from the National Institutes of Health, NIH Blueprint Initiative for Neuroscience Research grant U01MH093765, National Institutes of Health grant P41EB015896, and NIH NIBIB grant K99/R00EB012107.

Note that the MGH-UCLA Connectome scanner is a Work in Progress. The information about this product is preliminary. The product is under development and is not commercially available in the U.S. and its future availability cannot be assured.

Conflict of interest

The authors

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