Zero and first-order phase shift correction for field map estimation with dual-echo GRE using bipolar gradients

Quantitative assessment of the susceptibility artefact and its interaction with motion in diffusion MRI

In this paper we evaluate the three main methods for correcting the susceptibility-induced artefact in diffusion-weighted magnetic-resonance (DW-MR) data, and assess how correction is affected by the susceptibility field's interaction with motion. The susceptibility artefact adversely impacts analysis performed on the data and is typically corrected in post-processing. Correction strategies involve either registration to a structural image, the application of an acquired field-map or the use of additional images acquired with different phase-encoding. Unfortunately, the choice of which method to use is made difficult by the absence of any systematic comparisons of them. In this work we quantitatively evaluate these methods, by extending and employing a recently proposed framework that allows for the simulation of realistic DW-MR datasets with artefacts. Our analysis separately evaluates the ability for methods to correct for geometric distortions and to recover lost information in regions of signal compression. In terms of geometric distortions, we find that registration-based methods offer the poorest correction. Field-mapping techniques are better, but are influenced by noise and partial volume effects, whilst multiple phase-encode methods performed best. We use our simulations to validate a popular surrogate metric of correction quality, the comparison of corrected data acquired with AP and LR phase-encoding, and apply this surrogate to real datasets. Furthermore, we demonstrate that failing to account for the interaction of the susceptibility field with head movement leads to increased errors when analysing DW-MR data. None of the commonly used post-processing methods account for this interaction, and we suggest this may be a valuable area for future methods development.

An Actively Decoupled Dual Transceiver Coil System for Continuous ASL at 7 T

7 T arterial spin labeling (ASL) faces major challenges including the increased specific absorption rate (SAR) and increased B₀ and B₁ inhomogeneity. This work describes the design and implementation of a dual-coil system that allows for continuous ASL (CASL) at 7 T. This system consisted of an actively detunable eight-channel transceiver head coil, and a three-channel transceiver labeling coil. Four experiments were performed in 5 healthy subjects: (i) to demonstrate that active detuning during ASL labeling reduces magnetization transfer; (ii) to measure the B₁ profile at the labeling plane; (iii) to quantify B₀ off-resonance at the labeling plane; and (iv) to collect in vivo CASL data. The magnetization transfer ratio in the head coil was reduced to 0.0 ± 0.2% by active detuning during labeling. The measured B₁ profiles in all 5 subjects were sufficient to satisfy the flow-driven adiabatic inversion necessary for CASL, however the actual labeling efficiency was significantly impacted by B₀ off-resonance at the labeling plane. The measured CASL percent signal change in gray matter (0.94% ± 0.10%) corresponds with the low labeling efficiency predicted by the B₀ off-resonance. This work demonstrates progress in the technical implementation of 7 T CASL, and reinforces the need for improved B₀ homogeneity at the labeling plane.

Foundations of MRI phase imaging and processing for Quantitative Susceptibility Mapping (QSM)

Quantitative Susceptibility Mapping (QSM) is a novel MRI based technique that relies on estimates of the magnetic field distribution in the tissue under examination. Several sophisticated data processing steps are required to extract the magnetic field distribution from raw MRI phase measurements. The objective of this review article is to provide a general overview and to discuss several underlying assumptions and limitations of the pre-processing steps that need to be applied to MRI phase data before the final field-to-source inversion can be performed. Beginning with the fundamental relation between MRI signal and tissue magnetic susceptibility this review covers the reconstruction of magnetic field maps from multi-channel phase images, background field correction, and provides an overview of state of the art QSM solution strategies.

Evaluation of EPI distortion correction methods for quantitative MRI of the brain at high magnetic field

High field MRI has been applied to high-resolution structural and functional imaging of the brain. Echo planar imaging (EPI) is an ultrafast acquisition technique widely used in diffusion imaging, functional MRI and perfusion imaging. However, it suffers from geometric and intensity distortions caused by static magnetic field inhomogeneity, which is worse at higher field strengths. Such susceptibility artifacts are particularly severe in relation to the small size of the mouse brain. In this study we compared different distortion correction methods, including nonlinear registration, field map-based, and reversed phase-encoding-based approaches, on quantitative imaging of T1 and perfusion in the mouse brain acquired by spin-echo EPI with inversion recovery and pseudo-continuous arterial spin labeling, respectively, at 7 T. Our results showed that the 3D reversed phase-encoding correction outperformed other methods in terms of geometric fidelity, and that conventional field map-based correction could be improved by combination with affine transformation to reduce the bias in the field map. Both methods improved quantification with smaller fitting error and regional variation. These approaches offer robust correction of EPI distortions at high field strengths and hence could lead to more accurate co-registration and quantification of imaging biomarkers in both clinical and preclinical applications.

Phase-corrected bipolar gradients in multi-echo gradient-echo sequences for quantitative susceptibility mapping

OBJECTIVE

Large echo spacing of unipolar readout gradients in current multi-echo gradient-echo (GRE) sequences for mapping fields in quantitative susceptibility mapping (QSM) can be reduced using bipolar readout gradients thereby improving acquisition efficiency.

MATERIALS AND METHODS

Phase discrepancies between odd and even echoes in the bipolar readout gradients caused by non-ideal gradient behaviors were measured, modeled as polynomials in space and corrected for accordingly in field mapping. The bipolar approach for multi-echo GRE field mapping was compared with the unipolar approach for QSM.

RESULTS

The odd-even-echo phase discrepancies were approximately constant along the phase encoding direction and linear along the readout and slice-selection directions. A simple linear phase correction in all three spatial directions was shown to enable accurate QSM of the human brain using a bipolar multi-echo GRE sequence. Bipolar multi-echo acquisition provides QSM in good quantitative agreement with unipolar acquisition while also reducing noise.

CONCLUSION

With a linear phase correction between odd-even echoes, bipolar readout gradients can be used in multi-echo GRE sequences for QSM.

Phase-uncertainty quality map for two-point Dixon fat-water separation

This work investigates and compares two different phase-correction algorithms for Dixon fat-water separation and two different quality maps (QM) for region-growing: the original QM, based on phase gradients, and a QM based on phase uncertainty, proposed in this article. A spoiled dual-gradient-echo sequence was employed at 1.5 T to acquire in-phase and out-of-phase images of joints, parotid glands, abdomen and test objects. All 97 datasets were processed eight times each: with two different phase correction algorithms (original and hierarchical phase correction), with two different QM, and with/without removing linear component of the phase drifts associated with dual-echo acquisitions and bipolar readout gradient waveforms. The linear component of the phase drift along the readout direction was found to reach 4.1° pixel(-1), depending on the geometric parameters. Pre-processing to remove linear phase shifts has little impact on outcome. The hierarchic phase-correction algorithm outperformed the original phase-correction algorithm in all applications. The proposed phase-uncertainty QM provides a small performance improvement in clinical images, but can be vulnerable to flow-related phase shifts in bright vessels. Overall the most successful phase-correction technique employed phase-uncertainty QMs and hierarchic algorithms, with pre-processing to correct the linear phase drift associated with dual-echo acquisitions and bipolar readout gradient waveform.

Multi-parametric neuroimaging reproducibility: a 3-T resource study

Modern MRI image processing methods have yielded quantitative, morphometric, functional, and structural assessments of the human brain. These analyses typically exploit carefully optimized protocols for specific imaging targets. Algorithm investigators have several excellent public data resources to use to test, develop, and optimize their methods. Recently, there has been an increasing focus on combining MRI protocols in multi-parametric studies. Notably, these have included innovative approaches for fusing connectivity inferences with functional and/or anatomical characterizations. Yet, validation of the reproducibility of these interesting and novel methods has been severely hampered by the limited availability of appropriate multi-parametric data. We present an imaging protocol optimized to include state-of-the-art assessment of brain function, structure, micro-architecture, and quantitative parameters within a clinically feasible 60-min protocol on a 3-T MRI scanner. We present scan-rescan reproducibility of these imaging contrasts based on 21 healthy volunteers (11 M/10 F, 22-61 years old). The cortical gray matter, cortical white matter, ventricular cerebrospinal fluid, thalamus, putamen, caudate, cerebellar gray matter, cerebellar white matter, and brainstem were identified with mean volume-wise reproducibility of 3.5%. We tabulate the mean intensity, variability, and reproducibility of each contrast in a region of interest approach, which is essential for prospective study planning and retrospective power analysis considerations. Anatomy was highly consistent on structural acquisition (~1-5% variability), while variation on diffusion and several other quantitative scans was higher (~<10%). Some sequences are particularly variable in specific structures (ASL exhibited variation of 28% in the cerebral white matter) or in thin structures (quantitative T2 varied by up to 73% in the caudate) due, in large part, to variability in automated ROI placement. The richness of the joint distribution of intensities across imaging methods can be best assessed within the context of a particular analysis approach as opposed to a summary table. As such, all imaging data and analysis routines have been made publicly and freely available. This effort provides the neuroimaging community with a resource for optimization of algorithms that exploit the diversity of modern MRI modalities. Additionally, it establishes a baseline for continuing development and optimization of multi-parametric imaging protocols.

Linear phase-error correction for improved water and fat separation in dual-echo dixon techniques

Large and spatially-linear phase errors along the frequency-encode direction may be induced by several common and hard-to-avoid system imperfections such as eddy currents. For data acquired in dual-echo Dixon techniques, the linear phase error can be more aggravated when compared to that acquired in a single echo and can pose challenges to a phase-correction algorithm necessary for successful Dixon processing. In this work, we propose a two-step process that first corrects the linear component of the phase errors with a modified Ahn-Cho algorithm (Ahn CB and Cho ZH, IEEE Trans. Med. Imaging 6:32, 1987) and then corrects the residual phase errors with a previously-developed region-growing algorithm (Ma J, Magn. Res. Med. 52:415, 2004). We demonstrate that successive application of the two-step process to data from a dual-echo Dixon technique provides a "1-2 punch" to the overall phase errors and can overcome local water and fat separation failures that are observed when the region-growing-based algorithm is applied alone.