Steady-state diffusion-weighted imaging: theory, acquisition and analysis

Distortionless, free-breathing, and respiratory resolved 3D diffusion weighted imaging of the abdomen

PURPOSE

Abdominal imaging is frequently performed with breath holds or respiratory triggering to reduce the effects of respiratory motion. Diffusion weighted sequences provide a useful clinical contrast but have prolonged scan times due to low signal-to-noise ratio (SNR), and cannot be completed in a single breath hold. Echo-planar imaging (EPI) is the most commonly used trajectory for diffusion weighted imaging but it is susceptible to off-resonance artifacts. A respiratory resolved, three-dimensional (3D) diffusion prepared sequence that obtains distortionless diffusion weighted images during free-breathing is presented. Techniques to address the myriad of challenges including: 3D shot-to-shot phase correction, respiratory binning, diffusion encoding during free-breathing, and robustness to off-resonance are described.

METHODS

A twice-refocused, M1-nulled diffusion preparation was combined with an RF-spoiled gradient echo readout and respiratory resolved reconstruction to obtain free-breathing diffusion weighted images in the abdomen. Cartesian sampling permits a sampling density that enables 3D shot-to-shot phase navigation and reduction of transient fat artifacts. Theoretical properties of a region-based shot rejection are described. The region-based shot rejection method was evaluated with free-breathing (normal and exaggerated breathing), and respiratory triggering. The proposed sequence was compared in vivo with multishot DW-EPI.

RESULTS

The proposed sequence exhibits no evident distortion in vivo when compared to multishot DW-EPI, robustness to B0 and B1 field inhomogeneities, and robustness to motion from different respiratory patterns.

CONCLUSION

Acquisition of distortionless, diffusion weighted images is feasible during free-breathing with a b-value of 500 s/mm2, scan time of 6 min, and a clinically viable reconstruction time.

Robust multishot diffusion-weighted imaging of the abdomen with region-based shot rejection

PURPOSE

Diffusion-weighted (DW) imaging provides a useful clinical contrast, but is susceptible to motion-induced dephasing caused by the application of strong diffusion gradients. Phase navigators are commonly used to resolve shot-to-shot motion-induced phase in multishot reconstructions, but poor phase estimates result in signal dropout and Apparent Diffusion Coefficient (ADC) overestimation. These artifacts are prominent in the abdomen, a region prone to involuntary cardiac and respiratory motion. To improve the robustness of DW imaging in the abdomen, region-based shot rejection schemes that selectively weight regions where the shot-to-shot phase is poorly estimated were evaluated.

METHODS

Spatially varying weights for each shot, reflecting both the accuracy of the estimated phase and the degree of subvoxel dephasing, were estimated from the phase navigator magnitude images. The weighting was integrated into a multishot reconstruction using different formulations and phase navigator resolutions and tested with different phase navigator resolutions in multishot DW-echo Planar Imaging acquisitions of the liver and pancreas, using conventional monopolar and velocity-compensated diffusion encoding. Reconstructed images and ADC estimates were compared qualitatively.

RESULTS

The proposed region-based shot rejection reduces banding and signal dropout artifacts caused by physiological motion in the liver and pancreas. Shot rejection allows conventional monopolar diffusion encoding to achieve median ADCs in the pancreas comparable to motion-compensated diffusion encoding, albeit with a greater spread of ADCs.

CONCLUSION

Region-based shot rejection is a linear reconstruction that improves the motion robustness of multi-shot DWI and requires no sequence modifications.

Beyond the surface: how ex-vivo diffusion-weighted imaging reveals large animal brain microstructure and connectivity

Diffusion-weighted Imaging (DWI) is an effective and state-of-the-art neuroimaging method that non-invasively reveals the microstructure and connectivity of tissues. Recently, novel applications of the DWI technique in studying large brains through ex-vivo imaging enabled researchers to gain insights into the complex neural architecture in different species such as those of Perissodactyla (e.g., horses and rhinos), Artiodactyla (e.g., bovids, swines, and cetaceans), and Carnivora (e.g., felids, canids, and pinnipeds). Classical in-vivo tract-tracing methods are usually considered unsuitable for ethical and practical reasons, in large animals or protected species. Ex-vivo DWI-based tractography offers the chance to examine the microstructure and connectivity of formalin-fixed tissues with scan times and precision that is not feasible in-vivo. This paper explores DWI's application to ex-vivo brains of large animals, highlighting the unique insights it offers into the structure of sometimes phylogenetically different neural networks, the connectivity of white matter tracts, and comparative evolutionary adaptations. Here, we also summarize the challenges, concerns, and perspectives of ex-vivo DWI that will shape the future of the field in large brains.

Accelerated multislice MRI with patterned excitation

PURPOSE

Accelerate multislice 2D MRI by using RF pulses that simultaneously act on different slices to combine contrast preparation and image acquisition.

THEORY AND METHODS

MRI applications often require the use of multiple RF pulses to generate desired contrast and prepare the signal for readout. Examples are the use of inversion prepulses to generate T1 contrast, or the use of spin-echo preparations to generate T2 or diffusion contrast. In multislice MRI, this separation of contrast preparation and readout can render scans time-inefficient and lengthy. We introduce a class of pulse sequences that overcomes this inefficiency by combining contrast preparation and signal readout. This is accomplished by using RF pulses that manipulate the magnetization of multiple slices simultaneously and a gradient crusher scheme that selects a target slice for readout.

RESULTS

Feasibility of the method was demonstrated for spin echo-based measurement of water diffusion and tissue pulsation in human brain at 3 T. Increases in time-efficiency and reductions in scan time were highly dependent on specific implementation and reached as high as 25% and 53%, respectively.

CONCLUSION

A novel approach to multislice MRI is demonstrated that reduces scan time for specific applications.

Brain Pathways in LIS1-Associated Lissencephaly Revealed by Diffusion MRI Tractography

Lissencephaly (LIS) is a rare neurodevelopmental disorder with severe symptoms caused by abnormal neuronal migration during cortical development. It is caused by both genetic and non-genetic factors. Despite frequent studies about the cortex, comprehensive elucidation of structural abnormalities and their effects on the white matter is limited. The main objective of this study is to analyze abnormal neuronal migration pathways and white matter fiber organization in LIS1-associated LIS using diffusion MRI (dMRI) tractography. For this purpose, slabs of brain specimens with LIS (n = 3) and age and sex-matched controls (n = 4) were scanned with 3T dMRI. Our high-resolution ex vivo dMRI successfully identified common abnormalities across the samples. The results revealed an abnormal increase in radially oriented subcortical fibers likely associated with radial migration pathways and u-fibers and a decrease in association fibers in all LIS specimens.

Diffusion Breast MRI: Current Standard and Emerging Techniques

The role of diffusion weighted imaging (DWI) as a biomarker has been the subject of active investigation in the field of breast radiology. By quantifying the random motion of water within a voxel of tissue, DWI provides indirect metrics that reveal cellularity and architectural features. Studies show that data obtained from DWI may provide information related to the characterization, prognosis, and treatment response of breast cancer. The incorporation of DWI in breast imaging demonstrates its potential to serve as a non-invasive tool to help guide diagnosis and treatment. In this review, current technical literature of diffusion-weighted breast imaging will be discussed, in addition to clinical applications, advanced techniques, and emerging use in the field of radiomics.

High-resolution neural network-driven mapping of multiple diffusion metrics leveraging asymmetries in the balanced steady-state free precession frequency profile

We propose to utilize the rich information content about microstructural tissue properties entangled in asymmetric balanced steady-state free precession (bSSFP) profiles to estimate multiple diffusion metrics simultaneously by neural network (NN) parameter quantification. A 12-point bSSFP phase-cycling scheme with high-resolution whole-brain coverage is employed at 3 and 9.4 T for NN input. Low-resolution target diffusion data are derived based on diffusion-weighted spin-echo echo-planar-imaging (SE-EPI) scans, that is, mean, axial, and radial diffusivity (MD, AD, and RD), fractional anisotropy (FA), as well as the spherical coordinates (azimuth Φ and inclination ϴ) of the principal diffusion eigenvector. A feedforward NN is trained with incorporated probabilistic uncertainty estimation. The NN predictions yielded highly reliable results in white matter (WM) and gray matter structures for MD. The quantification of FA, AD, and RD was overall in good agreement with the reference but the dependence of these parameters on WM anisotropy was somewhat biased (e.g. in corpus callosum). The inclination ϴ was well predicted for anisotropic WM structures, while the azimuth Φ was overall poorly predicted. The findings were highly consistent across both field strengths. Application of the optimized NN to high-resolution input data provided whole-brain maps with rich structural details. In conclusion, the proposed NN-driven approach showed potential to provide distortion-free high-resolution whole-brain maps of multiple diffusion metrics at high to ultrahigh field strengths in clinically relevant scan times.

The Digital Brain Bank, an open access platform for post-mortem imaging datasets

Post-mortem magnetic resonance imaging (MRI) provides the opportunity to acquire high-resolution datasets to investigate neuroanatomy and validate the origins of image contrast through microscopy comparisons. We introduce the Digital Brain Bank (open.win.ox.ac.uk/DigitalBrainBank), a data release platform providing open access to curated, multimodal post-mortem neuroimaging datasets. Datasets span three themes-Digital Neuroanatomist: datasets for detailed neuroanatomical investigations; Digital Brain Zoo: datasets for comparative neuroanatomy; and Digital Pathologist: datasets for neuropathology investigations. The first Digital Brain Bank data release includes 21 distinctive whole-brain diffusion MRI datasets for structural connectivity investigations, alongside microscopy and complementary MRI modalities. This includes one of the highest-resolution whole-brain human diffusion MRI datasets ever acquired, whole-brain diffusion MRI in fourteen nonhuman primate species, and one of the largest post-mortem whole-brain cohort imaging studies in neurodegeneration. The Digital Brain Bank is the culmination of our lab's investment into post-mortem MRI methodology and MRI-microscopy analysis techniques. This manuscript provides a detailed overview of our work with post-mortem imaging to date, including the development of diffusion MRI methods to image large post-mortem samples, including whole, human brains. Taken together, the Digital Brain Bank provides cross-scale, cross-species datasets facilitating the incorporation of post-mortem data into neuroimaging studies.

Developing formalin-based fixative agents for post mortem brain MRI at 9.4 T

PURPOSE

To develop fixative agents for high-field MRI with suitable dielectric properties and measure MR properties in immersion-fixed brain tissue.

METHODS

Dielectric properties of formalin-based agents were assessed (100 MHz-4.5 GHz), and four candidate fixatives with/without polyvinylpyrrolidone (PVP) and different salt concentrations were formulated. B₁ field and MR properties (T₁ , R 2 ∗ , R₂ , R 2 ' , and magnetic susceptibility [QSM]) were observed in white and gray matter of pig brain samples during 0.5-35 days of immersion fixation. The kinetics were fitted using exponential functions. The immersion time required to reach maximum R 2 ∗ values at different tissue depths was used to estimate the Medawar coefficient for fixative penetration. The effect of replacing the fixatives with Fluoroinert and phosphate-buffered saline as embedding media was also evaluated.

RESULTS

The dielectric properties of formalin were nonlinearly modified by increasing amounts of additives. With 5% PVP and 0.04% NaCl, the dielectric properties and B₁ field reflected in vivo conditions. The highest B₁ values were found in white matter with PVP and varied significantly with tissue depth and embedding media, but not with immersion time. The MR properties depended on PVP yielding lower T₁ , higher R 2 ∗ , more paramagnetic QSM values, and a lower Medawar coefficient (0.9 mm / h ; without PVP: 1.5). Regardless of fixative, switching to phosphate-buffered saline as embedder caused a paramagnetic shift in QSM and decreased R 2 ∗ that progressed during 1 month of storage, whereas no differences were found with Fluorinert.

CONCLUSION

In vivo-like B₁ fields can be achieved in formalin fixatives using PVP and a low salt concentration, yielding lower T₁ , higher R 2 ∗ , and more paramagnetic QSM than without additives. The kinetics of R 2 ∗ allowed estimation of fixative tissue penetration.

A unifying view on extended phase graphs and Bloch simulations for quantitative MRI

Quantitative MRI methods and learning-based algorithms require exact forward simulations. One critical factor to correctly describe magnetization dynamics is the effect of slice-selective RF pulses. While contemporary simulation techniques correctly capture their influence, they only provide final magnetization distributions, require to be run for each parameter set separately, and make it hard to derive general theoretical conclusions and to generate a fundamental understanding of echo formation in the presence of slice-profile effects. This work aims to provide a mathematically exact framework, which is equally intuitive as extended phase graphs (EPGs), but also considers slice-profiles through their natural spatial representation. We show, through an analytical, hybrid Bloch-EPG formalism, that the spatially-resolved EPG approach allows to exactly predict the signal dependency on off-resonance, spoiling moment, microscopic dephasing, and echo time. We also demonstrate that our formalism allows to use the same phase graph to simulate both gradient-spoiled and balanced SSFP-based MR sequences. We present a derivation of the formalism and identify the connection to existing methods, i.e. slice-selective Bloch, slice-selective EPG, and the partitioned EPG. As a use case, the proposed hybrid Bloch-EPG framework is applied to MR Fingerprinting.

Three-dimensional spatially resolved phase graph framework

PURPOSE

An open-source spatially resolved phase graph framework is proposed for simulating arbitrary pulse sequences in the presence of piece-wise constant gradients with arbitrary orientations in three dimensions. It generalizes the extended phase graph algorithm for analysis of nonperiodic sequences while preserving its efficiency, and is able to estimate the signal modulation in the 3D spatial domain.

METHODS

The framework extends the recursive magnetization-evolution algorithm to account for anisotropic diffusion and exploits a novel 3D k-space grid-merging method to balance the computational effort and memory requirements against acceptable simulation errors. A new postsimulation module is proposed to track and visualize the signal evolution both in the k-space and in the image domain, which can be used for simulating image artifacts or finding frequency-response profiles. To illustrate the developed technique, three examples are presented: (1) fast off-resonance calculation for dictionary building in MR fingerprinting, (2) validation of a steady-state sequence with quasi-isotropic diffusion weighting, and (3) investigation of the magnetization evolution in PRESS-based spectroscopic imaging.

RESULTS

The grid-merging algorithm of the proposed framework demonstrates high calculation efficiency exemplified by frequency-response simulation of pseudo steady-state or diffusion-weighted steady-state sequences. It further helps to visualize the signal evolution in PRESS-based sequences.

CONCLUSIONS

The proposed simulation framework has been validated based on several different example applications for analyzing signal evolution in the frequency and spatial domain.

Diffusion-weighted double-echo steady-state with a three-dimensional cones trajectory for non-contrast-enhanced breast MRI

The image quality limitations of echo-planar diffusion-weighted imaging (DWI) are an obstacle to its widespread adoption in the breast. Steady-state DWI is an alternative DWI method with more robust image quality but its contrast for imaging breast cancer is not well-understood. The aim of this study was to develop and evaluate diffusion-weighted double-echo steady-state imaging with a three-dimensional cones trajectory (DW-DESS-Cones) as an alternative to conventional DWI for non-contrast-enhanced MRI in the breast. This prospective study included 28 women undergoing clinically indicated breast MRI and six asymptomatic volunteers. In vivo studies were performed at 3 T and included DW-DESS-Cones, DW-DESS-Cartesian, DWI, and CE-MRI acquisitions. Phantom experiments (diffusion phantom, High Precision Devices) and simulations were performed to establish framework for contrast of DW-DESS-Cones in comparison to DWI in the breast. Motion artifacts of DW-DESS-Cones were measured with artifact-to-noise ratio in volunteers and patients. Lesion-to-fibroglandular tissue signal ratios were measured, lesions were categorized as hyperintense or hypointense, and an image quality observer study was performed in DW-DESS-Cones and DWI in patients. Effect of DW-DESS-Cones method on motion artifacts was tested by mixed-effects generalized linear model. Effect of DW-DESS-Cones on signal in phantom was tested by quadratic regression. Correlation was calculated between DW-DESS-Cones and DWI lesion-to-fibroglandular tissue signal ratios. Inter-observer agreement was assessed with Gwet's AC. Simulations predicted hyperintensity of lesions with DW-DESS-Cones but at a 3% to 67% lower degree than with DWI. Motion artifacts were reduced with DW-DESS-Cones versus DW-DESS-Cartesian (p < 0.05). Lesion-to-fibroglandular tissue signal ratios were not correlated between DW-DESS-Cones and DWI (r = 0.25, p = 0.38). Concordant hyperintensity/hypointensity was observed between DW-DESS-Cones and DWI in 11/14 lesions. DW-DESS-Cones improved sharpness, distortion, and overall image quality versus DWI. DW-DESS-Cones may be able to eliminate motion artifacts in the breast allowing for investigation of higher degrees of steady-state diffusion weighting. Malignant breast lesions in DW-DESS-Cones demonstrated hyperintensity with respect to surrounding tissue without an injection of contrast. LEVEL OF EVIDENCE: 2. TECHNICAL EFFICACY STAGE: 1.

Comparison and evaluation of distortion correction techniques on an MR-guided radiotherapy system

PURPOSE

To evaluate two distortion correction techniques for diffusion-weighted single-shot echo-planar imaging (DW-ssEPI) on a 0.35 T magnetic resonance-guided radiotherapy (MRgRT) system.

METHODS

The effects of sequence optimization through enabling parallel imaging (PI) and selecting appropriate bandwidth on spatial distortion were first evaluated on the 0.35 T MRgRT system using a spatial integrity phantom. Field map (FM) and reversed gradient (RG) corrections were then performed on the optimized protocol to further reduce distortion. An open-source toolbox was used to quantify the spatial displacement before and after distortion correction. To evaluate ADC accuracy and repeatability of the optimized protocol, as well as impacts of distortion correction on ADC values, the optimized protocol was scanned twice on a diffusion phantom. The calculated ADC values were compared with reference ADCs using paired t-test. Intraclass correlation coefficient (ICC) between the two repetitions, as well as between before and after FM/RG correction was calculated to evaluate ADC repeatability and effects of distortion correction. Six patients were recruited to assess the in-vivo performance. The optimal distortion correction technique was identified by visual assessment. To quantify distortion reduction, tumor and critical structures were contoured on the turbo spin echo (TSE) image (reference image), the DW-ssEPI image, and the distortion corrected images independently by two radiation oncologists. Mean distance to agreement (MDA) and DICE coefficient between contours on the reference images and the diffusion images were calculated. Tumor apparent diffusion coefficient (ADC) values from the original DW-ssEPI images and the distortion corrected images were compared using Bland-Altman analysis.

RESULTS

Sequence optimization played a vital role in improving the spatial integrity, and spatial distortion was proportional to the total readout time. Before the correction, distortion of the optimized protocol (PI and high bandwidth) was 1.50 ± 0.89 mm in a 100 mm radius and 2.21 ± 1.39 mm in a 175 mm radius for the central plane. FM corrections reduced the distortions to 0.42 ± 0.27 mm and 0.67 ± 0.49 mm respectively, and RG reduced distortion to 0.40 ± 0.22 mm and 0.64 ± 0.47 mm, respectively. The optimized protocol provided accurate and repeatable ADC quantification on the diffusion phantom. The calculated ADC values were consistent before and after FM/RG correction. For the patient study, the FM correction was unable to reduce chemical shift artifacts whereas the RG method successfully mitigated the chemical shift. MDA reduced from 2.52 ± 1.29 mm to 1.11 ± 0.72 mm after the RG correction. The DICE coefficient increased from 0.80 ± 0.13 to 0.91 ± 0.06. A Bland-Altman plot showed that there was a good agreement between ADC measurements before and after application of the RG correction.

CONCLUSION

Two distortion correction techniques were evaluated on a commercial low-field MRgRT system. Overall, the RG correction was able to drastically improve spatial distortion and preserve ADC accuracy.

Alternating unbalanced SSFP for 3D R 2 ' mapping of the human brain

PURPOSE

Measuring the transverse-relaxation rate R 2 ' provides valuable information in quantitative evaluation of tissue microstructure, for example, in terms of oxygenation levels. Here, we propose an alternating unbalanced SSFP pulse sequence for rapid whole-brain 3D R 2 ' mapping.

METHODS

Unlike currently practiced, spin echo-based R 2 ' measurement techniques, the proposed method alternates between SSFP-FID and SSFP-ECHO modes for rapid 3D encoding of transverse relaxation rates expressed as R₂ + R 2 ' and R₂ - R 2 ' . Z-shimming gradients embedded into multi-echo trains of each SSFP module are designed to achieve relative immunity to large-scale magnetic-field variations (ΔB₀ ). Appropriate models for the temporal evolution of the two groups of SSFP signals were constructed with ΔB₀ -induced modulations accounted for, leading to ΔB₀ -corrected estimation of R₂ , R 2 ' , and R 2 ∗ (= R₂ + R 2 ' ). Additionally, relative magnetic susceptibility (Δχ) maps were obtained by quantitative susceptibility mapping of the phase data. Numerical simulations were performed to optimize scan parameters, followed by in vivo studies at 3 T in 7 healthy subjects. Measured parameters were evaluated in six brain regions, and subjected to interparameter correlation analysis.

RESULTS

The resultant maps of R 2 ' and additionally derived R₂ , R 2 ∗ , and Δχ all demonstrated the expected contrast across brain territories (eg, deep brain structures versus cortex), with the measured values in good agreement with previous reports. Furthermore, regression analyses yielded strong linear relationships for the transverse relaxation parameters ( R 2 ' , R₂ , and R 2 ∗ ) against Δχ.

CONCLUSION

Results suggest feasibility of the proposed method as a practical and reliable means for measuring R 2 ' , R₂ , R 2 ∗ , and Δχ across the entire brain.

Modeling an equivalent b-value in diffusion-weighted steady-state free precession

PURPOSE

Diffusion-weighted steady-state free precession (DW-SSFP) is shown to provide a means to probe non-Gaussian diffusion through manipulation of the flip angle. A framework is presented to define an effective b-value in DW-SSFP.

THEORY

The DW-SSFP signal is a summation of coherence pathways with different b-values. The relative contribution of each pathway is dictated by the flip angle. This leads to an apparent diffusion coefficient (ADC) estimate that depends on the flip angle in non-Gaussian diffusion regimes. By acquiring DW-SSFP data at multiple flip angles and modeling the variation in ADC for a given form of non-Gaussianity, the ADC can be estimated at a well-defined effective b-value.

METHODS

A gamma distribution is used to model non-Gaussian diffusion, embedded in the Buxton signal model for DW-SSFP. Monte-Carlo simulations of non-Gaussian diffusion in DW-SSFP and diffusion-weighted spin-echo sequences are used to verify the proposed framework. Dependence of ADC on flip angle in DW-SSFP is verified with experimental measurements in a whole, human postmortem brain.

RESULTS

Monte-Carlo simulations reveal excellent agreement between ADCs estimated with diffusion-weighted spin-echo and the proposed framework. Experimental ADC estimates vary as a function of flip angle over the corpus callosum of the postmortem brain, estimating the mean and standard deviation of the gamma distribution as 1.50 · 10 - 4  mm2 /s and 2.10 · 10 - 4  mm2 /s.

CONCLUSION

DW-SSFP can be used to investigate non-Gaussian diffusion by varying the flip angle. By fitting a model of non-Gaussian diffusion, the ADC in DW-SSFP can be estimated at an effective b-value, comparable to more conventional diffusion sequences.

Unipolar MR elastography: Theory, numerical analysis and implementation

In MR elastography (MRE), zeroth moment balanced motion-encoding gradients (MEGs) are incorporated into MRI sequences to induce a phase shift proportional to the local displacement caused by external actuation. To maximize the signal-to-noise ratio (SNR), fractional encoding is employed, i.e., the MEG duration is reduced below the wave period. Here, gradients encode primarily the velocity of the motion-reducing encoding efficiency. Thus, in GRE-MRE, T₂ * decay and motion sensitivity have to be balanced, imposing a lower limit on repetition times (TRs). We propose to use a single trapezoidal gradient, a "unipolar gradient", to directly encode spin displacement. Such gradients cannot be used in conventional sequences as they exhibit a large zeroth moment and dephase magnetization. By time-reversing a spoiled SSFP sequence, the spoiling gradient becomes an efficient unipolar MEG. The proposed "unipolar MRE" technique benefits from this approach in three ways: first, displacement encoding is split over multiple TRs increasing motion sensitivity; second, spoiler and MEG coincide, allowing a reduction in TR; third, motion sensitivity of a typical unipolar lobe is of an order of magnitude higher than a bipolar MEG of equal duration. In this work, motion encoding using unipolar MRE is analyzed using the extended phase graph (EPG) formalism with a periodic motion propagator. As an approximation, the two-transverse TR approximation for diffusion-weighted SSFP is extended to incorporate cyclic motion. A complex encoding efficiency metric is introduced to compare the displacement fields of unipolar and conventional GRE-MRE sequences in both magnitude and phase. The derived theoretical encoding equations are used to characterize the proposed sequence using an extensive parameter study. Unipolar MRE is validated against conventional GRE-MRE in a phantom study showing excellent agreement between measured displacement fields. In addition, unipolar MRE yields significantly increased octahedral shear strain-SNR relative to conventional GRE-MRE and allows for the recovery of high stiffness inclusions, where conventional GRE-MRE fails.

Ex vivo diffusion MRI of the human brain: Technical challenges and recent advances

This review discusses ex vivo diffusion magnetic resonance imaging (dMRI) as an important research tool for neuroanatomical investigations and the validation of in vivo dMRI techniques, with a focus on the human brain. We review the challenges posed by the properties of post-mortem tissue, and discuss state-of-the-art tissue preparation methods and recent advances in pulse sequences and acquisition techniques to tackle these. We then review recent ex vivo dMRI studies of the human brain, highlighting the validation of white matter orientation estimates and the atlasing and mapping of large subcortical structures. We also give particular emphasis to the delineation of layered gray matter structure with ex vivo dMRI, as this application illustrates the strength of its mesoscale resolution over large fields of view. We end with a discussion and outlook on future and potential directions of the field.

Post mortem high resolution diffusion MRI for large specimen imaging at 11.7 T with 3D segmented echo-planar imaging

BACKGROUND

Diffusion weighted imaging (DWI) is the only in vivo technique allowing for the mapping of tissue fiber architecture. Post mortem DWI is an increasingly popular method, since longer acquisition times (compared to in vivo) allow higher spatial and angular resolutions to be achieved. However, DWI protocols must be adapted to post mortem tissue (e.g., tuning acquisition parameters to account for changes in T1/T2). New method: In this work, we developed a framework to obtain high quality diffusion weighted images on post mortem large samples by using a combination of fast imaging with 3D diffusion-weighted segmented EPI (3D-DW seg-EPI), Gadolinium soaking and data denoising. Analyses including tractography were used to check the quality of the acquired data, including a comparison with 3D-DW SE acquisitions. Comparison with existing method: Effects on diffusion data of each of the components of the framework were tested: 3D-DW seg-EPI versus 3D-DW SE EPI; with and without data denoising; with and without Gd-soaking.

CONCLUSIONS

Our study demonstrated the feasibility of analysing anatomical connectivity using diffusion imaging of a post mortem macaque brain with a 3D-DW seg-EPI sequence acquired at ultra-high field. The combination of high angular and spatial resolution DWI with Gd-soaking and denoising provided data allowing us to perform diffusion tractography with results very similar to those obtained with a 3D-DW SE acquisition (with shorter acquisition times: 222 h versus 37 h for 3D-DW seg-EPI).

Microstructural imaging of the human brain with a 'super-scanner': 10 key advantages of ultra-strong gradients for diffusion MRI

The key component of a microstructural diffusion MRI 'super-scanner' is a dedicated high-strength gradient system that enables stronger diffusion weightings per unit time compared to conventional gradient designs. This can, in turn, drastically shorten the time needed for diffusion encoding, increase the signal-to-noise ratio, and facilitate measurements at shorter diffusion times. This review, written from the perspective of the UK National Facility for In Vivo MR Imaging of Human Tissue Microstructure, an initiative to establish a shared 300 mT/m-gradient facility amongst the microstructural imaging community, describes ten advantages of ultra-strong gradients for microstructural imaging. Specifically, we will discuss how the increase of the accessible measurement space compared to a lower-gradient systems (in terms of Δ, b-value, and TE) can accelerate developments in the areas of 1) axon diameter distribution mapping; 2) microstructural parameter estimation; 3) mapping micro-vs macroscopic anisotropy features with gradient waveforms beyond a single pair of pulsed-gradients; 4) multi-contrast experiments, e.g. diffusion-relaxometry; 5) tractography and high-resolution imaging in vivo and 6) post mortem; 7) diffusion-weighted spectroscopy of metabolites other than water; 8) tumour characterisation; 9) functional diffusion MRI; and 10) quality enhancement of images acquired on lower-gradient systems. We finally discuss practical barriers in the use of ultra-strong gradients, and provide an outlook on the next generation of 'super-scanners'.

Diffusion-Tensor Imaging Versus Digitization in Reconstructing the Masseter Architecture

Accurate characterization of the craniomaxillofacial (CMF) skeleton using finite element (FE) modeling requires representation of complex geometries, heterogeneous material distributions, and physiological loading. Musculature in CMF FE models are often modeled with simple link elements that do not account for fiber bundles (FBs) and their differential activation. Magnetic resonance (MR) diffusion-tensor imaging (DTI) enables reconstruction of the three-dimensional (3D) FB arrangement within a muscle. However, 3D quantitative validation of DTI-generated FBs is limited. This study compares 3D FB arrangement in terms of pennation angle (PA) and fiber bundle length (FBL) generated through DTI in a human masseter to manual digitization. CT, MR-proton density, and MR-DTI images were acquired from a single cadaveric specimen. Bone and masseter surfaces were reconstructed from CT and MR-proton density images, respectively. PA and FBL were estimated from FBs reconstructed from MR-DTI images using a streamline tracking (STT) algorithm (n = 193) and FBs identified through manual digitization (n = 181) and compared using the Mann–Whitney test. DTI-derived PAs did not differ from the digitized data (p = 0.411), suggesting that MR-DTI can be used to simulate FB orientation and the directionality of transmitted forces. Conversely, a significant difference was observed in FBL (p < 0.01) which may have resulted due to the tractography stopping criterion leading to early tract termination and greater length variability. Overall, this study demonstrated that DTI can yield muscle FB orientation data suitable to representative directionality of physiologic muscle loading in patient-specific CMF FE modeling.

Dissecting the pathobiology of altered MRI signal in amyotrophic lateral sclerosis: A post mortem whole brain sampling strategy for the integration of ultra-high-field MRI and quantitative neuropathology

BACKGROUND

Amyotrophic lateral sclerosis (ALS) is a clinically and histopathologically heterogeneous neurodegenerative disorder, in which therapy is hindered by the rapid progression of disease and lack of biomarkers. Magnetic resonance imaging (MRI) has demonstrated its potential for detecting the pathological signature and tracking disease progression in ALS. However, the microstructural and molecular pathological substrate is poorly understood and generally defined histologically. One route to understanding and validating the pathophysiological correlates of MRI signal changes in ALS is to directly compare MRI to histology in post mortem human brains.

RESULTS

The article delineates a universal whole brain sampling strategy of pathologically relevant grey matter (cortical and subcortical) and white matter tracts of interest suitable for histological evaluation and direct correlation with MRI. A standardised systematic sampling strategy that was compatible with co-registration of images across modalities was established for regions representing phosphorylated 43-kDa TAR DNA-binding protein (pTDP-43) patterns that were topographically recognisable with defined neuroanatomical landmarks. Moreover, tractography-guided sampling facilitated accurate delineation of white matter tracts of interest. A digital photography pipeline at various stages of sampling and histological processing was established to account for structural deformations that might impact alignment and registration of histological images to MRI volumes. Combined with quantitative digital histology image analysis, the proposed sampling strategy is suitable for routine implementation in a high-throughput manner for acquisition of large-scale histology datasets. Proof of concept was determined in the spinal cord of an ALS patient where multiple MRI modalities (T1, T2, FA and MD) demonstrated sensitivity to axonal degeneration and associated heightened inflammatory changes in the lateral corticospinal tract. Furthermore, qualitative comparison of R2* and susceptibility maps in the motor cortex of 2 ALS patients demonstrated varying degrees of hyperintense signal changes compared to a control. Upon histological evaluation of the same region, intensity of signal changes in both modalities appeared to correspond primarily to the degree of microglial activation.

CONCLUSION

The proposed post mortem whole brain sampling methodology enables the accurate intraindividual study of pathological propagation and comparison with quantitative MRI data, to more fully understand the relationship of imaging signal changes with underlying pathophysiology in ALS.

A Method for Whole Brain Ex Vivo Magnetic Resonance Imaging with Minimal Susceptibility Artifacts

Magnetic resonance imaging (MRI) is a non-destructive technique that is capable of localizing pathologies and assessing other anatomical features (e.g., tissue volume, microstructure, and white matter connectivity) in postmortem, ex vivo human brains. However, when brains are removed from the skull and cerebrospinal fluid (i.e., their normal in vivo magnetic environment), air bubbles and air–tissue interfaces typically cause magnetic susceptibility artifacts that severely degrade the quality of ex vivo MRI data. In this report, we describe a relatively simple and cost-effective experimental setup for acquiring artifact-free ex vivo brain images using a clinical MRI system with standard hardware. In particular, we outline the necessary steps, from collecting an ex vivo human brain to the MRI scanner setup, and have also described changing the formalin (as might be necessary in longitudinal postmortem studies). Finally, we share some representative ex vivo MRI images that have been acquired using the proposed setup in order to demonstrate the efficacy of this approach. We hope that this protocol will provide both clinicians and researchers with a straight-forward and cost-effective solution for acquiring ex vivo MRI data from whole postmortem human brains.

Intrinsic diffusion sensitivity of the balanced steady-state free precession (bSSFP) imaging sequence

The purpose of this work was to analyze the intrinsic diffusion sensitivity of the balanced steady-state free precession (bSSFP) imaging sequence, meaning the observation of diffusion-induced attenuation of the bSSFP steady-state signal due to the imaging gradients. Although these diffusion effects are usually neglected for most clinical gradient systems, such strong gradient systems are employed for high resolution imaging of small animals or MR Microscopy. The impact on the bSSFP signal of the imaging gradients characterized by their b-values was analyzed with simulations and experiments at a 7T animal scanner using a gradient system with maximum gradient amplitude of approx. 700 mT/m. It was found that the readout gradients have a stronger impact on the attenuation than the phase encoding gradients. Also, as the PE gradients are varying with each repetition interval, the diffusion effects induce strong modulations of the bSSFP signal over the sequence repetition cycles depending on the phase encoding gradient table. It is shown that a signal gain can be obtained through a change of flip angle as a new optimal flip angle maximizing the signal can be defined. The dependency of the diffusion effects on relaxation times and b-values were explored with simulations. The attenuation increases with T2. In conclusion, diffusion attenuation of the bSSFP signal becomes significant for high resolution imaging voxel size (roughly < 100 μm) of long T2 substances.

Spatial variations in magnetic resonance-based diffusion of articular cartilage in knee osteoarthritis

PURPOSE

To evaluate a pulse sequence combining stimulated echo diffusion preparation with a 3D segmented spoiled gradient echo (SPGR) acquisition for diffusion tensor imaging (DTI) of knee cartilage in healthy and osteoarthritis (OA) populations for early diagnosis and characterization of OA.

METHODS

Diffusion-weighted images of 40 subjects (20 healthy, 20 OA) at baseline and 20 subjects (10 healthy, 10 OA) at one year were obtained. The subjects were classified according to Kellgren Lawrence (KL) and whole organ magnetic resonance imaging scoring (WORMS) method acquired at 3 T. Cartilage full thickness and laminar mean diffusivity (MD) and fractional anisotropy (FA) values were quantified. The reproducibility of MD and FA values was assessed in five healthy human subjects based on test-retest scans.

RESULTS

In general, the full thickness MD values were higher in subjects with knee OA compared to healthy controls in both the baseline and follow up cohort. Laminar analysis MD and FA results were significantly different (p<0.05) between the bone-articular and articular layer with the articular layer having higher MD and lower FA value compared to the bone layer. The global reproducibility error was 6.5% for MD and 11.6% for FA.

CONCLUSION

The diffusion-weighted stimulated echo-based sequence may be used as a valuable tool for early diagnosis and characterization of knee OA at 3 T in the future.

Improving diffusion-weighted imaging of post-mortem human brains: SSFP at 7 T

Post-mortem diffusion imaging of whole, human brains has potential to provide data for validation or high-resolution anatomical investigations. Previous work has demonstrated improvements in data acquired with diffusion-weighted steady-state free precession (DW-SSFP) compared with conventional diffusion-weighted spin echo at 3T. This is due to the ability of DW-SSFP to overcome signal-to-noise and diffusion contrast losses brought about by tissue fixation related decreases in T2 and ADC. In this work, data of four post-mortem human brains were acquired at 3T and 7 T, using DW-SSFP with similar effective b-values (b(eff)~5150 s/mm(2)) for inter-field strength comparisons; in addition, DW-SSFP data were acquired at 7 T with higher b(eff) (~8550 s/mm(2)) for intra-field strength comparisons. Results demonstrate that both datasets acquired at 7 T had higher SNR and diffusion contrast than data acquired at 3T, and data acquired at higher b(eff) had improved diffusion contrast than at lower b(eff) at 7 T. These results translate to improved estimates of secondary fiber orientations leading to higher fidelity tractography results compared with data acquired at 3T. Specifically, tractography streamlines of cortical projections originating from the corpus callosum, corticospinal tract, and superior longitudinal fasciculus were more successful at crossing the centrum semiovale and projected closer to the cortex. Results suggest that DW-SSFP at 7 T is a preferential method for acquiring diffusion-weighted data of post-mortem human brain, specifically where the primary region of interest involves crossing white matter tracts.

High-resolution, three-dimensional diffusion-weighted breast imaging using DESS

PURPOSE

To evaluate the use of the double-echo steady-state (DESS) sequence for acquiring high-resolution breast images with diffusion and T2 weighting.

MATERIALS AND METHODS

Phantom scans were used to verify the T2 and diffusion weighting of the DESS sequence. Image distortion was evaluated in volunteers by comparing DESS images and conventional diffusion-weighted images (DWI) to spoiled gradient-echo images. The DESS sequence was added to a standard clinical protocol, and the resulting patient images were used to evaluate overall image quality and image contrast in lesions.

RESULTS

The diffusion weighting of the DESS sequence can be easily modulated by changing the spoiler gradient area and flip angle. Radiologists rated DESS images as having higher resolution and less distortion than conventional DWI. Lesion-to-tissue contrast ratios are strongly correlated between DWI and DESS images (R=0.83) and between T2-weighted fast spin-echo and DESS images (R=0.80).

CONCLUSION

The DESS sequence is able to acquire high-resolution 3D diffusion- and T2-weighted images in short scan times, with image quality that facilitates morphological assessment of lesions.

Multiple-echo diffusion tensor acquisition technique (MEDITATE) on a 3T clinical scanner

This article describes the concepts and implementation of an MRI method, the multiple-echo diffusion tensor acquisition technique (MEDITATE), which is capable of acquiring apparent diffusion tensor maps in two scans on a 3T clinical scanner. In each MEDITATE scan, a set of RF pulses generates multiple echoes, the amplitudes of which are diffusion weighted in both magnitude and direction by a pattern of diffusion gradients. As a result, two scans acquired with different diffusion weighting strengths suffice for accurate estimation of diffusion tensor imaging (DTI) parameters. The MEDITATE variation presented here expands previous MEDITATE approaches to adapt to the clinical scanner platform, such as exploiting longitudinal magnetization storage to reduce T2 weighting. Fully segmented multi-shot Cartesian encoding is used for image encoding. MEDITATE was tested on isotropic (agar gel), anisotropic diffusion phantoms (asparagus) and in vivo skeletal muscle in healthy volunteers with cardiac gating. Comparisons of accuracy were performed with standard twice-refocused spin echo (TRSE) DTI in each case and good quantitative agreement was found between diffusion eigenvalues, mean diffusivity and fractional anisotropy derived from TRSE DTI and from the MEDITATE sequence. Orientation patterns were correctly reproduced in both isotropic and anisotropic phantoms, and approximately for in vivo imaging. This illustrates that the MEDITATE method of compressed diffusion encoding is feasible on the clinical scanner platform. With future development and employment of appropriate view-sharing image encoding, this technique may be used in clinical applications requiring time-sensitive acquisition of DTI parameters such as dynamical DTI in muscle.

Challenges of High-resolution Diffusion Imaging of the Human Medial Temporal Lobe in Alzheimer Disease

The human medial temporal lobe performs an essential role in memory formation and retrieval. Diseases involving the hippocampus such as Alzheimer disease present a unique opportunity for advanced imaging techniques to detect abnormalities at an early stage. In particular, it is possible that diffusion imaging will measure abnormal microarchitecture beyond the realm of macroscopic imaging. However, this task is formidable because of the detailed anatomy of the medial temporal lobe, the difficulties in obtaining high-quality diffusion images of adequate resolution, and the challenges in diffusion data processing. Moreover, it is unclear if any differences will be significant for an individual patient or simply groups of patients. Successful endeavors will need to address each of these challenges in an integrated fashion. The rewards of such analysis may be detection of microscopic disease in vivo, which could represent a landmark accomplishment for the field of neuroradiology.

Simultaneous estimation of T(2) and apparent diffusion coefficient in human articular cartilage in vivo with a modified three-dimensional double echo steady state (DESS) sequence at 3 T

T(2) mapping and diffusion-weighted imaging complement morphological imaging for assessing cartilage disease and injury. The double echo steady state sequence has been used for morphological imaging and generates two echoes with markedly different T(2) and diffusion weighting. Modifying the spoiler gradient area and flip angle of the double echo steady state sequence allows greater control of the diffusion weighting of both echoes. Data from two acquisitions with different spoiler gradient areas and flip angles are used to simultaneously estimate the T(2) and apparent diffusion coefficient of each voxel. This method is verified in phantoms and validated in vivo in the knee; estimates from different regions of interest in the phantoms and cartilage are compared to those obtained using standard spin-echo methods. The Pearson correlations were 0.984 for T(2) (∼2% relative difference between spin-echo and double echo steady state estimates) and 0.997 for apparent diffusion coefficient (˜1% relative difference between spin-echo and double echo steady state estimates) for the phantom study and 0.989 for T(2) and 0.987 for apparent diffusion coefficient in regions of interest in the human knee in vivo. High accuracy for simultaneous three-dimensional T(2) and apparent diffusion coefficient measurements are demonstrated, while also providing morphologic three-dimensional images without blurring or distortion in reasonable scan times.

Fast diffusion-weighted steady state free precession imaging of in vivo knee cartilage

Quantification of molecular diffusion with steady state free precession (SSFP) is complicated by the fact that diffusion effects accumulate over several repetition times (TR) leading to complex signal dependencies on transverse and longitudinal magnetization paths. This issue is commonly addressed by setting TR > T(2), yielding strong attenuation of all higher modes, except of the shortest ones. As a result, signal attenuation from diffusion becomes T(2) independent but signal-to-noise ratio (SNR) and sequence efficiency are remarkably poor. In this work, we present a new approach for fast in vivo steady state free precession diffusion-weighted imaging of cartilage with TR << T(2) offering a considerable increase in signal-to-noise ratio and sequence efficiency. At a first glance, prominent coupling between magnetization paths seems to complicate quantification issues in this limit, however, it is observed that diffusion effects become rather T(2) (ΔD ≈ 1/10 ΔT(2)) but not T(1) independent (ΔD ≈ 1/2 ΔT(1)) for low flip angles α ≈ 10 - 15°. As a result, fast high-resolution (0.35 × 0.35 - 0.50 × 0.50 mm(2) in-plane resolution) quantitative diffusion-weighted imaging of human articular cartilage is demonstrated at 3.0 T in a clinical setup using estimated T(1) and T(2) or a combination of measured T(1) and estimated T(2) values.

GPU accelerated Monte Carlo simulation of pulsed-field gradient NMR experiments

The simulation of diffusion by Monte Carlo methods is often essential to describing NMR measurements of diffusion in porous media. However, simulation timescales must often span hundreds of milliseconds, with large numbers of trajectories required to ensure statistical convergence. Here we demonstrate that by parallelising code to run on graphics processing units (GPUs), these calculations may be accelerated by over three orders of magnitude, opening new frontiers in experimental design and analysis. As such cards are commonly installed on most desktop computers, we expect that this will prove useful in many cases where simple analytical descriptions are not available or appropriate, e.g. in complex geometries or where short gradient pulse approximations do not hold, or for the analysis of diffusion-weighted MRI in complex tissues such as the lungs and brain.