Mechanisms of T2 * anisotropy and gradient echo myelin water imaging

So You Want to Image Myelin Using MRI: Magnetic Susceptibility Source Separation for Myelin Imaging

In MRI, researchers have long endeavored to effectively visualize myelin distribution in the brain, a pursuit with significant implications for both scientific research and clinical applications. Over time, various methods such as myelin water imaging, magnetization transfer imaging, and relaxometric imaging have been developed, each carrying distinct advantages and limitations. Recently, an innovative technique named as magnetic susceptibility source separation has emerged, introducing a novel surrogate biomarker for myelin in the form of a diamagnetic susceptibility map. This paper comprehensively reviews this cutting-edge method, providing the fundamental concepts of magnetic susceptibility, susceptibility imaging, and the validation of the diamagnetic susceptibility map as a myelin biomarker that indirectly measures myelin content. Additionally, the paper explores essential aspects of data acquisition and processing, offering practical insights for readers. A comparison with established myelin imaging methods is also presented, and both current and prospective clinical and scientific applications are discussed to provide a holistic understanding of the technique. This work aims to serve as a foundational resource for newcomers entering this dynamic and rapidly expanding field.

Quantitative magnetic resonance imaging reflects different levels of histologically determined myelin densities in multiple sclerosis, including remyelination in inactive multiple sclerosis lesions

Magnetic resonance imaging (MRI) of focal or diffuse myelin damage or remyelination may provide important insights into disease progression and potential treatment efficacy in multiple sclerosis (MS). We performed post-mortem MRI and histopathological myelin measurements in seven progressive MS cases to evaluate the ability of three myelin-sensitive MRI scans to distinguish different stages of MS pathology, particularly chronic demyelinated and remyelinated lesions. At 3 Tesla, we acquired two different myelin water imaging (MWI) scans and magnetisation transfer ratio (MTR) data. Histopathology included histochemical stainings for myelin phospholipids (LFB) and iron as well as immunohistochemistry for myelin proteolipid protein (PLP), CD68 (phagocytosing microglia/macrophages) and BCAS1 (remyelinating oligodendrocytes). Mixed-effects modelling determined which histopathological metric best predicted MWF and MTR in normal-appearing and diffusely abnormal white matter, active/inactive, inactive, remyelinated and ischemic lesions. Both MWI measures correlated well with each other and histology across regions, reflecting the different stages of MS pathology. MTR data showed a considerable influence of components other than myelin and a strong dependency on tissue storage duration. Both MRI and histology revealed increased myelin densities in inactive compared with active/inactive lesions. Chronic inactive lesions harboured single scattered myelin fibres indicative of low-level remyelination. Mixed-effects modelling showed that smaller differences between white matter areas were linked to PLP densities and only to a small extent confounded by iron. MWI reflects differences in myelin lipids and proteins across various levels of myelin densities encountered in MS, including low-level remyelination in chronic inactive lesions.

Orientation dependent proton transverse relaxation in the human brain white matter: The magic angle effect on a cylindrical helix

PURPOSE

To overcome some limitations of previous proton orientation-dependent transverse relaxation formalisms in human brain white matter (WM) by a generalized magic angle effect function.

METHODS

A cylindrical helix model was developed embracing anisotropic rotational and translational diffusion of restricted molecules in WM, with the former characterized by an axially symmetric system. Transverse relaxation rates R₂ and R₂^∗ were divided into isotropic R₂ⁱ and anisotropic parts, R₂^a ∗ f(α,Φ - ε₀), with α denoting an open angle and ε₀ an orientation (Φ) offset from DTI-derived primary diffusivity direction. The proposed framework (Fit A) was compared to prior models without ε₀ on previously published water and methylene proton transverse relaxation rates from developing, healthy, and pathological WM at 3 T. Goodness of fit was represented by root-mean-square error (RMSE). F-test and linear correlation were used with statistical significance set to P ≤ 0.05.

RESULTS

Fit A significantly (P < 0.01) outperformed prior models as demonstrated by reduced RMSEs, e.g., 0.349 vs. 0.724 in myelin water. Fitted ε₀ was in good agreement with calculated ε₀ from directional diffusivities. Compared with those from healthy adult, the fitted R₂ⁱ, R₂^a, and α from neonates were substantially reduced but ε₀ increased, consistent with developing myelination. Significant positive (R₂ⁱ) and negative (α and R₂^a) correlations were found with aging (demyelination) in elderly.

CONCLUSION

The developed framework can better characterize orientation dependences from a wide range of proton transverse relaxation measurements in the human brain WM, thus shedding new light on myelin microstructural alterations at the molecular level.

On the performance of multi-compartment relaxometry for myelin water imaging (MCR-MWI) - test-retest repeatability and inter-protocol reproducibility

In this study, we optimized the variable flip angle (VFA) acquisition scheme using numerical simulations to shorten the acquisition time of multicompartment relaxometry for myelin water imaging (MCR-MWI) to a clinically practical range in the absence of advanced image reconstruction methods. As the primary objective of this study, the test-retest repeatability of myelin water fraction (MWF) measurements of MCR-MWI is evaluated on three gradient echo (GRE) sequence settings using the optimized VFA schemes with different echo times and repetition times, emulating various scanner setups. The cross-protocol reproducibility of MCR-MWI and MCR with diffusion-informed myelin water imaging (MCR-DIMWI) is also examined. As a secondary objective, we explore the bundle-specific profiles of various microstructural parameters from MCR-(DI)MWI and their cross-correlations to determine if these parameters possess supplementary microstructure information beyond myelin concentration. Numerical simulations indicate that MCR-MWI can be performed with a minimum of three flip angles covering a wide range of T₁ weightings without adding significant bias. This is supported by the results of an in vivo experiment, allowing whole-brain 1.5 mm isotropic MWF maps to be acquired in 9 min, reducing the total scan time to 40% of the original implementation without significant quality degradation. Good test-retest repeatability is observed for MCR-MWI for all three GRE protocols. While good correlations can also be found in MWF across protocols, systematic differences are observed. Bundle-specific MWF analysis reveals that certain white matter bundles are similar in all participants. We also found that microstructure relaxation parameters have low linear correlations with MWF. MCR-MWI is a reproducible measure of myelin. However, attention should be paid to the protocol related MWF differences when comparing different studies, as the MWF bias up to 0.5% can be observed across the protocols examined in this work.

Orientation dependence of R2 relaxation in the newborn brain

In MRI the transverse relaxation rate, R₂ = 1/T₂^, shows dependence on the orientation of ordered tissue relative to the main magnetic field. In previous studies, orientation effects of R₂ relaxation in the mature brain's white matter have been found to be described by a susceptibility-based model of diffusion through local magnetic field inhomogeneities created by the diamagnetic myelin sheaths. Orientation effects in human newborn white matter have not yet been investigated. The newborn brain is known to contain very little myelin and is therefore expected to exhibit a decrease in orientation dependence driven by susceptibility-based effects. We measured R₂ orientation dependence in the white matter of human newborns. R₂ data were acquired with a 3D Gradient and Spin Echo (GRASE) sequence and fiber orientation was mapped with diffusion tensor imaging (DTI). We found orientation dependence in newborn white matter that is not consistent with the susceptibility-based model and is best described by a model of residual dipolar coupling. In the near absence of myelin in the newborn brain, these findings suggest the presence of residual dipolar coupling between rotationally restricted water molecules. This has important implications for quantitative imaging methods such as myelin water imaging, and suggests orientation dependence of R₂ as a potential marker in early brain development.

Inconsistencies in atlas-based volumetric measures of the human nucleus basalis of Meynert: A need for high-resolution alternatives

The nucleus basalis of Meynert (nbM) is the major source of cortical acetylcholine (ACh) and has been related to cognitive processes and to neurological disorders. However, spatially delineating the human nbM in MRI studies remains challenging. Due to the absence of a functional localiser for the human nbM, studies to date have localised it using nearby neuroanatomical landmarks or using probabilistic atlases. To understand the feasibility of MRI of the nbM we set our four goals; our first goal was to review current human nbM region-of-interest (ROI) selection protocols used in MRI studies, which we found have reported highly variable nbM volume estimates. Our next goal was to quantify and discuss the limitations of existing atlas-based volumetry of nbM. We found that the identified ROI volume depends heavily on the atlas used and on the probabilistic threshold set. In addition, we found large disparities even for data/studies using the same atlas and threshold. To test whether spatial resolution contributes to volume variability, as our third goal, we developed a novel nbM mask based on the normalized BigBrain dataset. We found that as long as the spatial resolution of the target data was 1.3 mm isotropic or above, our novel nbM mask offered realistic and stable volume estimates. Finally, as our last goal we tried to discern nbM using publicly available and novel high resolution structural MRI ex vivo MRI datasets. We find that, using an optimised 9.4T quantitative T₂^⁎ ex vivo dataset, the nbM can be visualised using MRI. We conclude caution is needed when applying the current methods of mapping nbM, especially for high resolution MRI data. Direct imaging of the nbM appears feasible and would eliminate the problems we identify, although further development is required to allow such imaging using standard (f)MRI scanning.

A new advanced MRI biomarker for remyelinated lesions in Multiple Sclerosis

Objectives

Neuropathological studies have shown that multiple sclerosis (MS) lesions are heterogeneous in terms of myelin/axon damage and repair as well as iron content. However, it remains a challenge to identify specific chronic lesion types, especially remyelinated lesions, in vivo in patients with MS.

Methods

We performed 3 studies: (1) a cross‐sectional study in a prospective cohort of 115 patients with MS and 76 healthy controls, who underwent 3 T magnetic resonance imaging (MRI) for quantitative susceptibility mapping (QSM), myelin water fraction (MWF), and neurite density index (NDI) maps. White matter (WM) lesions in QSM were classified into 5 QSM lesion types (iso‐intense, hypo‐intense, hyperintense, lesions with hypo‐intense rims, and lesions with paramagnetic rim legions [PRLs]); (2) a longitudinal study of 40 patients with MS to study the evolution of lesions over 2 years; (3) a postmortem histopathology‐QSM validation study in 3 brains of patients with MS to assess the accuracy of QSM classification to identify neuropathological lesion types in 63 WM lesions.

Results

At baseline, hypo‐ and isointense lesions showed higher mean MWF and NDI values compared to other QSM lesion types (p < 0.0001). Further, at 2‐year follow‐up, hypo‐/iso‐intense lesions showed an increase in MWF. Postmortem analyses revealed that QSM highly accurately identifies (1) fully remyelinated areas as hypo‐/iso‐intense (sensitivity = 88.89% and specificity = 100%), (2) chronic inactive lesions as hyperintense (sensitivity = 71.43% and specificity = 92.00%), and (3) chronic active/smoldering lesions as PRLs (sensitivity = 92.86% and specificity = 86.36%).

Interpretation

These results provide the first evidence that it is possible to distinguish chronic MS lesions in a clinical setting, hereby supporting with new biomarkers to develop and assess remyelinating treatments. ANN NEUROL 2022;92:486–502

Imaging white matter microstructure with gradient-echo phase imaging: Is ex vivo imaging with formalin-fixed tissue a good approximation of the in vivo brain?

Purpose

Ex vivo imaging is a commonly used approach to investigate the biophysical mechanism of orientation‐dependent signal phase evolution in white matter. Yet, how phase measurements are influenced by the structural alteration in the tissue after formalin fixation is not fully understood. Here, we study the effects on magnetic susceptibility, microstructural compartmentalization, and chemical exchange measurement with a postmortem formalin‐fixed whole‐brain human tissue.

Methods

A formalin‐fixed, postmortem human brain specimen was scanned with multiple orientations to the main magnetic field direction for robust bulk magnetic susceptibility measurement with conventional quantitative susceptibility imaging models. White matter samples were subsequently excised from the whole‐brain specimen and scanned in multiple rotations on an MRI scanner to measure the anisotropic magnetic susceptibility and microstructure‐related contributions in the signal phase and to validate the findings of the whole‐brain data.

Results

The bulk isotropic magnetic susceptibility of ex vivo whole‐brain imaging is comparable to in vivo imaging, with noticeable enhanced nonsusceptibility contributions. The excised specimen experiment reveals that anisotropic magnetic susceptibility and compartmentalization phase effect were considerably reduced in the formalin‐fixed white matter specimens.

Conclusions

Formalin‐fixed postmortem white matter exhibits comparable isotropic magnetic susceptibility to previous in vivo imaging findings. However, the measured phase and magnitude data of the fixed white matter tissue shows a significantly weaker orientation dependency and compartmentalization effect. Alternatives to formalin fixation are needed to better reproduce the in vivo microstructural effects in postmortem samples.

Improved magnetic resonance myelin water imaging using multi-channel denoising convolutional neural networks (MCDnCNN)

BACKGROUND

Myelin water imaging (MWI) is powerful and important for studying and diagnosing neurological and psychiatric diseases. In particular, myelin water fraction (MWF) is derived from MWI data for quantifying myelination. However, MWF estimation is typically sensitive to noise. Improving the accuracy of MWF estimation based on WMI data acquired using a magnetic resonance (MR) multiple gradient recalled echo (mGRE) imaging sequence is desired.

METHODS

The proposed method employs a recently introduced the multi-channel denoising convolutional neural networks (MCDnCNN). Five different MCDnCNN models, denoted as Delevel1, Delevel2, Delevel3, Delevel4 and DelevelMix corresponding to five noise levels (Level1, Level2, Level3, Level4 and LevelMix), were trained using the data of the first echo of the mGRE brain images acquired from 15 healthy human subjects. Using simulated noisy data that employed a hollow cylinder model, we first evaluated the improvement in estimating MWF based on data denoised by the five different MCDnCNNs, by comparing the MWF maps calculated from the denoised data with ground truth. Next, we again evaluated the improvement using real-world in vivo datasets of 11 human participants acquired using the mGRE sequence. The datasets were first denoised by five different MCDnCNNs (Delevel1, 2, 3, 4 and DelevelMix), and subsequently their MWF maps were calculated and compared with the MWF maps directly calculated from the raw mGRE images without being denoised.

RESULTS

Experiments using the simulation data denoised by the appropriate MCDnCNN models showed that the standard deviation (SD) of the absolute error (AE) of the derived MWF results was significantly reduced (maximal reduction =15.5%, Level3 simulated noisy data, orientation angle =0, all the five MCDnCNN models). In the test using in vivo data, estimating MWF based on data particularly denoised by the appropriate MCDnCNN models was found to be the best, compared to otherwise not using the appropriate models. The results demonstrated that the appropriate MCDnCNN models may permit high-quality MWF mapping, i.e., substantial reduction of random variation in estimating MWF-maps while preserving accuracy and structural details.

CONCLUSIONS

Appropriate MCDnCNN models as proposed may improve both the accuracy and precision in estimating MWF maps, thereby making it a more clinically feasible alternative.

Whole-brain 3D mapping of oxygen metabolism using constrained quantitative BOLD

Quantitative BOLD (qBOLD) MRI permits noninvasive evaluation of hemodynamic and metabolic states of the brain by quantifying parametric maps of deoxygenated blood volume (DBV) and hemoglobin oxygen saturation level of venous blood (Y_v), and along with a measurement of cerebral blood flow (CBF), the cerebral metabolic rate of oxygen (CMRO₂). The method, thus should have potential to provide important information on many neurological disorders as well as normal cerebral physiology. One major challenge in qBOLD is to separate de-oxyhemoglobin’s contribution to R₂′ from other sources modulating the voxel signal, for instance, R₂, R₂′ from non-heme iron (R′_2,nh), and macroscopic magnetic field variations. Further, even with successful separation of the several confounders, it is still challenging to extract DBV and Y_v from the heme-originated R₂′ because of limited sensitivity of the qBOLD model. These issues, which have not been fully addressed in currently practiced qBOLD methods, have so far precluded 3D whole-brain implementation of qBOLD. Thus, the purpose of this work was to develop a new 3D MRI oximetry technique that enables robust qBOLD parameter mapping across the entire brain. To achieve this goal, we employed a rapid, R₂′-sensitive, steady-state 3D pulse sequence (termed ‘AUSFIDE’) for data acquisition, and implemented a prior-constrained qBOLD processing pipeline that exploits a plurality of preliminary parameters obtained via AUSFIDE, along with additionally measured cerebral venous blood volume. Numerical simulations and in vivo studies at 3 T were performed to evaluate the performance of the proposed, constrained qBOLD mapping in comparison to the parent qBOLD method. Measured parameters (Y_v, DBV, R′_2,nh, nonblood magnetic susceptibility) in ten healthy subjects demonstrate the expected contrast across brain territories, while yielding group-averages of 64.0 ± 2.3 % and 62.2 ± 3.1 % for Y_v and 2.8 ± 0.5 % and 1.8 ± 0.4 % for DBV in cortical gray and white matter, respectively. Given the Y_v measurements, additionally quantified CBF in seven of the ten study subjects enabled whole-brain 3D CMRO₂ mapping, yielding group averages of 134.2 ± 21.1 and 79.4 ± 12.6 µmol/100 g/min for cortical gray and white matter, in good agreement with literature values. The results suggest feasibility of the proposed method as a practical and reliable means for measuring neurometabolic parameters over an extended brain coverage.

Improved Multi-Echo Gradient-Echo-Based Myelin Water Fraction Mapping Using Dimensionality Reduction

Multi-echo gradient-echo (mGRE)-based myelin water fraction (MWF) mapping is a promising myelin water imaging (MWI) modality but is vulnerable to noise and artifact corruption. The linear dimensionality reduction (LDR) method has recently shown improvements with regard to these challenges. However, the magnitude value based low rank operators have been shown to misestimate the MWF for regions with [Formula: see text] anisotropy. This paper presents a nonlinear dimensionality reduction (NLDR) method to estimate the MWF map better by encouraging nonlinear low dimensionality of mGRE signal sources. Specifically, we implemented a fully connected deep autoencoder to extract the low-dimensional features of complex-valued signals and incorporated a sparse regularization to separate the anomaly sources that do not reside in the low-dimensional manifold. Simulations and in vivo experiments were performed to evaluate the accuracy of the MWF map under various situations. The proposed NLDR-based MWF improves the accuracy of the MWF map over the conventional nonlinear least-squares method and the LDR-based MWF and maintains robustness against noise and artifact corruption.

Brain myelin water fraction is associated with APOE4 allele status in patients with cognitive impairment

BACKGROUND AND PURPOSE

Apolipoprotein E4 (APOE4) is a major genetic risk factor for Alzheimer's disease. However, the effect of APOE4 status on myelin remains unclear. This study investigated the effect of APOE4 on myelin content in cognitively impaired individuals using T2* gradient echo (GRE)-based myelin water fraction (MWF) imaging.

METHODS

Between August 2017 and January 2019, we evaluated 39 cognitively impaired patients (median age, 75 years; male:female = 8:31; Alzheimer's disease: mild cognitive impairment = 11:28). We obtained brain MWF values from white matter hyperintensities (WMHs) and normal-appearing white matter (NAWM). Linear regression analysis was performed to investigate the relationship between the APOE4 status and MWF and cognitive function and MWF.

RESULTS

Among the 39 cognitively impaired patients, nine (23.1%) were APOE4 carriers and 30 (76.9%) were noncarriers. APOE4 carriers had a lower hippocampal volume than noncarriers (p = .045), but other brain volume parameters were not differed. After age adjustment, the APOE4 status was significantly associated with reduced MWF in NAWM (β = -0.310 per allele; p = .049) but not in WMH (β = -0.258 per allele; p = .113). After age adjustment, MWF in NAWM was significantly associated with Mini-Mental State Examination score (β = 0.313, p = .031).

CONCLUSIONS

T2* GRE-based MWF imaging can reveal myelin loss, particularly in NAWM, in cognitively impaired patients among APOE4 carriers. In vivo MWF in NAWM might be a novel imaging marker of Alzheimer's disease, for clarifying the interactions between the white matter and cognitive dysfunction with respect to the APOE4 status.

Sensitivity of fiber orientation dependent R 2 ∗ to temperature and post mortem interval

PURPOSE

R 2 ∗ imaging of brain white matter is well known for being sensitive to the orientation of nerve fibers with respect to the B₀ field of the MRI scanner. The goal of this study was to evaluate whether and to which extent fiber orientation dependent R 2 ∗ differs between in vivo and post mortem in situ examinations, and to investigate the influence of varying temperatures and post mortem intervals (PMI).

METHODS

Post mortem in situ and in vivo MRI scans were conducted at 3T. R 2 ∗ was acquired with a multi-echo gradient-echo sequence, and the orientation of white matter fibers was computed using diffusion tensor imaging (DTI). Fitting of the measured fiber orientation dependent R 2 ∗ was performed using three different formulations of a previously proposed model.

RESULTS

R 2 ∗ increased with increasing fiber angle for in vivo and post mortem in situ examinations, whereby the orientation dependency was lower post mortem. The different formulations of the fiber orientation model resulted in an identical fit, but showed large variations of the estimated parameters. The higher order orientation dependent R 2 ∗ components significantly decreased with decreasing temperature, while the orientation independent R 2 ∗ components showed no significant correlation with either temperature or PMI.

CONCLUSION

Although the mean diffusivity is strongly reduced post mortem, we could successfully estimate the fiber angle using DTI. Due to the strong correlation of the higher order orientation dependent R 2 ∗ components with temperature, the decreased R 2 ∗ fiber orientation dependency post mortem in situ might primarily be attributed to the lower brain temperature.

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.

Artificial neural network for multi-echo gradient echo-based myelin water fraction estimation

PURPOSE

To demonstrate robust myelin water fraction (MWF) mapping using an artificial neural network (ANN) with multi-echo gradient-echo (GRE) signal.

METHODS

Multi-echo gradient-echo signals simulated with a three-pool exponential model were used to generate the training data set for the ANN, which was designed to yield the MWF. We investigated the performance of our proposed ANN for various conditions using both numerical simulations and in vivo data. Simulations were conducted with various SNRs to investigate the performance of the ANN. In vivo data with high spatial resolutions were applied in the analyses, and results were compared with MWFs derived by the nonlinear least-squares algorithm using a complex three-pool exponential model.

RESULTS

The network results for the simulations show high accuracies against noise compared with nonlinear least-squares MWFs: RMS-error value of 5.46 for the nonlinear least-squares MWF and 3.56 for the ANN MWF at an SNR of 150 (relative gain = 34.80%). These effects were also found in the in vivo data, with reduced SDs in the region-of-interest analyses. These effects of the ANN demonstrate the feasibility of acquiring high-resolution myelin water images.

CONCLUSION

The simulation results and in vivo data suggest that the ANN facilitates more robust MWF mapping in multi-echo gradient-echo sequences compared with the conventional nonlinear least-squares method.

Characterizing white matter fiber orientation effects on multi-parametric quantitative BOLD assessment of oxygen extraction fraction

Relative oxygen extraction fraction (rOEF) is a fundamental indicator of cerebral metabolic function. An easily applicable method for magnetic resonance imaging (MRI) based rOEF mapping is the multi-parametric quantitative blood oxygenation level dependent (mq-BOLD) approach with separate acquisitions of transverse relaxation times   T 2 * and T2 and dynamic susceptibility contrast (DSC) based relative cerebral blood volume (rCBV). Given that transverse relaxation and rCBV in white matter (WM) strongly depend on nerve fiber orientation, mq-BOLD derived rOEF is expected to be affected as well. To investigate fiber orientation related rOEF artefacts, we present a methodological study characterizing anisotropy effects of WM as measured by diffusion tensor imaging (DTI) on mq-BOLD in 30 healthy volunteers. Using a 3T clinical MRI-scanner, we performed a comprehensive correlation of all parameters (  T 2 * , T2, R 2 ' , rCBV, rOEF, where R 2 ' =1/  T 2 * -1/T2) with DTI-derived fiber orientation towards the main magnetic field (B0). Our results confirm strong dependencies of transverse relaxation and rCBV on the nerve fiber orientation towards B0, with anisotropy-driven variations up to 37%. Comparably weak orientation-dependent variations of mq-BOLD derived rOEF (3.8%) demonstrate partially counteracting influences of R 2 ' and rCBV effects, possibly suggesting applicability of rOEF as an oxygenation sensitive biomarker. However, unresolved issues warrant caution when applying mq-BOLD to WM.

So You Want to Image Myelin Using MRI: An Overview and Practical Guide for Myelin Water Imaging

Myelin water imaging (MWI) is an MRI imaging biomarker for myelin. This method can generate an in vivo whole-brain myelin water fraction map in approximately 10 minutes. It has been applied in various applications including neurodegenerative disease, neurodevelopmental, and neuroplasticity studies. In this review we start with a brief introduction of myelin biology and discuss the contributions of myelin in conventional MRI contrasts. Then the MRI properties of myelin water and four different MWI methods, which are categorized as T₂ -, T₂ *-, T₁ -, and steady-state-based MWI, are summarized. After that, we cover more practical issues such as availability, interpretation, and validation of these methods. To illustrate the utility of MWI as a clinical research tool, MWI studies for two diseases, multiple sclerosis and neuromyelitis optica, are introduced. Additional topics about imaging myelin in gray matter and non-MWI methods for myelin imaging are also included. Although technical and physiological limitations exist, MWI is a potent surrogate biomarker of myelin that carries valuable and useful information of myelin. Evidence Level: 5 Technical Efficacy: 1 J. MAGN. RESON. IMAGING 2021;53:360-373.

Visualization of Nigrosome 1 from the Viewpoint of Anatomic Structure

BACKGROUND AND PURPOSE

Parkinson disease is related to neurodegeneration and iron deposition in the substantia nigra pars compacta and nigrosome 1. However, visualization of nigrosome 1 via MR imaging is poor owing to the bilateral asymmetry, regardless of whether it is healthy. We focused on the magic angle and susceptibility effect and evaluated the anatomic slant structure of nigrosome 1 by tilting subjects' heads in the B₀ direction.

MATERIALS AND METHODS

To investigate the effectiveness of the magic angle, we tilted the volunteers' heads to the right and left in the B₀ direction or not at all for evaluating correlations between the degree of head tilting and visualization of the right nigrosome 1 and left nigrosome 1 using 3D spoiled gradient-echo sequences with multiecho acquisitions. We evaluated the susceptibility of nigrosome 1 and the local field using quantitative susceptibility mapping to assess static magnetic field inhomogeneity.

RESULTS

The heads tilted to the right and left showed significantly higher contrasts of nigrosome 1 and the substantia nigra pars compacta than the nontilted heads. No significant differences were observed in the visualization and susceptibility between the right nigrosome 1 and left nigrosome 1 for each head tilt. The effect of the magic angle was remarkable in the nontilted heads. This finding was supported by quantitative susceptibility mapping because the anatomic slant structure of nigrosome 1 was coherent between the axis of nigrosome 1 and the magic angle.

CONCLUSIONS

The asymmetric visualization of nigrosome 1 is affected by the magic angle and susceptibility. The anatomic slant structure of nigrosome 1 causes these challenges in visualization.

In vivo magnetic resonance imaging and spectroscopy. Technological advances and opportunities for applications continue to abound

Over the past decades, the field of in vivo magnetic resonance (MR) has built up an impressive repertoire of data acquisition and analysis technologies for anatomical, functional, physiological, and molecular imaging, the description of which requires many book volumes. As such it is impossible for a few authors to have an authoritative overview of the field and for a brief article to be inclusive. We will therefore focus mainly on data acquisition and attempt to give some insight into the principles underlying current advanced methods in the field and the potential for further innovation. In our view, the foreseeable future is expected to show continued rapid progress, for instance in imaging of microscopic tissue properties in vivo, assessment of functional and anatomical connectivity, higher resolution physiologic and metabolic imaging, and even imaging of receptor binding. In addition, acquisition speed and information content will continue to increase due to the continuous development of approaches for parallel imaging (including simultaneous multi-slice imaging), compressed sensing, and MRI fingerprinting. Finally, artificial intelligence approaches are becoming more realistic and will have a tremendous effect on both acquisition and analysis strategies. Together, these developments will continue to provide opportunity for scientific discovery and, in combination with large data sets from other fields such as genomics, allow the ultimate realization of precision medicine in the clinic.

hMRI - A toolbox for quantitative MRI in neuroscience and clinical research

Neuroscience and clinical researchers are increasingly interested in quantitative magnetic resonance imaging (qMRI) due to its sensitivity to micro-structural properties of brain tissue such as axon, myelin, iron and water concentration. We introduce the hMRI-toolbox, an open-source, easy-to-use tool available on GitHub, for qMRI data handling and processing, presented together with a tutorial and example dataset. This toolbox allows the estimation of high-quality multi-parameter qMRI maps (longitudinal and effective transverse relaxation rates R1 and R2⋆, proton density PD and magnetisation transfer MT saturation) that can be used for quantitative parameter analysis and accurate delineation of subcortical brain structures. The qMRI maps generated by the toolbox are key input parameters for biophysical models designed to estimate tissue microstructure properties such as the MR g-ratio and to derive standard and novel MRI biomarkers. Thus, the current version of the toolbox is a first step towards in vivo histology using MRI (hMRI) and is being extended further in this direction. Embedded in the Statistical Parametric Mapping (SPM) framework, it benefits from the extensive range of established SPM tools for high-accuracy spatial registration and statistical inferences and can be readily combined with existing SPM toolboxes for estimating diffusion MRI parameter maps. From a user's perspective, the hMRI-toolbox is an efficient, robust and simple framework for investigating qMRI data in neuroscience and clinical research.

Signal compartments in ultra-high field multi-echo gradient echo MRI reflect underlying tissue microstructure in the brain

Gradient recalled echo magnetic resonance imaging (GRE-MRI) at ultra-high field holds great promise for new contrast mechanisms and delineation of putative tissue compartments that contribute to the multi-echo GRE-MRI signal may aid structural characterization. Several studies have adopted the three water-pool compartment model to study white matter brain regions, associating individual compartments with myelin, axonal and extracellular water. However, the number and identifiability of GRE-MRI signal compartments has not been fully explored. We undertook this task for human brain imaging data. Multiple echo time GRE-MRI data were acquired in five healthy participants, specific anatomical structures were segmented in each dataset (substantia nigra, caudate, insula, putamen, thalamus, fornix, internal capsule, corpus callosum and cerebrospinal fluid), and the signal fitted with models comprising one to six signal compartments using a complex-valued plane wave formulation. Information criteria and cluster analysis methods were used to ascertain the number of distinct compartments within the signal from each structure and to determine their respective frequency shifts. We identified five principal signal compartments with different relative contributions to each structure's signal. Voxel-based maps of the volume fraction of each of these compartments were generated and demonstrated spatial correlation with brain anatomy.

Quantifying MRI frequency shifts due to structures with anisotropic magnetic susceptibility using pyrolytic graphite sheet

Magnetic susceptibility is an important source of contrast in magnetic resonance imaging (MRI), with spatial variations in the susceptibility of tissue affecting both the magnitude and phase of the measured signals. This contrast has generally been interpreted by assuming that tissues have isotropic magnetic susceptibility, but recent work has shown that the anisotropic magnetic susceptibility of ordered biological tissues, such as myelinated nerves and cardiac muscle fibers, gives rise to unexpected image contrast. This behavior occurs because the pattern of field variation generated by microstructural elements formed from material of anisotropic susceptibility can be very different from that predicted by modelling the effects in terms of isotropic susceptibility. In MR images of tissue, such elements are manifested at a sub-voxel length-scale, so the patterns of field variation that they generate cannot be directly visualized. Here, we used pyrolytic graphite sheet which has a large magnetic susceptibility anisotropy to form structures of known geometry with sizes large enough that the pattern of field variation could be mapped directly using MRI. This allowed direct validation of theoretical expressions describing the pattern of field variation from anisotropic structures with biologically relevant shapes (slabs, spherical shells and cylindrical shells).

Investigating magnetic susceptibility of human knee joint at 7 Tesla

PURPOSE

To evaluate the magnetic susceptibility properties of different anatomical structures within the knee joint using quantitative susceptibility mapping (QSM).

METHODS

A collagen tissue model was simulated and ex vivo animal cartilage experiments were conducted at 9.4 Tesla (T) to evaluate the B₀ orientation-dependent magnetic susceptibility contrast observed in cartilage. Furthermore, nine volunteers (six healthy subjects without knee pain history and three patients with known knee injury, between 29 and 58 years old) were scanned using gradient-echo acquisitions on a high-field 7T MR scanner. Susceptibility values of different tissues were quantified and diseased cartilage and meniscus were compared against that of healthy volunteers.

RESULTS

Simulation and ex vivo animal cartilage experiments demonstrated that collagen fibrils exhibit an anisotropic susceptibility. A gradual change of magnetic susceptibility was observed in the articular cartilage from the superficial zone to the deep zone, forming a multilayer ultrastructure consistent with anisotropy of collagen fibrils. Meniscal tears caused a clear reduction of susceptibility contrast between the injured meniscus and surrounding cartilage illustrated by a loss of the sharp boundaries between the two. Moreover, QSM showed more dramatic contrast in the focal degenerated articular cartilage than R2* mapping.

CONCLUSION

The arrangement of the collagen fibrils is significant, and likely the most dominant source of magnetic susceptibility anisotropy. Quantitative susceptibility mapping offers a means to characterize magnetic susceptibility properties of tissues in the knee joint. It is sensitive to collagen damage or degeneration and may be useful for evaluating the status of knee diseases, such as meniscal tears and cartilage disease. Magn Reson Med 78:1933-1943, 2017. © 2017 International Society for Magnetic Resonance in Medicine.

Test-retest reliability and concurrent validity of in vivo myelin content indices: Myelin water fraction and calibrated T1 w/T2 w image ratio

In an age-heterogeneous sample of healthy adults, we examined test-retest reliability (with and without participant repositioning) of two popular MRI methods of estimating myelin content: modeling the short spin-spin (T₂ ) relaxation component of multi-echo imaging data and computing the ratio of T₁ -weighted and T₂ -weighted images (T₁ w/T₂ w). Taking the myelin water fraction (MWF) index of myelin content derived from the multi-component T₂ relaxation data as a standard, we evaluate the concurrent and differential validity of T₁ w/T₂ w ratio images. The results revealed high reliability of MWF and T₁ w/T₂ w ratio. However, we found significant correlations of low to moderate magnitude between MWF and the T₁ w/T₂ w ratio in only two of six examined regions of the cerebral white matter. Notably, significant correlations of the same or greater magnitude were observed for T₁ w/T₂ w ratio and the intermediate T₂ relaxation time constant, which is believed to reflect differences in the mobility of water between the intracellular and extracellular compartments. We conclude that although both methods are highly reliable and thus well-suited for longitudinal studies, T₁ w/T₂ w ratio has low criterion validity and may be not an optimal index of subcortical myelin content. Hum Brain Mapp 38:1780-1790, 2017. © 2017 Wiley Periodicals, Inc.

Rapid simultaneous high-resolution mapping of myelin water fraction and relaxation times in human brain using BMC-mcDESPOT

A number of central nervous system (CNS) diseases exhibit changes in myelin content and magnetic resonance longitudinal, T₁, and transverse, T₂, relaxation times, which therefore represent important biomarkers of CNS pathology. Among the methods applied for measurement of myelin water fraction (MWF) and relaxation times, the multicomponent driven equilibrium single pulse observation of T₁ and T₂ (mcDESPOT) approach is of particular interest. mcDESPOT permits whole brain mapping of multicomponent T₁ and T₂, with data acquisition accomplished within a clinically realistic acquisition time. Unfortunately, previous studies have indicated the limited performance of mcDESPOT in the setting of the modest signal-to-noise range of high-resolution mapping, required for the depiction of small structures and to reduce partial volume effects. Recently, we showed that a new Bayesian Monte Carlo (BMC) analysis substantially improved determination of MWF from mcDESPOT imaging data. However, our previous study was limited in that it did not discuss determination of relaxation times. Here, we extend the BMC analysis to the simultaneous determination of whole-brain MWF and relaxation times using the two-component mcDESPOT signal model. Simulation analyses and in-vivo human brain studies indicate the overall greater performance of this approach compared to the stochastic region contraction (SRC) algorithm, conventionally used to derive parameter estimates from mcDESPOT data. SRC estimates of the transverse relaxation time of the long T₂ fraction, T_2,l, and the longitudinal relaxation time of the short T₁ fraction, T_1,s, clustered towards the lower and upper parameter search space limits, respectively, indicating failure of the fitting procedure. We demonstrate that this effect is absent in the BMC analysis. Our results also showed improved parameter estimation for BMC as compared to SRC for high-resolution mapping. Overall we find that the combination of BMC analysis and mcDESPOT, BMC-mcDESPOT, shows excellent performance for accurate high-resolution whole-brain mapping of MWF and bi-component transverse and longitudinal relaxation times within a clinically realistic acquisition time.