Reproducibility of the Standard Model of diffusion in white matter on clinical MRI systems

MATI: A GPU-accelerated toolbox for microstructural diffusion MRI simulation and data fitting with a graphical user interface

PURPOSE

To introduce MATI (Microstructural Analysis Toolbox for Imaging), a versatile MATLAB-based toolbox that combines both simulation and data fitting capabilities for microstructural dMRI research.

METHODS

MATI provides a user-friendly, graphical user interface that enables researchers, including those without much programming experience, to perform advanced simulations and data analyses for microstructural MRI research. For simulation, MATI supports arbitrary microstructural tissues and pulse sequences. For data fitting, MATI supports a range of fitting methods, including traditional non-linear least squares, Bayesian approaches, machine learning, and dictionary matching methods, allowing users to tailor analyses based on specific research needs.

RESULTS

Optimized with vectorized matrix operations and high-performance numerical libraries, MATI achieves high computational efficiency, enabling rapid simulations and data fitting on CPU and GPU hardware. While designed for microstructural dMRI, MATI's generalized framework can be extended to other imaging methods, making it a flexible and scalable tool for quantitative MRI research.

CONCLUSION

MATI offers a significant step toward translating advanced microstructural MRI techniques into clinical applications.

Juvenile Myoclonic Epilepsy Imaging Endophenotypes and Relationship With Cognition and Resting-State EEG

Structural neuroimaging studies of patients with Juvenile Myoclonic Epilepsy (JME) typically present two findings: 1-volume reduction of subcortical gray matter structures, and 2-abnormalities of cortical thickness. The general trend has been to observe increased cortical thickness primarily in medial frontal regions, but heterogeneity across studies is common, including reports of decreased cortical thickness. These differences have not been explained. The cohort of patients investigated here originates from the Juvenile Myoclonic Epilepsy Connectome Project, which included comprehensive neuropsychological testing, 3 T MRI, and high-density 256-channel EEG. 64 JME patients aged 12-25 and 41 age and sex-matched healthy controls were included. Data-driven approaches were used to compare cortical thickness and subcortical volumes between the JME and control participants. After differences were identified, supervised machine learning was used to confirm their classification power. K-means clustering was used to generate imaging endophenotypes, which were then correlated with cognition, EEG frequency band lagged coherence from resting state high-density EEG, and white and grey matter based spatial statistics from diffusion imaging. The volumes of subcortical gray matter structures, particularly the thalamus and the motor-associated thalamic nuclei (ventral anterior), were found to be smaller in JME. In addition, the right hemisphere (primarily) sulcal pre-motor cortex was abnormally thicker in an age-dependent manner in JME with an asymmetry in the pre-motor cortical findings. These results suggested that for some patients JME may be an asymmetric disease, at least at the cortical level. Cluster analysis revealed three discrete imaging endophenotypes (left, right, symmetric). Clinically, the groups were not substantially different except for cognition, where left hemisphere disease was linked with a lower performance on a general cognitive factor ("g"). HD-EEG demonstrated statistically significant differences between imaging endophenotypes. Tract-based spatial statistics showed significant changes between endophenotypes as well. The left dominant disease group exhibited diffuse white matter changes. JME patients present with heterogeneity in underlying imaging endophenotypes that are defined by the presence and laterality of asymmetric abnormality at the level of the pre-motor sulcal cortex; these endophenotypes are linked to orderly relationships with cognition, EEG, and white matter pathology. The relationship of JME's adolescent onset, age-dependent cortical thickness loss, and seizure upon awakening all suggest that synaptic pruning may be a key element in the pathogenesis of JME. Individualized treatment approaches for neuromodulation are needed to target the most relevant cortical and subcortical structures as well as develop disease-modifying and neuroprotective strategies.

A deep learning approach to multi-fiber parameter estimation and uncertainty quantification in diffusion MRI

Diffusion MRI (dMRI) is the primary imaging modality used to study brain microstructure in vivo. Reliable and computationally efficient parameter inference for common dMRI biophysical models is a challenging inverse problem, due to factors such as variable dimensionalities (reflecting the unknown number of distinct white matter fiber populations in a voxel), low signal-to-noise ratios, and non-linear forward models. These challenges have led many existing methods to use biologically implausible simplified models to stabilize estimation, for instance, assuming shared microstructure across all fiber populations within a voxel. In this work, we introduce a novel sequential method for multi-fiber parameter inference that decomposes the task into a series of manageable subproblems. These subproblems are solved using deep neural networks tailored to problem-specific structure and symmetry, and trained via simulation. The resulting inference procedure is largely amortized, enabling scalable parameter estimation and uncertainty quantification across all model parameters. Simulation studies and real imaging data analysis using the Human Connectome Project (HCP) demonstrate the advantages of our method over standard alternatives. In the case of the standard model of diffusion, our results show that under HCP-like acquisition schemes, estimates for extra-cellular parallel diffusivity are highly uncertain, while those for the intra-cellular volume fraction can be estimated with relatively high precision.

Isotropic sampling of tensor-encoded diffusion MRI

PURPOSE

The purpose of this study is to develop a method for selecting uniform wave vectors for double diffusion encoding (DDE) to improve the accuracy and reliability of diffusion measurements.

METHODS

The method relies on identifying orthogonal wave vectors with rotations, and representing these rotations as points on a three-dimensional sphere in four dimensions using quaternions. This enables an electrostatic repulsion algorithm to achieve a uniform distribution of these points. The optimal points are then converted back into orthogonal wave vectors (or rotations).

RESULTS

The method was validated by comparing the distribution of directions to those generated by uniform sampling and by evaluating the error in the powder-averaged signal for various models. Our results demonstrate that the electrostatic repulsion approach effectively achieves a uniform distribution of wave vectors.

CONCLUSION

The proposed method provides a systematic way to generate uniform diffusion directions suitable, for example, for DDE, enhancing the precision of diffusion measurements and reducing potential bias in experimental results. The method is also capable of generating uniform sets of B-tensors, and is thus applicable for general free waveform encoding.

White matter microstructure links with brain, bodily and genetic attributes in adolescence, mid- and late life

Advanced diffusion magnetic resonance imaging (dMRI) allows one to probe and assess brain white matter (WM) organisation and microstructure in vivo. Various dMRI models with different theoretical and practical assumptions have been developed, representing partly overlapping characteristics of the underlying brain biology with potentially complementary value in the cognitive and clinical neurosciences. To which degree the different dMRI metrics relate to clinically relevant geno- and phenotypes is still debated. Hence, we investigate how tract-based and whole WM skeleton parameters from different dMRI approaches associate with clinically relevant and white matter-related phenotypes (sex, age, pulse pressure (PP), body-mass-index (BMI), brain asymmetry) and genetic markers in the UK Biobank (UKB, n=52,140) and the Adolescent Brain Cognitive Development (ABCD) Study (n=5,844). In general, none of the imaging approaches could explain all examined phenotypes, though the approaches were overall similar in explaining variability of the examined phenotypes. Nevertheless, particular diffusion parameters of the used dMRI approaches stood out in explaining some important phenotypes known to correlate with general human health outcomes. A multi-compartment Bayesian dMRI approach provided the strongest WM associations with age, and together with diffusion tensor imaging, the largest accuracy for sex-classifications. We find a similar pattern of metric and tract-dependent asymmetries across datasets, with stronger asymmetries in ABCD data. The magnitude of WM associations with polygenic scores as well as PP depended more on the sample, and likely age, than dMRI metrics. However, kurtosis was most indicative of BMI and potentially of bipolar disorder polygenic scores. We conclude that WM microstructure is differentially associated with clinically relevant pheno- and genotypes at different points in life.

Estimating Brain Similarity Networks with Diffusion MRI

Structural similarity has emerged as a promising tool in mapping the network organization of an individual, living human brain. Here, we propose diffusion similarity networks (DSNs), which employ rotationally invariant spherical harmonic features derived from diffusion magnetic resonance imaging (dMRI), to map gray matter structural organization. Compared to prior approaches, DSNs showed clearer laminar, cytoarchitectural, and micro-architectural organization; greater sensitivity to age, cognition, and sex; higher heritability in a large dataset of healthy young adults; and straightforward extension to non-cortical regions. We show DSNs are correlated with functional, structural, and gene expression connectomes and their gradients align with the sensory-fugal and sensorimotor-association axes of the cerebral cortex, including neuronal oscillatory dynamics, metabolism, immunity, and dopaminergic and glutaminergic receptor densities. DSNs can be easily integrated into conventional dMRI analysis, adding information complementary to structural white matter connectivity, and could prove useful in investigating a wide array of neurological and psychiatric conditions.

Metrology for MRI: the field you've never heard of

Quantitative MRI has been an active area of research for decades and has produced a huge range of approaches with enormous potential for patient benefit. In many cases, however, there are challenges with reproducibility which have hampered clinical translation. Quantitative MRI is a form of measurement and like any other form of measurement it requires a supporting metrological framework to be fully consistent and compatible with the international system of units. This means not just expressing results in terms of seconds, meters, etc., but demonstrating consistency to their internationally recognized definitions. Such a framework for MRI is not yet complete, but a considerable amount of work has been done internationally towards building one. This article describes the current state of the art for MRI metrology, including a detailed description of metrological principles and how they are relevant to fully quantitative MRI. It also undertakes a gap analysis of where we are versus where we need to be to support reproducibility in MRI. It focusses particularly on the role and activities of national measurement institutes across the globe, illustrating the genuinely international and collaborative nature of the field.

Denoising Improves Cross-Scanner and Cross-Protocol Test-Retest Reproducibility of Diffusion Tensor and Kurtosis Imaging

The clinical translation of diffusion magnetic resonance imaging (dMRI)-derived quantitative contrasts hinges on robust reproducibility, minimizing both same-scanner and cross-scanner variability. As multi-site data sets, including multi-shell dMRI, expand in scope, enhancing reproducibility across variable MRI systems and MRI protocols becomes crucial. This study evaluates the reproducibility of diffusion kurtosis imaging (DKI) metrics (beyond conventional diffusion tensor imaging (DTI)), at the voxel and region-of-interest (ROI) levels on magnitude and complex-valued dMRI data, using denoising with and without harmonization. We compared same-scanner, cross-scanner, and cross-protocol variability for a multi-shell dMRI protocol (2-mm isotropic resolution, b = 0, 1000, 2000 s/mm2) in 20 subjects. We first evaluated the effectiveness of Marchenko-Pastur Principal Component Analysis (MPPCA) based denoising strategies for both magnitude and complex data to mitigate noise-induced bias and variance, to improve dMRI parametric maps and reproducibility. Next, we examined the impact of denoising under different population analysis approaches, specifically comparing voxel-wise versus region of interest (ROI)-based methods. We also evaluated the role of denoising when harmonizing dMRI across scanners and protocols. The results indicate that DTI and DKI maps visually improve after MPPCA denoising, with noticeably fewer outliers in kurtosis maps. Denoising, either using magnitude or complex dMRI, enhances voxel-wise reproducibility, with test-retest variability of kurtosis indices reduced from 15%-20% without denoising to 5%-10% after denoising. Complex dMRI denoising reduces the noise floor by up to 60%. Denoising not only reduced variability across scans and protocols, but also increased statistical power for low SNR voxel-wise comparisons when comparing cross sectional groups. In conclusion, MPPCA denoising, either over magnitude or complex dMRI data, enhances the reproducibility and precision of higher-order diffusion metrics across same-scanner, cross-scanner, and cross-protocol assessments. The enhancement in data quality and precision facilitates the broader application and acceptance of these advanced imaging techniques in both clinical practice and large-scale neuroimaging studies.

Characterization of neurite and soma organization in the brain and spinal cord with diffusion MRI

The central nervous system (CNS), comprised of both the brain and spinal cord, and is a complex network of white and gray matter responsible for sensory, motor, and cognitive functions. Advanced diffusion MRI (dMRI) techniques offer a promising mechanism to non-invasively characterize CNS architecture, however, most studies focus on the brain or spinal cord in isolation. Here, we implemented a clinically feasible dMRI protocol on a 3T scanner to simultaneously characterize neurite and soma microstructure of both the brain and spinal cord. The protocol enabled the use of Diffusion Tensor Imaging (DTI), Standard Model Imaging (SMI), and Soma and Neurite Density Imaging (SANDI), representing the first time SMI and SANDI have been evaluated in the cord, and in the cord and brain simultaneously. Our results demonstrate high image quality even at high diffusion weightings, reproducibility of SMI and SANDI derived metrics similar to those of DTI with few exceptions, and biologically feasible contrasts between and within white and gray matter regions. Reproducibility and contrasts were decreased in the cord compared to that of the brain, revealing challenges due to partial volume effects and image preprocessing. This study establishes a harmonized approach for brain and cord microstructural imaging, and the opportunity to study CNS pathologies and biomarkers of structural integrity across the neuroaxis.

Improving the Assessment of Axonal Injury in Early Multiple Sclerosis

RATIONALE AND OBJECTIVES

Several quantitative magnetic resonance imaging (MRI) methods are available to measure tissue injury in multiple sclerosis (MS), but their pathological specificity remains limited. The multi-compartment diffusion imaging using the spherical mean technique (SMT) overcomes several technical limitations of the diffusion-weighted image signal, thus delivering metrics with increased pathological specificity. Given these premises, here we assess whether the SMT-derived apparent axonal volume (Vax) provides a better tissue classifier than the diffusion tensor imaging (DTI)-derived axial diffusivity (AD) in the white matter (WM) of MS brains.

METHODS

Forty-three treatment-naïve people with newly diagnosed MS, clinically isolated syndrome, or radiologically isolated syndrome and 18 healthy controls (HCs) underwent a 3.0 Tesla MRI inclusive of T1-weighted (T1-w) and T2-w fluid-attenuated inversion recovery (FLAIR) sequences, and multi-b shell diffusion-weighted imaging. In patients only, pre- and post-gadolinium diethylenetriamine penta-acetic acid T1-w sequences were obtained for the evaluation of contrast-active lesions (CELs). Vax and AD were calculated in T2-lesions, chronic black holes (cBHs), and normal appearing (NAWM) in patients and normal WM (NWM) in HCs. Vax and AD values were compared across all the possible combinations of these regions. CELs were excluded from the analyses.

RESULTS

Vax differed in all comparisons (p ≤ 0.047 by paired t-test); AD differed in most comparisons (p < 0.001) except between NAWM and NWM, and between cBHs and T2-lesions. Vax had higher accuracy (p ≤ 0.029 by DeLong test) and larger effect size (p ≤ 0.038 by paired t-test) than AD in differentiating areas with even minimal tissue injury.

CONCLUSIONS

Vax provides a better radiological quantitative discriminator of different degrees of axonal-mediated tissue injury even between areas with expected minimal pathology. Our data support further studies to assess the readiness of Vax as a measure of outcome for clinical trials on neuroprotection in MS.

Multi-tensor fixel-based metrics in tractometry: application to multiple sclerosis

Traditional Diffusion Tensor Imaging (DTI) metrics are affected by crossing fibers and lesions. Most of the previous tractometry works use the single diffusion tensor, which leads to limited sensitivity and challenging interpretation of the results in crossing fiber regions. In this work, we propose a tractometry pipeline that combines white matter tractography with multi-tensor fixel-based metrics. These multi-tensors are estimated using the stable, accurate and robust to noise Multi-Resolution Discrete Search method (MRDS). The spatial coherence of the multi-tensor field estimated with MRDS, which includes up to three anisotropic and one isotropic tensors, is tractography-regularized using the Track Orientation Density Imaging method. Our end-to-end tractometry pipeline goes from raw data to track-specific multi-tensor-metrics tract profiles that are robust to noise and crossing fibers. A comprehensive evaluation conducted in a phantom simulating healthy and damaged tissue with the standard model, as well as in a healthy cohort of 20 individuals scanned along 5 time points, demonstrates the advantages of using multi-tensor metrics over traditional single-tensor metrics in tractometry. Qualitative assessment in a cohort of patients with relapsing-remitting multiple sclerosis reveals that the pipeline effectively detects white matter anomalies in the presence of crossing fibers and lesions.

In vivo human neurite exchange imaging (NEXI) at 500 mT/m diffusion gradients

Evaluating tissue microstructure and membrane integrity in the living human brain through diffusion-water exchange imaging is challenging due to requirements for a high signal-to-noise ratio and short diffusion times dictated by relatively fast exchange processes. The goal of this work was to demonstrate the feasibility of in vivo imaging of tissue micro-geometries and water exchange within the brain gray matter using the state-of-the-art Connectome 2.0 scanner equipped with an ultra-high-performance gradient system (maximum gradient strength=500 mT/m, maximum slew rate=600 T/m/s). We performed diffusion MRI measurements in 15 healthy volunteers at multiple diffusion times (13-30 ms) and b -values up to 17.5 ms/μm2. The anisotropic Kärger model was applied to estimate the exchange time between intra-neurite and extracellular water in gray matter. The estimated exchange time across the cortical ribbon was around (median±interquartile range) 13±8 ms on Connectome 2.0, substantially faster than that measured using an imaging protocol compatible with Connectome 1.0-alike systems on the same cohort. Our investigation suggested that the NEXI exchange time estimation using a Connectome 1.0 compatible protocol was more prone to residual noise floor biases due to the small time-dependent signal contrasts across diffusion times when the exchange is fast (≤20 ms). Furthermore, spatial variation of exchange time was observed across the cortex, where the motor cortex, somatosensory cortex and visual cortex exhibit longer exchange times compared to other cortical regions. Non-linear fitting for the anisotropic Kärger model was accelerated 100 times using a GPU-based pipeline compared to the conventional CPU-based approach. This study highlighted the importance of the chosen diffusion times and measures to address Rician noise in dMRI data, which can have a substantial impact on the estimated NEXI exchange time and require extra attention when comparing NEXI results between various hardware setups.

Application of preoperative advanced diffusion magnetic resonance imaging in evaluating the postoperative recurrence of lower grade gliomas

BACKGROUND

Recurrence of lower grade glioma (LrGG) appeared to be unavoidable despite considerable research performed in last decades. Thus, we evaluated the postoperative recurrence within two years after the surgery in patients with LrGG by preoperative advanced diffusion magnetic resonance imaging (dMRI).

MATERIALS AND METHODS

48 patients with lower-grade gliomas (23 recurrence, 25 nonrecurrence) were recruited into this study. Different models of dMRI were reconstructed, including apparent fiber density (AFD), white matter tract integrity (WMTI), diffusion tensor imaging (DTI), diffusion kurtosis imaging (DKI), neurite orientation dispersion and density imaging (NODDI), Bingham NODDI and standard model imaging (SMI). Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA) was used to construct a multiparametric prediction model for the diagnosis of postoperative recurrence.

RESULTS

The parameters derived from each dMRI model, including AFD, axon water fraction (AWF), mean diffusivity (MD), mean kurtosis (MK), fractional anisotropy (FA), intracellular volume fraction (ICVF), extra-axonal perpendicular diffusivity (De⊥), extra-axonal parallel diffusivity (De∥) and free water fraction (fw), showed significant differences between nonrecurrence group and recurrence group. The extra-axonal perpendicular diffusivity (De⊥) had the highest area under curve (AUC = 0.885), which was significantly higher than others. The variable importance for the projection (VIP) value of De⊥ was also the highest. The AUC value of the multiparametric prediction model merging AFD, WMTI, DTI, DKI, NODDI, Bingham NODDI and SMI was up to 0.96.

CONCLUSION

Preoperative advanced dMRI showed great efficacy in evaluating postoperative recurrence of LrGG and De⊥ of SMI might be a valuable marker.

White Matter Microstructural Changes Using Ultra-Strong Diffusion Gradient MRI in Adult-Onset Idiopathic Focal Cervical Dystonia

BACKGROUND AND OBJECTIVES

Adult-onset idiopathic focal cervical dystonia (AOIFCD) involves abnormal posturing of the cervical musculature and, in some individuals, an associated head tremor. Existing neuroimaging studies have implicated key motor networks. However, measures used to date lack specificity toward underlying pathophysiologic differences. We aim to assess white matter motor pathways for localized, microstructural differences, which may aid in understanding underlying mechanisms.

METHODS

Individuals diagnosed with AOIFCD and an age- and sex-matched control group were prospectively recruited through the Welsh Movement Disorders Research Network. All participants underwent in-depth clinical phenotyping and MRI (structural and diffusion sequences) using ultra-strong diffusion gradients. Tractography (whole-tract median values) and tractometry (along tract profiling) were performed for key white matter motor pathways assessing diffusion kurtosis imaging (DKI), neurite orientation dispersion and density imaging (NODDI), and standard model parameters. Groups were compared using linear model analysis with Bonferroni multiple comparison correction.

RESULTS

Fifty participants with AOIFCD and 30 healthy control participants were recruited, with 46 with AOIFCD and 30 healthy controls included for analysis (33 without head tremor, 13 with head tremor). Significant differences were observed in the anterior thalamic radiations (lower mid-tract fractional anisotropy [estimate = -0.046, p = 3.07 × 10-3], radial kurtosis [estimate = -0.165, p = 1.42 × 10-4], f-intra-axonal signal fraction [estimate = -0.044, p = 2.78 × 10-3], p2 orientation coherence [estimate = -0.043, p = 1.64 × 10-3], higher Orientation Dispersion Index [ODI, estimate = 0.023, p = 2.22 × 10-3]) and thalamopremotor tracts (higher mid-tract mean kurtosis [estimate = 0.064, p = 7.56 × 10-4], lower Neurite Density Index [estimate = 0.062, p = 2.1 × 10-3], higher distal tract ODI [estimate = 0.062, p = 3.1 × 10-3], lower f [estimate = -0.1, p = 2.3 × 10-3], and striatopremotor tracts [proximal lower f: estimate = -0.075, p = 1.06 × 10-3]). These measures correlated with clinical measures: dystonia duration (right thalamopremotor distal ODI: r = -0.9, p = 1.29 × 10-14), psychiatric symptoms (obsessive compulsive symptoms: left anterior thalamic radiation p2 r = 0.92, p = 2.797 × 10-11), sleep quality (Sleep Disorders Questionnaire Score: left anterior thalamic radiation ODI: r = -0.84, p = 4.84 × 10-11), pain (left anterior thalamic radiation ODI: r = -0.89, p = 1.4 × 10-13), and cognitive functioning (paired associated learning task p2, r = 0.94, p = 6.68 × 10-20).

DISCUSSION

Overall, localized microstructural differences were identified within tracts linking the prefrontal and premotor cortices with thalamic and basal ganglia regions, suggesting pathophysiologic processes involve microstructural aberrances of motor system modulatory pathways, particularly involving intra-axonal and fiber orientation dispersion measures.

Callosal Interhemispheric Communication in Mild Traumatic Brain Injury: A Mediation Analysis on WM Microstructure Effects

BACKGROUND AND PURPOSE

Because the corpus callosum connects the left and right hemispheres and a variety of WM bundles across the brain in complex ways, damage to the neighboring WM microstructure may specifically disrupt interhemispheric communication through the corpus callosum following mild traumatic brain injury. Here we use a mediation framework to investigate how callosal interhemispheric communication is affected by WM microstructure in mild traumatic brain injury.

MATERIALS AND METHODS

Multishell diffusion MR imaging was performed on 23 patients with mild traumatic brain injury within 1 month of injury and 17 healthy controls, deriving 11 diffusion metrics, including DTI, diffusional kurtosis imaging, and compartment-specific standard model parameters. Interhemispheric processing speed was assessed using the interhemispheric speed of processing task (IHSPT) by measuring the latency between word presentation to the 2 hemivisual fields and oral word articulation. Mediation analysis was performed to assess the indirect effect of neighboring WM microstructures on the relationship between the corpus callosum and IHSPT performance. In addition, we conducted a univariate correlation analysis to investigate the direct association between callosal microstructures and IHSPT performance as well as a multivariate regression analysis to jointly evaluate both callosal and neighboring WM microstructures in association with IHSPT scores for each group.

RESULTS

Several significant mediators in the relationships between callosal microstructure and IHSPT performance were found in healthy controls. However, patients with mild traumatic brain injury appeared to lose such normal associations when microstructural changes occurred compared with healthy controls.

CONCLUSIONS

This study investigates the effects of neighboring WM microstructure on callosal interhemispheric communication in healthy controls and patients with mild traumatic brain injury, highlighting that neighboring noncallosal WM microstructures are involved in callosal interhemispheric communication and information transfer. Further longitudinal studies may provide insight into the temporal dynamics of interhemispheric recovery following mild traumatic brain injury.

Cerebral microstructural alterations in Post-COVID-condition are related to cognitive impairment, olfactory dysfunction and fatigue

After contracting COVID-19, a substantial number of individuals develop a Post-COVID-Condition, marked by neurologic symptoms such as cognitive deficits, olfactory dysfunction, and fatigue. Despite this, biomarkers and pathophysiological understandings of this condition remain limited. Employing magnetic resonance imaging, we conduct a comparative analysis of cerebral microstructure among patients with Post-COVID-Condition, healthy controls, and individuals that contracted COVID-19 without long-term symptoms. We reveal widespread alterations in cerebral microstructure, attributed to a shift in volume from neuronal compartments to free fluid, associated with the severity of the initial infection. Correlating these alterations with cognition, olfaction, and fatigue unveils distinct affected networks, which are in close anatomical-functional relationship with the respective symptoms.

Optimisation of quantitative brain diffusion-relaxation MRI acquisition protocols with physics-informed machine learning

Diffusion-relaxation MRI aims to extract quantitative measures that characterise microstructural tissue properties such as orientation, size, and shape, but long acquisition times are typically required. This work proposes a physics-informed learning framework to extract an optimal subset of diffusion-relaxation MRI measurements for enabling shorter acquisition times, predict non-measured signals, and estimate quantitative parameters. In vivo and synthetic brain 5D-Diffusion-T1-T2∗-weighted MRI data obtained from five healthy subjects were used for training and validation, and from a sixth participant for testing. One fully data-driven and two physics-informed machine learning methods were implemented and compared to two manual selection procedures and Cramér-Rao lower bound optimisation. The physics-informed approaches could identify measurement-subsets that yielded more consistently accurate parameter estimates in simulations than other approaches, with similar signal prediction error. Five-fold shorter protocols yielded error distributions of estimated quantitative parameters with very small effect sizes compared to estimates from the full protocol. Selected subsets commonly included a denser sampling of the shortest and longest inversion time, lowest echo time, and high b-value. The proposed framework combining machine learning and MRI physics offers a promising approach to develop shorter imaging protocols without compromising the quality of parameter estimates and signal predictions.

Insights and improvements in correspondence between axonal volume fraction measured with diffusion-weighted MRI and electron microscopy

Biophysical diffusion-weighted imaging (DWI) models are increasingly used in neuroscience to estimate the axonal water fraction (f AW ), which in turn is key for noninvasive estimation of the axonal volume fraction (f A ). These models require thorough validation by comparison with a reference method, for example, electron microscopy (EM). While EM studies often neglect the unmyelinated axons and solely report the fraction of myelinated axons, in DWI both myelinated and unmyelinated axons contribute to the DWI signal. However, DWI models often include simplifications, for example, the neglect of differences in the compartmental relaxation times or fixed diffusivities, which in turn might affect the estimation off AW . We investigate whether linear calibration parameters (scaling and offset) can improve the comparability between EM- and DWI-based metrics off A . To this end, we (a) used six DWI models based on the so-called standard model of white matter (WM), including two models with fixed compartmental diffusivities (e.g., neurite orientation dispersion and density imaging, NODDI) and four models that fitted the compartmental diffusivities (e.g., white matter tract integrity, WMTI), and (b) used a multimodal data set including ex vivo diffusion DWI and EM data in mice with a broad dynamic range of fibre volume metrics. We demonstrated that the offset is associated with the volume fraction of unmyelinated axons and the scaling factor is associated with different compartmentalT 2 and can substantially enhance the comparability between EM- and DWI-based metrics off A . We found that DWI models that fitted compartmental diffusivities provided the most accurate estimates of the EM-basedf A . Finally, we introduced a more efficient hybrid calibration approach, where only the offset is estimated but the scaling is fixed to a theoretically predicted value. Using this approach, a similar one-to-one correspondence to EM was achieved for WMTI. The method presented can pave the way for use of validated DWI-based models in clinical research and neuroscience.

Assessment of Precision and Accuracy of Brain White Matter Microstructure using Combined Diffusion MRI and Relaxometry

Joint modeling of diffusion and relaxation has seen growing interest due to its potential to provide complementary information about tissue microstructure. For brain white matter, we designed an optimal diffusion-relaxometry MRI protocol that samples multiple b-values, B-tensor shapes, and echo times (TE). This variable-TE protocol (27 min) has as subsets a fixed-TE protocol (15 min) and a 2-shell dMRI protocol (7 min), both characterizing diffusion only. We assessed the sensitivity, specificity and reproducibility of these protocols with synthetic experiments and in six healthy volunteers. Compared with the fixed-TE protocol, the variable-TE protocol enables estimation of free water fractions while also capturing compartmental T 2 relaxation times. Jointly measuring diffusion and relaxation offers increased sensitivity and specificity to microstructure parameters in brain white matter with voxelwise coefficients of variation below 10%.

Changes in Cortical Microstructure of the Human Brain Resulting from Long-Term Motor Learning

The mechanisms subserving motor skill acquisition and learning in the intact human brain are not fully understood. Previous studies in animals have demonstrated a causal relationship between motor learning and structural rearrangements of synaptic connections, raising the question of whether neurite-specific changes are also observable in humans. Here, we use advanced diffusion magnetic resonance imaging (MRI), sensitive to dendritic and axonal processes, to investigate neuroplasticity in response to long-term motor learning. We recruited healthy male and female human participants (age range 19-29) who learned a challenging dynamic balancing task (DBT) over four consecutive weeks. Diffusion MRI signals were fitted using Neurite Orientation Dispersion and Density Imaging (NODDI), a theory-driven biophysical model of diffusion, yielding measures of tissue volume, neurite density and the organizational complexity of neurites. While NODDI indices were unchanged and reliable during the control period, neurite orientation dispersion increased significantly during the learning period mainly in primary sensorimotor, prefrontal, premotor, supplementary, and cingulate motor areas. Importantly, reorganization of cortical microstructure during the learning phase predicted concurrent behavioral changes, whereas there was no relationship between microstructural changes during the control phase and learning. Changes in neurite complexity were independent of alterations in tissue density, cortical thickness, and intracortical myelin. Our results are in line with the notion that structural modulation of neurites is a key mechanism supporting complex motor learning in humans.SIGNIFICANCE STATEMENT The structural correlates of motor learning in the human brain are not fully understood. Results from animal studies suggest that synaptic remodeling (e.g., reorganization of dendritic spines) in sensorimotor-related brain areas is a crucial mechanism for the formation of motor memory. Using state-of-the-art diffusion magnetic resonance imaging (MRI), we found a behaviorally relevant increase in the organizational complexity of neocortical microstructure, mainly in primary sensorimotor, prefrontal, premotor, supplementary, and cingulate motor regions, following training of a challenging dynamic balancing task (DBT). Follow-up analyses suggested structural modulation of synapses as a plausible mechanism driving this increase, while colocalized changes in cortical thickness, tissue density, and intracortical myelin could not be detected. These results advance our knowledge about the neurobiological basis of motor learning in humans.

A simulation-driven supervised learning framework to estimate brain microstructure using diffusion MRI

We propose a framework to train supervised learning models on synthetic data to estimate brain microstructure parameters using diffusion magnetic resonance imaging (dMRI). Although further validation is necessary, the proposed framework aims to seamlessly incorporate realistic simulations into dMRI microstructure estimation. Synthetic data were generated from over 1,000 neuron meshes converted from digital neuronal reconstructions and linked to their neuroanatomical parameters (such as soma volume and neurite length) using an optimized diffusion MRI simulator that produces intracellular dMRI signals from the solution of the Bloch-Torrey partial differential equation. By combining random subsets of simulated neuron signals with a free diffusion compartment signal, we constructed a synthetic dataset containing dMRI signals and 40 tissue microstructure parameters of 1.45 million artificial brain voxels. To implement supervised learning models we chose multilayer perceptrons (MLPs) and trained them on a subset of the synthetic dataset to estimate some microstructure parameters, namely, the volume fractions of soma, neurites, and the free diffusion compartment, as well as the area fractions of soma and neurites. The trained MLPs perform satisfactorily on the synthetic test sets and give promising in-vivo parameter maps on the MGH Connectome Diffusion Microstructure Dataset (CDMD). Most importantly, the estimated volume fractions showed low dependence on the diffusion time, the diffusion time independence of the estimated parameters being a desired property of quantitative microstructure imaging. The synthetic dataset we generated will be valuable for the validation of models that map between the dMRI signals and microstructure parameters. The surface meshes and microstructures parameters of the aforementioned neurons have been made publicly available.

Mapping tissue microstructure across the human brain on a clinical scanner with soma and neurite density image metrics

Soma and neurite density image (SANDI) is an advanced diffusion magnetic resonance imaging biophysical signal model devised to probe in vivo microstructural information in the gray matter (GM). This model requires acquisitions that include b values that are at least six times higher than those used in clinical practice. Such high b values are required to disentangle the signal contribution of water diffusing in soma from that diffusing in neurites and extracellular space, while keeping the diffusion time as short as possible to minimize potential bias due to water exchange. These requirements have limited the use of SANDI only to preclinical or cutting-edge human scanners. Here, we investigate the potential impact of neglecting water exchange in the SANDI model and present a 10-min acquisition protocol that enables to characterize both GM and white matter (WM) on 3 T scanners. We implemented analytical simulations to (i) evaluate the stability of the fitting of SANDI parameters when diminishing the number of shells; (ii) estimate the bias due to potential exchange between neurites and extracellular space in such reduced acquisition scheme, comparing it with the bias due to experimental noise. Then, we demonstrated the feasibility and assessed the repeatability and reproducibility of our approach by computing microstructural metrics of SANDI with AMICO toolbox and other state-of-the-art models on five healthy subjects. Finally, we applied our protocol to five multiple sclerosis patients. Results suggest that SANDI is a practical method to characterize WM and GM tissues in vivo on performant clinical scanners.

Neurite orientation dispersion and density imaging of white matter microstructure in sensory processing dysfunction with versus without comorbid ADHD

Introduction

Sensory Processing Dysfunction (SPD) is common yet understudied, affecting up to one in six children with 40% experiencing co-occurring challenges with attention. The neural architecture of SPD with Attention Deficit and Hyperactivity Disorder (ADHD) (SPD+ADHD) versus SPD without ADHD (SPD-ADHD) has yet to be explored in diffusion tensor imaging (DTI) and Neurite Orientation Dispersion and Density Imaging (NODDI) has yet to be examined.

Methods

The present study computed DTI and NODDI biophysical model parameter maps of one hundred children with SPD. Global, regional and voxel-level white matter tract measures were analyzed and compared between SPD+ADHD and SPD-ADHD groups.

Results

SPD+ADHD children had global WM Fractional Anisotropy (FA) and Neurite Density Index (NDI) that trended lower than SPD-ADHD children, primarily in boys only. Data-driven voxelwise and WM tract-based analysis revealed statistically significant decreases of NDI in boys with SPD+ADHD compared to those with SPD-ADHD, primarily in projection tracts of the internal capsule and commissural fibers of the splenium of the corpus callosum.

Conclusion

We conclude that WM microstructure is more delayed/disrupted in boys with SPD+ADHD compared to SPD-ADHD, with NODDI showing a larger effect than DTI. This may represent the combined WM pathology of SPD and ADHD, or it may result from a greater degree of SPD WM pathology causing the development of ADHD.

Differentiation of white matter histopathology using b-tensor encoding and machine learning

Diffusion-weighted magnetic resonance imaging (DW-MRI) is a non-invasive technique that is sensitive to microstructural geometry in neural tissue and is useful for the detection of neuropathology in research and clinical settings. Tensor-valued diffusion encoding schemes (b-tensor) have been developed to enrich the microstructural data that can be obtained through DW-MRI. These advanced methods have proven to be more specific to microstructural properties than conventional DW-MRI acquisitions. Additionally, machine learning methods are particularly useful for the study of multidimensional data sets. In this work, we have tested the reach of b-tensor encoding data analyses with machine learning in different histopathological scenarios. We achieved this in three steps: 1) We induced different levels of white matter damage in rodent optic nerves. 2) We obtained ex vivo DW-MRI data with b-tensor encoding schemes and calculated quantitative metrics using Q-space trajectory imaging. 3) We used a machine learning model to identify the main contributing features and built a voxel-wise probabilistic classification map of histological damage. Our results show that this model is sensitive to characteristics of microstructural damage. In conclusion, b-tensor encoded DW-MRI data analyzed with machine learning methods, have the potential to be further developed for the detection of histopathology and neurodegeneration.

Parameter estimation for WMTI-Watson model of white matter using encoder-decoder recurrent neural network

PURPOSE

Biophysical modeling of the diffusion MRI (dMRI) signal provides estimates of specific microstructural tissue properties. Although non-linear least squares (NLLS) is the most widespread fitting method, it suffers from local minima and high computational cost. Deep learning approaches are steadily replacing NLLS, but come with the limitation that the model needs to be retrained for each acquisition protocol and noise level. In this study, a novel fitting approach was proposed based on the encoder-decoder recurrent neural network (RNN) to accelerate model estimation with good generalization to various datasets.

METHODS

The white matter tract integrity (WMTI)-Watson model as an implementation of the Standard Model of diffusion in white matter derives its parameters indirectly from the diffusion and kurtosis tensors (DKI). The RNN-based solver, which estimates the WMTI-Watson model from DKI, is therefore more readily translatable to various data, irrespective of acquisition protocols as long as the DKI was pre-computed from the signal. An embedding approach was also used to render the model insensitive to potential differences in distributions between training data and experimental data. The analytical solution, NLLS, RNN-, and a multilayer perceptron (MLP)-based methods were evaluated on synthetic and in vivo datasets of rat and human brain.

RESULTS

The proposed RNN solver showed highly reduced computation time over the analytical solution and NLLS, with similar accuracy but improved robustness, and superior generalizability over MLP.

CONCLUSION

The RNN estimator can be easily applied to various datasets without retraining, which shows great potential for a widespread use.