Prevalence of white matter pathways coming into a single white matter voxel orientation: The bottleneck issue in tractography

Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 1: In vivo small-animal imaging

Small-animal diffusion MRI (dMRI) has been used for methodological development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. The steps from animal setup and monitoring, to acquisition, analysis, and interpretation are complex, with many decisions that may ultimately affect what questions can be answered using the resultant data. This work aims to present selected considerations and recommendations from the diffusion community on best practices for preclinical dMRI of in vivo animals. We describe the general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in animal species and disease models and discuss why some may be more or less appropriate for different studies. We, then, give recommendations for in vivo acquisition protocols, including decisions on hardware, animal preparation, and imaging sequences, followed by advice for data processing including preprocessing, model-fitting, and tractography. Finally, we provide an online resource that lists publicly available preclinical dMRI datasets and software packages to promote responsible and reproducible research. In each section, we attempt to provide guides and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should focus. Although we mainly cover the central nervous system (on which most preclinical dMRI studies are focused), we also provide, where possible and applicable, recommendations for other organs of interest. An overarching goal is to enhance the rigor and reproducibility of small animal dMRI acquisitions and analyses, and thereby advance biomedical knowledge.

Imaging the structural connectome with hybrid MRI-microscopy tractography

Mapping how neurons are structurally wired into whole-brain networks can be challenging, particularly in larger brains where 3D microscopy is not available. Multi-modal datasets combining MRI and microscopy provide a solution, where high resolution but 2D microscopy can be complemented by whole-brain but lowresolution MRI. However, there lacks unified approaches to integrate and jointly analyse these multi-modal data in an insightful way. To address this gap, we introduce a data-fusion method for hybrid MRI-microscopy fibre orientation and connectome reconstruction. Specifically, we complement precise "in-plane" orientations from microscopy with "through-plane" information from MRI to construct 3D hybrid fibre orientations at resolutions far exceeding that of MRI whilst preserving microscopy's myelin specificity, resulting in superior fibre tracking. Our method is openly available, can be deployed on standard 2D microscopy, including different microscopy contrasts, and is species agnostic, facilitating neuroanatomical investigation in both animal models and human brains.

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.

The scientific value of tractography: accuracy vs usefulness

Tractography has emerged as a central tool for mapping the cerebral white matter architecture. However, its scientific value continues to be a subject of debate, given its inherent limitations in anatomical accuracy. This concise communication showcases key points of a debate held at the 2024 Tract-Anat Retreat, addressing the trade-offs between the accuracy and utility of tractography. While tractography remains constrained by limitations related to resolution, sensitivity, and validation, its usefulness and utility in areas such as surgical planning, disorder prediction, and the elucidation of brain development are emphasized. These perspectives highlight the necessity of context-specific interpretation, anatomically informed algorithms, and the continuous refinement of tractography workflows to achieve an optimal balance between accuracy and utility.

Fiber Microstructure Quantile (FMQ) Regression: A Novel Statistical Approach for Analyzing White Matter Bundles from Periphery to Core

The structural connections of the brain's white matter are critical for brain function. Diffusion MRI tractography enables the in-vivo reconstruction of white matter fiber bundles and the study of their relationship to covariates of interest, such as neurobehavioral or clinical factors. In this work, we introduce Fiber Microstructure Quantile (FMQ) Regression, a new statistical approach for studying the association between white matter fiber bundles and scalar factors (e.g., cognitive scores). Our approach analyzes tissue microstructure measures based on quantile-specific bundle regions . These regions are defined in a data-driven fashion according to the quantiles of fractional anisotropy (FA) of a population fiber bundle, which pools all individuals' bundles. The FA quantiles induce a natural subdivision of a fiber bundle, defining regions from the periphery (low FA) to the core (high FA) of the population fiber bundle. To investigate how fiber bundle tissue microstructure relates to covariates of interest, we employ the statistical technique of quantile regression. Unlike ordinary regression, which only models a conditional mean, quantile regression models the conditional quantiles of a response variable. This enables the proposed analysis, where a quantile regression is fitted for each quantile-specific bundle region. To demonstrate FMQ Regression, we perform an illustrative study in a large healthy young adult tractography dataset derived from the Human Connectome Project-Young Adult (HCP-YA), focusing on particular bundles expected to relate to particular aspects of cognition and motor function. In comparison with traditional regression analyses based on FA Mean and Automated Fiber Quantification (AFQ), we find that FMQ Regression provides a superior model fit with the lowest mean squared error. This demonstrates that FMQ Regression captures the relationship between scalar factors and white matter microstructure more effectively than the compared approaches. Our results suggest that FMQ Regression, which enables FA analysis in data-driven regions defined by FA quantiles, is more powerful for detecting brain-behavior associations than AFQ, which enables FA analysis in regions defined along the trajectory of a bundle. FMQ Regression finds significant brain-behavior associations in multiple bundles, including findings unique to males or to females. In both males and females, language performance is significantly associated with FA in the left arcuate fasciculus, with stronger associations in the bundle's periphery. In males only, memory performance is significantly associated with FA in the left uncinate fasciculus, particularly in intermediate regions of the bundle. In females only, motor performance is significantly associated with FA in the left and right corticospinal tracts, with a slightly lower relationship at the bundle periphery and a slightly higher relationship toward the bundle core. No significant relationships are found between executive function and cingulum bundle FA. Our study demonstrates that FMQ Regression is a powerful statistical approach that can provide insight into associations from bundle periphery to bundle core. Our results also identify several brain-behavior relationships unique to males or to females, highlighting the importance of considering sex differences in future research.

TractGraphFormer: Anatomically informed hybrid graph CNN-transformer network for interpretable sex and age prediction from diffusion MRI tractography

The relationship between brain connections and non-imaging phenotypes is increasingly studied using deep neural networks. However, the local and global properties of the brain's white matter networks are often overlooked in convolutional network design. We introduce TractGraphFormer, a hybrid Graph CNN-Transformer deep learning framework tailored for diffusion MRI tractography. This model leverages local anatomical characteristics and global feature dependencies of white matter structures. The Graph CNN module captures white matter geometry and grey matter connectivity to aggregate local features from anatomically similar white matter connections, while the Transformer module uses self-attention to enhance global information learning. Additionally, TractGraphFormer includes an attention module for interpreting predictive white matter connections. We apply TractGraphFormer to tasks of sex and age prediction. TractGraphFormer shows strong performance in large datasets of children (n = 9345) and young adults (n = 1065). Overall, our approach suggests that widespread connections in the WM are predictive of the sex and age of an individual. For each prediction task, consistent predictive anatomical tracts are identified across the two datasets. The proposed approach highlights the potential of integrating local anatomical information and global feature dependencies to improve prediction performance in machine learning with diffusion MRI tractography.

Tutorial: a guide to diffusion MRI and structural connectomics

Diffusion magnetic resonance imaging (dMRI) is a versatile imaging technique that has gained popularity thanks to its sensitive ability to measure displacement of water molecules within a living tissue on a micrometer scale. Although dMRI has been around since the early 1990s, its applications are constantly evolving, primarily regarding the inference of structural connectomics from nerve fiber trajectories. However, these applications require expertise in image processing and statistics, and it can be difficult for a newcomer to choose an appropriate pipeline to fit their research needs, not least because dMRI is such a flexible methodology that dozens of acquisition and analysis pipelines have been developed over the years. This introductory guide is designed for graduate students and researchers in the neuroscience community who are interested in integrating this new methodology regardless of their background in neuroimaging and computational tools. The guide provides a brief overview of the basic dMRI methodologies but focuses on its applications in neuroplasticity and connectomics. The guide starts with dMRI experimental designs and a complete step-by-step pipeline for structural connectomics. The following section covers the basics of dMRI, including parameters and clinical applications (apparent diffusion coefficient, mean diffusivity, fractional anisotropy and microscopic fractional anisotropy), as well as different approaches and models. The final section focuses on structural connectomics, covering subjects from fiber tracking (techniques, evaluation and limitations) to structural networks (constructing, analyzing and visualizing a network).

Deep learning based tractography with TractSeg in patients with hemispherotomy: Evaluation and refinement

Deep learning-based tractography implicitly learns anatomical prior knowledge that is required to resolve ambiguities inherent in traditional streamline tractography. TractSeg is a particularly widely used example of such an approach. Even though it has exclusively been trained on healthy subjects, a certain level of generalization to different pathologies has been demonstrated, and TractSeg is now increasingly used for clinical cases. We explore the limits of TractSeg by evaluating it on a unique dataset of 25 patients with epilepsy who underwent hemispherotomy, a type of surgery in which the two hemispheres are surgically separated. We compare results to those on 25 healthy controls who have been imaged with the same setup. We find that TractSeg generalizes remarkably well, given the severity of the abnormalities. However, to our knowledge, we are the first to document cases in which TractSeg erroneously reconstructs ("hallucinates") tracts that are known to have been surgically disconnected, and we found cases in which it implausibly continues tracts through obvious lesions. At the same time, TractSeg failed to reconstruct or undersegmented some tracts that are known to be preserved. We subsequently propose a refinement of TractSeg which aims to improve its applicability to data with pathologies, by using its Tract Orientation Maps as an anatomical prior in low-rank tensor approximation based tractography such that tracking is guaranteed to continue only where presence of the tract is directly supported by the data ("data fidelity"). We demonstrate that our extension not only eliminates hallucinated tracts and reconstructions within lesions, but that it also increases the ability to reconstruct the preserved tracts, and leads to more complete reconstructions even in healthy controls. Despite these advances, we recommend caution and manual quality control when applying deep learning based tractography to patient data.

White Matter Tract Crossing and Bottleneck Regions in the Fetal Brain

There is a growing interest in using diffusion MRI to study the white matter tracts and structural connectivity of the fetal brain. Recent progress in data acquisition and processing suggests that this imaging modality has a unique role in elucidating the normal and abnormal patterns of neurodevelopment in utero. However, there have been no efforts to quantify the prevalence of crossing tracts and bottleneck regions, important issues that have been investigated for adult brains. In this work, we determined the brain regions with crossing tracts and bottlenecks between 23 and 36 gestational weeks. We performed probabilistic tractography on 62 fetal brain scans and extracted a set of 51 distinct white matter tracts, which we grouped into 10 major tract bundle groups. We analyzed the results to determine the patterns of tract crossings and bottlenecks. Our results showed that 20%-25% of the white matter voxels included two or three crossing tracts. Bottlenecks were more prevalent. Between 75% and 80% of the voxels were characterized as bottlenecks, with more than 40% of the voxels involving four or more tracts. These results highlight the relevance of these regions to key developmental processes, specifically, the dispersion of projection fibers, the protracted growth of commissural pathways, and the emergence of association tracts that contribute to the formation of complex intersection regions. These developmental interactions lead to a high prevalence of crossing fibers and bottleneck areas, reflecting the intricate organization required for establishing structural and functional connectivity. Additionally, our results highlight the challenge of fetal brain tractography and structural connectivity assessment and call for innovative image acquisition and analysis methods to mitigate these problems.

Sex-Specific White Matter Abnormalities Across the Dynamic Pain Connectome in Neuropathic Pain: A Fixel-Based Analysis Study

A fundamental issue in neuroscience is a lack of understanding regarding the relationship between brain function and the white matter architecture that supports it. Individuals with chronic neuropathic pain (NP) exhibit functional abnormalities throughout brain networks collectively termed the "dynamic pain connectome" (DPC), including the default mode network (DMN), salience network, and ascending nociceptive and descending pain modulation systems. These functional abnormalities are often observed in a sex-dependent fashion. However, the enigmatic white matter structural features underpinning these functional networks and the relationship between structure and function/dysfunction in NP remain poorly understood. Here we used fixel-based analysis of diffusion weighted imaging data in 80 individuals (40 with NP [21 female, 19 male] and 40 sex- and age-matched healthy controls [HCs]) to evaluate white matter microstructure (fiber density [FD]), macrostructure (fiber bundle cross section) and combined microstructure and macrostructure (fiber density and cross section) within anatomical connections that support the DPC. We additionally examined whether there are sex-specific abnormalities in NP white matter structure. We performed fixel-wise and connection-specific mean analyses and found three main ways in which individuals with NP differed from HCs: (1) people with NP exhibited abnormally low FD and FDC within the corona radiata consistent with the ascending nociceptive pathway between the sensory thalamus and primary somatosensory cortex (S1). Furthermore, the entire sensory thalamus-S1 pathway exhibited abnormally low FD and FDC in people with NP, and this effect was driven by the females with NP; (2) females, but not males, with NP had abnormally low FD within the cingulum consistent with the right medial prefrontal cortex-posterior cingulate cortex DMN pathway; and (3) individuals with NP had higher connection-specific mean FDC than HCs in the anterior insula-temporoparietal junction and sensory thalamus-posterior insula pathways. However, sex-specific analyses did not corroborate these connection-specific findings in either females or males with NP. Our findings suggest that females with NP exhibit microstructural and macrostructural white matter abnormalities within the DPC networks including the ascending nociceptive system and DMN. We propose that aberrant white matter structure contributes to or is driven by functional abnormalities associated with NP. Our sex-specific findings highlight the utility and importance of using sex-disaggregated analyses to identify white matter abnormalities in clinical conditions such as chronic pain.

Changing the Paradigm for Tractography Segmentation in Neurosurgery: Validation of a Streamline-Based Approach

In glioma surgery, maximizing the extent of resection while preserving cognitive functions requires an understanding of the unique architecture of the white matter (WM) pathways of the single patient and of their spatial relationship with the tumor. Tractography enables the reconstruction of WM pathways, and bundle segmentation allows the identification of critical connections for functional preservation. This study evaluates the effectiveness of a streamline-based approach for bundle segmentation on a clinical dataset as compared to the traditional ROI-based approach. We performed bundle segmentation of the arcuate fasciculus, of its indirect anterior and posterior segments, and of the inferior fronto-occipital fasciculus in the healthy hemisphere of 25 high-grade glioma patients using both ROI- and streamline-based approaches. ROI-based segmentation involved manually delineating ROIs on MR anatomical images in Trackvis (V0.6.2.1). Streamline-based segmentations were performed in Tractome, which integrates clustering algorithms with the visual inspection and manipulation of streamlines. Shape analysis was conducted on each bundle. A paired t-test was performed on the irregularity measurement to compare segmentations achieved with the two approaches. Qualitative differences were evaluated through visual inspection. Streamline-based segmentation consistently yielded significantly lower irregularity scores (p < 0.001) compared to ROI-based segmentation for all the examined bundles, indicating more compact and accurate bundle reconstructions. Qualitative assessment identified common biases in ROI-based segmentations, such as the inclusion of anatomically implausible streamlines or streamlines with undesired trajectories. Streamline-based bundle segmentation with Tractome provides reliable and more accurate reconstructions compared to the ROI-based approach. By directly manipulating streamlines rather than relying on voxel-based ROI delineations, Tractome allows us to discern and discard implausible or undesired streamlines and to identify the course of WM bundles even when the anatomy is distorted by the lesion. These features make Tractome a robust tool for bundle segmentation in clinical contexts.

Midlife dynamics of white matter architecture in lexical production

We aimed to examine the white matter changes associated with lexical production difficulties, beginning in midlife with increased naming latencies. To delay lexical production decline, middle-aged adults may rely on domain-general and language-specific compensatory mechanisms proposed by the LARA model (Lexical Access and Retrieval in Aging). However, the white matter changes supporting these mechanisms remains largely unknown. Using data from the CAMCAN cohort, we employed an unsupervised and data-driven methodology to examine the relationships between diffusion-weighted imaging and lexical production. Our findings indicate that midlife is marked by alterations in brain structure within distributed dorsal, ventral, and anterior cortico-subcortical networks, marking the onset of lexical production decline around ages 53-54. Middle-aged adults may initially adopt a "semantic strategy" to compensate for lexical production challenges, but this strategy seems compromised later (ages 55-60) as semantic control declines. These insights underscore the interplay between domain-general and language-specific processes in the trajectory of lexical production performance in healthy aging and hint at potential biomarkers for language-related neurodegenerative pathologies.

Microstructure of the cerebellum and its afferent pathways underpins dystonia in myoclonus dystonia

BACKGROUND AND PURPOSE

Myoclonus dystonia due to a pathogenic variant in SGCE (MYC/DYT-SGCE) is a rare condition involving a motor phenotype associating myoclonus and dystonia. Dysfunction within the networks relying on the cortex, cerebellum, and basal ganglia was presumed to underpin the clinical manifestations. However, the microarchitectural abnormalities within these structures and related pathways are unknown. Here, we investigated the microarchitectural brain abnormalities related to the motor phenotype in MYC/DYT-SGCE.

METHODS

We used neurite orientation dispersion and density imaging, a multicompartment tissue model of diffusion neuroimaging, to compare microarchitectural neurite organization in MYC/DYT-SGCE patients and healthy volunteers (HVs). Neurite density index (NDI), orientation dispersion index (ODI), and isotropic volume fraction (ISOVF) were derived and correlated with the severity of motor symptoms. Fractional anisotropy (FA) and mean diffusivity (MD) derived from the diffusion tensor approach were also analyzed. In addition, we studied the pathways that correlated with motor symptom severity using tractography analysis.

RESULTS

Eighteen MYC/DYT-SGCE patients and 24 HVs were analyzed. MYC/DYT-SGCE patients showed an increase of ODI and a decrease of FA within their motor cerebellum. More severe dystonia was associated with lower ODI and NDI and higher FA within motor cerebellar cortex, as well as with lower NDI and higher ISOVF and MD within the corticopontocerebellar and spinocerebellar pathways. No association was found between myoclonus severity and diffusion parameters.

CONCLUSIONS

In MYC/DYT-SGCE, we found microstructural reorganization of the motor cerebellum. Structural change in the cerebellar afferent pathways that relay inputs from the spinal cord and the cerebral cortex were specifically associated with the severity of dystonia.

In Vivo visualization of white matter fiber tracts in the brainstem using low flip angle double echo 3D gradient echo imaging at 3T

BACKGROUND

White matter (WM) fiber tracts in the brainstem communicate with various regions in the cerebrum, cerebellum, and spinal cord. Clinically, small lesions, malformations, or histopathological changes in the brainstem can cause severe neurological disorders. A direct and non-invasive assessment approach could bring valuable information about the intricate anatomical variations of the white matter fiber tracts and nuclei. Although tractography from diffusion tensor imaging has been commonly used to map the WM fiber tracts connectivity, it is difficult to differentiate the complex WM tracts anatomically. Both high field MRI methods and ultrahigh-field MRI methods at 7T and 11.7 T have been used to enhance the contrast of WM fiber tracts. Despite their promising results, it is still challenging to achieve wide clinical adoption at 3T. In this study, we explored a clinically feasible method using a proton density weighted (PDW) 3D gradient echo (GRE) sequence to directly image the WM fiber tracts in the brainstem at 3T in vivo.

METHODS

We optimized a 3D high resolution, double echo, short TR, PDW GRE sequence on 5 healthy volunteers using a clinical 3T scanner to visualize the complicated anatomy of WM fiber tracts in the brain stem. Tissue properties including T1, proton density and T2* from in vivo quantitative MRI data were used for simulations to determine the optimal flip angle for the sequence. The visualization of multiple WM fiber tracts in the brainstem was assessed qualitatively and quantitatively using relative contrast and contrast-to-noise ratio (CNR). To improve the CNR, the final images were created by averaging over all echoes from two consecutive scans at the optimal flip angle. The results were compared to anatomical atlases and histology sections to identify the major fiber tracts. All the identified major fiber tracts were labeled on axial, sagittal and coronal slices.

RESULTS

The WM fiber tracts were found to have distinct hypointense signal throughout the brainstem and most of the major WM fiber tracts, such as the corticospinal tract, medial lemniscus, medial longitudinal fasciculus, and central tegmental tract, in the brainstem up to and including the thalamus were identified in all subjects. Both qualitative and quantitative evaluations showed that the 3° scan offered the best contrast for WM fiber tracts for a TR of 20 ms. The average over the first two echo times and two consecutive 3° scans gave a CNR of 47.8 ± 6.2 for the pyramidal tracts in particular and CNRs values greater than 6.5 ± 2.4 for the rest of the fiber tracts.

CONCLUSIONS

All the major fiber tracts in the brainstem could be visualized. Given the reasonably short scan time of 10 min at 3T, double echo PDW GRE sequence is a very practical approach for clinical adoption.

Developmental differences in canonical cortical networks: Insights from microstructure-informed tractography

In response to a growing interest in refining brain connectivity assessments, this study focuses on integrating white matter fiber-specific microstructural properties into structural connectomes. Spanning ages 8-19 years in a developmental sample, it explores age-related patterns of microstructure-informed network properties at both local and global scales. First, the diffusion-weighted signal fraction associated with each tractography-reconstructed streamline was constructed. Subsequently, the convex optimization modeling for microstructure-informed tractography (COMMIT) approach was employed to generate microstructure-informed connectomes from diffusion MRI data. To complete the investigation, network characteristics within eight functionally defined networks (visual, somatomotor, dorsal attention, ventral attention, limbic, fronto-parietal, default mode, and subcortical networks) were evaluated. The findings underscore a consistent increase in global efficiency across child and adolescent development within the visual, somatomotor, and default mode networks (p < 0.005). Additionally, mean strength exhibits an upward trend in the somatomotor and visual networks (p < 0.001). Notably, nodes within the dorsal and ventral visual pathways manifest substantial age-dependent changes in local efficiency, aligning with existing evidence of extended maturation in these pathways. The outcomes strongly support the notion of a prolonged developmental trajectory for visual association cortices. This study contributes valuable insights into the nuanced dynamics of microstructure-informed brain connectivity throughout different developmental stages.

Modeling the impact of MRI acquisition bias on structural connectomes: Harmonizing structural connectomes

One way to increase the statistical power and generalizability of neuroimaging studies is to collect data at multiple sites or merge multiple cohorts. However, this usually comes with site-related biases due to the heterogeneity of scanners and acquisition parameters, negatively impacting sensitivity. Brain structural connectomes are not an exception: Being derived from T1-weighted and diffusion-weighted magnetic resonance images, structural connectivity is impacted by differences in imaging protocol. Beyond minimizing acquisition parameter differences, removing bias with postprocessing is essential. In this work we create, from the exhaustive Human Connectome Project Young Adult dataset, a resampled dataset of different b-values and spatial resolutions, modeling a cohort scanned across multiple sites. After demonstrating the statistical impact of acquisition parameters on connectivity, we propose a linear regression with explicit modeling of b-value and spatial resolution, and validate its performance on separate datasets. We show that b-value and spatial resolution affect connectivity in different ways and that acquisition bias can be reduced using a linear regression informed by the acquisition parameters while retaining interindividual differences and hence boosting fingerprinting performance. We also demonstrate the generative potential of our model, and its generalization capability in an independent dataset reflective of typical acquisition practices in clinical settings.

Ground-truth effects in learning-based fiber orientation distribution estimation in neonatal brains

Diffusion Magnetic Resonance Imaging (dMRI) is a noninvasive method for depicting brain microstructure in vivo. Fiber orientation distributions (FODs) are mathematical representations extensively used to map white matter fiber configurations. Recently, FOD estimation with deep neural networks has seen growing success, in particular, those of neonates estimated with fewer diffusion measurements. These methods are mostly trained on target FODs reconstructed with multi-shell multi-tissue constrained spherical deconvolution (MSMT-CSD), which might not be the ideal ground truth for developing brains. Here, we investigate this hypothesis by training a state-of-the-art model based on the U-Net architecture on both MSMT-CSD and single-shell three-tissue constrained spherical deconvolution (SS3T-CSD). Our results suggest that SS3T-CSD might be more suited for neonatal brains, given that the ratio between single and multiple fiber-estimated voxels with SS3T-CSD is more realistic compared to MSMT-CSD. Additionally, increasing the number of input gradient directions significantly improves performance with SS3T-CSD over MSMT-CSD. Finally, in an age domain-shift setting, SS3T-CSD maintains robust performance across age groups, indicating its potential for more accurate neonatal brain imaging.

Pretreatment Brain White Matter Integrity Associated With Neuropathic Pain Relief and Changes in Temporal Summation of Pain Following Ketamine

Neuropathic pain (NP) is a prevalent condition often associated with heightened pain responsiveness suggestive of central sensitization. Neuroimaging biomarkers of treatment outcomes may help develop personalized treatment strategies, but white matter (WM) properties have been underexplored for this purpose. Here we assessed whether WM pathways of the default mode network (DMN: medial prefrontal cortex [mPFC], posterior cingulate cortex, and precuneus) and descending pain modulation system (periaqueductal gray [PAG]) are associated with ketamine analgesia and attenuated temporal summation of pain (TSP, reflecting central sensitization) in NP. We used a fixel-based analysis of diffusion-weighted imaging data to evaluate WM microstructure (fiber density [FD]) and macrostructure (fiber bundle cross-section) within the DMN and mPFC-PAG pathways in 70 individuals who underwent magnetic resonance imaging and TSP testing; 35 with NP who underwent ketamine treatment and 35 age- and sex-matched pain-free individuals. Individuals with NP were assessed before and 1 month after treatment; those with ≥30% pain relief were considered responders (n = 18), or otherwise as nonresponders (n = 17). We found that WM structure within the DMN and mPFC-PAG pathways did not differentiate responders from nonresponders. However, pretreatment FD in the anterior limb of the internal capsule correlated with pain relief (r=.48). Moreover, pretreatment FD in the DMN (left mPFC-precuneus/posterior cingulate cortex; r=.52) and mPFC-PAG (r=.42) negatively correlated with changes in TSP. This suggests that WM microstructure in the DMN and mPFC-PAG pathway is associated with the degree to which ketamine reduces central sensitization. Thus, fixel metrics of WM structure may hold promise to predict ketamine NP treatment outcomes. PERSPECTIVE: We used advanced fixel-based analyses of MRI diffusion-weighted imaging data to identify pretreatment WM microstructure associated with ketamine outcomes, including analgesia and markers of attenuated central sensitization. Exploring associations between brain structure and treatment outcomes could contribute to a personalized approach to treatment for individuals with NP.

Exploring White Matter Microstructure with Symptom Severity and Outcomes Following Deep Brain Stimulation in Tremor Syndromes

Background

Essential tremor (ET) and dystonic tremor (DT) are movement disorders that cause debilitating symptoms, significantly impacting daily activities and quality of life. A poor understanding of their pathophysiology, as well as the mediators of clinical outcomes following deep brain stimulation (DBS), highlights the need for biomarkers to accurately characterise and optimally treat patients.

Objectives

We assessed the white matter microstructure of pathways implicated in the pathophysiology and therapeutic intervention in a retrospective cohort of patients with DT (n = 17) and ET (n = 19). We aimed to identity associations between white matter microstructure, upper limb tremor severity, and tremor improvement following DBS.

Methods

A fixel-based analysis pipeline was implemented to investigate white matter microstructural metrics in the whole brain, cerebello-thalamic pathways and tracts connected to stimulation volumes following DBS. Associations with preoperative and postoperative severity were analysed within each disorder group and across combined disorder groups.

Results

DBS led to significant improvements in both groups. No group differences in stimulation positions were identified. When white matter microstructural data was aligned according to the maximally affected upper limb, increased fiber density, and combined fiber density & cross-section of fixels in the left cerebellum were associated with greater tremor severity across DT and ET patients. White matter microstructure did not show associations with postoperative changes in cerebello-thalamic pathways, or tracts connected to stimulation volumes.

Discussion

Diffusion changes of the cerebellum are associated with the severity of upper limb tremor and appear to overlap in essential or dystonic tremor disorders.

Streamline tractography of the fetal brain in utero with machine learning

Diffusion-weighted magnetic resonance imaging (dMRI) is the only non-invasive tool for studying white matter tracts and structural connectivity of the brain. These assessments rely heavily on tractography techniques, which reconstruct virtual streamlines representing white matter fibers. Much effort has been devoted to improving tractography methodology for adult brains, while tractography of the fetal brain has been largely neglected. Fetal tractography faces unique difficulties due to low dMRI signal quality, immature and rapidly developing brain structures, and paucity of reference data. To address these challenges, this work presents the first machine learning model, based on a deep neural network, for fetal tractography. The model input consists of five different sources of information: (1) Voxel-wise fiber orientation, inferred from a diffusion tensor fit to the dMRI signal; (2) Directions of recent propagation steps; (3) Global spatial information, encoded as normalized distances to keypoints in the brain cortex; (4) Tissue segmentation information; and (5) Prior information about the expected local fiber orientations supplied with an atlas. In order to mitigate the local tensor estimation error, a large spatial context around the current point in the diffusion tensor image is encoded using convolutional and attention neural network modules. Moreover, the diffusion tensor information at a hypothetical next point is included in the model input. Filtering rules based on anatomically constrained tractography are applied to prune implausible streamlines. We trained the model on manually-refined whole-brain fetal tractograms and validated the trained model on an independent set of 11 test scans with gestational ages between 23 and 36 weeks. Results show that our proposed method achieves superior performance across all evaluated tracts. The new method can significantly advance the capabilities of dMRI for studying normal and abnormal brain development in utero.

Associations between prenatal adversity and neonatal white matter microstructure on language outcomes at age 2 years

Background

Early life adversity is associated with microstructural alterations in white matter regions that subserve language. However, the mediating and moderating pathways between adversities experienced in utero and key neonatal white matter tracts including the corpus callosum (CC), superior longitudinal fasciculus (SLF), arcuate fasciculus (AF), inferior fronto- occipital fasciculus (IFOF), and uncinate on early language outcomes remains unknown.

Methods

This longitudinal study includes 160 neonates, oversampled for prenatal exposure to adversity, who underwent diffusion MRI (dMRI) in the first weeks of life. dMRI parameters were obtained using probabilistic tractography in FSL. Maternal Social Disadvantage and Psychosocial Stress was assessed throughout pregnancy. At age 2 years, the Bayley Scales of Infant and Toddler Development-III evaluated language outcomes. Linear regression, mediation, and moderation assessed associations between prenatal adversities and neonatal white matter on language outcomes.

Results

Prenatal exposure to Social Disadvantage (p<.001) and Maternal Psychosocial Stress (p<.001) were correlated with poorer language outcomes. When Social Disadvantage and maternal Psychosocial Stress were modeled simultaneously in relation to language outcomes, only Social Disadvantage was significant (p<.001). Independent of Social Disadvantage (p<.001), lower neonatal CC fractional anisotropy (FA) was related to poorer global (p=.02) and receptive (p=.02) language outcomes. CC FA did not mediate the association between Social Disadvantage and language outcomes (indirect effect 95% CIs -0.96-0.15), and there was no interaction between Social Disadvantage and CC FA on language outcomes (p>.05). Bilateral SLF/AF, IFOF, and uncinate were not significant (p>.05).

Conclusions

Prenatal exposure to Social Disadvantage and neonatal CC FA were independently related to language problems by age 2, with no evidence of mediating or moderating associations with language outcomes. These findings elucidate the early neural underpinnings of language development and suggest that the prenatal period may be an important time to provide poverty- reducing support to expectant mothers to promote offspring neurodevelopmental outcomes.

White matter tract crossing and bottleneck regions in the fetal brain

There is a growing interest in using diffusion MRI to study the white matter tracts and structural connectivity of the fetal brain. Recent progress in data acquisition and processing suggests that this imaging modality has a unique role in elucidating the normal and abnormal patterns of neurodevelopment in utero. However, there have been no efforts to quantify the prevalence of crossing tracts and bottleneck regions, important issues that have been extensively researched for adult brains. In this work, we determined the brain regions with crossing tracts and bottlenecks between 23 and 36 gestational weeks. We performed probabilistic tractography on 59 fetal brain scans and extracted a set of 51 distinct white tracts, which we grouped into 10 major tract bundle groups. We analyzed the results to determine the patterns of tract crossings and bottlenecks. Our results showed that 20-25% of the white matter voxels included two or three crossing tracts. Bottlenecks were more prevalent. Between 75-80% of the voxels were characterized as bottlenecks, with more than 40% of the voxels involving four or more tracts. The results of this study highlight the challenge of fetal brain tractography and structural connectivity assessment and call for innovative image acquisition and analysis methods to mitigate these problems.

Deep Normative Tractometry for Identifying Joint White Matter Macro- and Micro-structural Abnormalities in Alzheimer's Disease

This study introduces the Deep Normative Tractometry (DNT) framework, that encodes the joint distribution of both macrostructural and microstructural profiles of the brain white matter tracts through a variational autoencoder (VAE). By training on data from healthy controls, DNT learns the normative distribution of tract data, and can delineate along-tract micro- and macro-structural abnormalities. Leveraging a large sample size via generative pre-training, we assess DNT's generalizability using transfer learning on data from an independent cohort acquired in India. Our findings demonstrate DNT's capacity to detect widespread diffusivity abnormalities along tracts in mild cognitive impairment and Alzheimer's disease, aligning closely with results from the Bundle Analytics (BUAN) tractometry pipeline. By incorporating tract geometry information, DNT may be able to distinguish disease-related abnormalities in anisotropy from tract macrostructure, and shows promise in enhancing fine-scale mapping and detection of white matter alterations in neurodegenerative conditions.

Multimodal study of multilevel pulvino-temporal connections: a new piece in the puzzle of lexical retrieval networks

Advanced methods of imaging and mapping the healthy and lesioned brain have allowed for the identification of the cortical nodes and white matter tracts supporting the dual neurofunctional organization of language networks in a dorsal phonological and a ventral semantic stream. Much less understood are the anatomical correlates of the interaction between the two streams; one hypothesis being that of a subcortically mediated interaction, through crossed cortico-striato-thalamo-cortical and cortico-thalamo-cortical loops. In this regard, the pulvinar is the thalamic subdivision that has most regularly appeared as implicated in the processing of lexical retrieval. However, descriptions of its connections with temporal (language) areas remain scarce. Here we assess this pulvino-temporal connectivity using a combination of state-of-the-art techniques: white matter stimulation in awake surgery and postoperative diffusion MRI (n = 4), virtual dissection from the Human Connectome Project 3 and 7 T datasets (n = 172) and operative microscope-assisted post-mortem fibre dissection (n = 12). We demonstrate the presence of four fundamental fibre contingents: (i) the anterior component (Arnold's bundle proper) initially described by Arnold in the 19th century and destined to the anterior temporal lobe; (ii) the optic radiations-like component, which leaves the pulvinar accompanying the optical radiations and reaches the posterior basal temporal cortices; (iii) the lateral component, which crosses the temporal stem orthogonally and reaches the middle temporal gyrus; and (iv) the auditory radiations-like component, which leaves the pulvinar accompanying the auditory radiations to the superomedial aspect of the temporal operculum, just posteriorly to Heschl's gyrus. Each of those components might correspond to a different level of information processing involved in the lexical retrieval process of picture naming.

Probing Evidence of Cerebral White Matter Microstructural Disruptions in Ischemic Heart Disease Before and Following Cardiac Rehabilitation: A Diffusion Tensor MR Imaging Study

BACKGROUND

Ischemic heart disease (IHD) is linked to brain white matter (WM) breakdown but how age or disease effects WM integrity, and whether it is reversible using cardiac rehabilitation (CR), remains unclear.

PURPOSE

To assess the effects of brain aging, cardiovascular disease, and CR on WM microstructure in brains of IHD patients following a cardiac event.

STUDY TYPE

Retrospective.

POPULATION

Thirty-five IHD patients (9 females; mean age = 59 ± 8 years), 21 age-matched healthy controls (10 females; mean age = 59 ± 8 years), and 25 younger controls (14 females; mean age = 26 ± 4 years).

FIELD STRENGTH/SEQUENCE

3 T diffusion-weighted imaging with single-shot echo planar imaging acquired at 3 months and 9 months post-cardiac event.

ASSESSMENT

Tract-based spatial statistics (TBSS) and tractometry were used to compare fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) in cerebral WM between: 1) older and younger controls to distinguish age-related from disease-related WM changes; 2) IHD patients at baseline (pre-CR) and age-matched controls to investigate if cardiovascular disease exacerbates age-related WM changes; and 3) IHD patients pre-CR and post-CR to investigate the neuroplastic effect of CR on WM microstructure.

STATISTICAL TESTS

Two-sample unpaired t-test (age: older vs. younger controls; IHD: IHD pre-CR vs. age-matched controls). One-sample paired t-test (CR: IHD pre- vs. post-CR). Statistical threshold: P < 0.05 (FWE-corrected).

RESULTS

TBSS and tractometry revealed widespread WM changes in older controls compared to younger controls while WM clusters of decreased FA in the fornix and increased MD in body of corpus callosum were observed in IHD patients pre-CR compared to age-matched controls. Robust WM improvements (increased FA, increased AD) were observed in IHD patients post-CR.

DATA CONCLUSION

In IHD, both brain aging and cardiovascular disease may contribute to WM disruptions. IHD-related WM disruptions may be favorably modified by CR.

LEVEL OF EVIDENCE

3 TECHNICAL EFFICACY: Stage 2.

Understanding Wellbeing Profiles According to White Matter Structural Connectivity Sub-types in Early Adolescents: The First Hundred Brains Cohort from the Longitudinal Adolescent Brain Study

Wellbeing is protective against the emergence of psychopathology. Neurobiological markers associated with mental wellbeing during adolescence are important to understand. Limited research has examined neural networks (white matter tracts) and mental wellbeing in early adolescence specifically. A cross-sectional diffusion tensor imaging analysis approach was conducted, from the Longitudinal Adolescent Brain study, First Hundred Brains cohort (N = 99; 46.5% female; Mage = 13.01, SD = 0.55). Participants completed self-report measures including wellbeing, quality-of-life, and psychological distress. Potential neurobiological profiles using fractional anisotropy, axial, and radial diffusivity were determined via a whole brain voxel-wise approach, and hierarchical cluster analysis of fractional anisotropy values, obtained from 21 major white matter tracts. Three cluster groups with significantly different neurobiological profiles were distinguished. No significant differences were found between the three cluster groups and measures of wellbeing, but two left lateralized significant associations between white matter tracts and wellbeing measures were found. These results provide preliminary evidence for potential neurobiological markers of mental health and wellbeing in early adolescence and should be tracked longitudinally to provide more detailed and robust findings.

White matter microstructural plasticity associated with educational intervention in reading disability

Children's reading progress typically slows during extended breaks in formal education, such as summer vacations. This stagnation can be especially concerning for children with reading difficulties or disabilities, such as dyslexia, because of the potential to exacerbate the skills gap between them and their peers. Reading interventions can prevent skill loss and even lead to appreciable gains in reading ability during the summer. Longitudinal studies relating intervention response to brain changes can reveal educationally relevant insights into rapid learning-driven brain plasticity. The current work focused on reading outcomes and white matter connections, which enable communication among the brain regions required for proficient reading. We collected reading scores and diffusion-weighted images at the beginning and end of summer for 41 children with reading difficulties who had completed either 1st or 2nd grade. Children were randomly assigned to either receive an intensive reading intervention (n = 26; Seeing Stars from Lindamood-Bell which emphasizes orthographic fluency) or be deferred to a wait-list group (n = 15), enabling us to analyze how white matter properties varied across a wide spectrum of skill development and regression trajectories. On average, the intervention group had larger gains in reading compared to the non-intervention group, who declined in reading scores. Improvements on a proximal measure of orthographic processing (but not other more distal reading measures) were associated with decreases in mean diffusivity within core reading brain circuitry (left arcuate fasciculus and left inferior longitudinal fasciculus) and increases in fractional anisotropy in the left corticospinal tract. Our findings suggest that responses to intensive reading instruction are related predominantly to white matter plasticity in tracts most associated with reading.

Deep Normative Tractometry for Identifying Joint White Matter Macro- and Micro-structural Abnormalities in Alzheimer's Disease

This study introduces the Deep Normative Tractometry (DNT) framework, that encodes the joint distribution of both macrostructural and microstructural profiles of the brain white matter tracts through a variational autoencoder (VAE). By training on data from healthy controls, DNT learns the normative distribution of tract data, and can delineate along-tract micro-and macro-structural abnormalities. Leveraging a large sample size via generative pre-training, we assess DNT's generalizability using transfer learning on data from an independent cohort acquired in India. Our findings demonstrate DNT's capacity to detect widespread diffusivity abnormalities along tracts in mild cognitive impairment and Alzheimer's disease, aligning closely with results from the Bundle Analytics (BUAN) tractometry pipeline. By incorporating tract geometry information, DNT may be able to distinguish disease-related abnormalities in anisotropy from tract macrostructure, and shows promise in enhancing fine-scale mapping and detection of white matter alterations in neurodegenerative conditions.

Fibre orientation atlas guided rapid segmentation of white matter tracts

Fibre tract delineation from diffusion magnetic resonance imaging (MRI) is a valuable clinical tool for neurosurgical planning and navigation, as well as in research neuroimaging pipelines. Several popular methods are used for this task, each with different strengths and weaknesses making them more or less suited to different contexts. For neurosurgical imaging, priorities include ease of use, computational efficiency, robustness to pathology and ability to generalise to new tracts of interest. Many existing methods use streamline tractography, which may require expert neuroimaging operators for setting parameters and delineating anatomical regions of interest, or suffer from as a lack of generalisability to clinical scans involving deforming tumours and other pathologies. More recently, data-driven approaches including deep-learning segmentation models and streamline clustering methods have improved reproducibility and automation, although they can require large amounts of training data and/or computationally intensive image processing at the point of application. We describe an atlas-based direct tract mapping technique called 'tractfinder', utilising tract-specific location and orientation priors. Our aim was to develop a clinically practical method avoiding streamline tractography at the point of application while utilising prior anatomical knowledge derived from only 10-20 training samples. Requiring few training samples allows emphasis to be placed on producing high quality, neuro-anatomically accurate training data, and enables rapid adaptation to new tracts of interest. Avoiding streamline tractography at the point of application reduces computational time, false positives and vulnerabilities to pathology such as tumour deformations or oedema. Carefully filtered training streamlines and track orientation distribution mapping are used to construct tract specific orientation and spatial probability atlases in standard space. Atlases are then transformed to target subject space using affine registration and compared with the subject's voxel-wise fibre orientation distribution data using a mathematical measure of distribution overlap, resulting in a map of the tract's likely spatial distribution. This work includes extensive performance evaluation and comparison with benchmark techniques, including streamline tractography and the deep-learning method TractSeg, in two publicly available healthy diffusion MRI datasets (from TractoInferno and the Human Connectome Project) in addition to a clinical dataset comprising paediatric and adult brain tumour scans. Tract segmentation results display high agreement with established techniques while requiring less than 3 min on average when applied to a new subject. Results also display higher robustness than compared methods when faced with clinical scans featuring brain tumours and resections. As well as describing and evaluating a novel proposed tract delineation technique, this work continues the discussion on the challenges surrounding the white matter segmentation task, including issues of anatomical definitions and the use of quantitative segmentation comparison metrics.

Diagnostic and Therapeutic Issues in Glioma Using Imaging Data: The Challenge of Numerical Twinning

Glial tumors represent the leading etiology of primary brain tumors. Their particularities lie in (i) their location in a highly functional organ that is difficult to access surgically, including for biopsy, and (ii) their rapid, anisotropic mode of extension, notably via the fiber bundles of the white matter, which further limits the possibilities of resection. The use of mathematical tools enables the development of numerical models representative of the oncotype, genotype, evolution, and therapeutic response of lesions. The significant development of digital technologies linked to high-resolution NMR exploration, coupled with the possibilities offered by AI, means that we can envisage the creation of digital twins of tumors and their host organs, thus reducing the use of physical sampling.

Reconstructing the somatotopic organization of the corticospinal tract remains a challenge for modern tractography methods

The corticospinal tract (CST) is a critically important white matter fiber tract in the human brain that enables control of voluntary movements of the body. The CST exhibits a somatotopic organization, which means that the motor neurons that control specific body parts are arranged in order within the CST. Diffusion magnetic resonance imaging (MRI) tractography is increasingly used to study the anatomy of the CST. However, despite many advances in tractography algorithms over the past decade, modern, state-of-the-art methods still face challenges. In this study, we compare the performance of six widely used tractography methods for reconstructing the CST and its somatotopic organization. These methods include constrained spherical deconvolution (CSD) based probabilistic (iFOD1) and deterministic (SD-Stream) methods, unscented Kalman filter (UKF) tractography methods including multi-fiber (UKF2T) and single-fiber (UKF1T) models, the generalized q-sampling imaging (GQI) based deterministic tractography method, and the TractSeg method. We investigate CST somatotopy by dividing the CST into four subdivisions per hemisphere that originate in the leg, trunk, hand, and face areas of the primary motor cortex. A quantitative and visual comparison is performed using diffusion MRI data (N = 100 subjects) from the Human Connectome Project. Quantitative evaluations include the reconstruction rate of the eight anatomical subdivisions, the percentage of streamlines in each subdivision, and the coverage of the white matter-gray matter (WM-GM) interface. CST somatotopy is further evaluated by comparing the percentage of streamlines in each subdivision to the cortical volumes for the leg, trunk, hand, and face areas. Overall, UKF2T has the highest reconstruction rate and cortical coverage. It is the only method with a significant positive correlation between the percentage of streamlines in each subdivision and the volume of the corresponding motor cortex. However, our experimental results show that all compared tractography methods are biased toward generating many trunk streamlines (ranging from 35.10% to 71.66% of total streamlines across methods). Furthermore, the coverage of the WM-GM interface in the largest motor area (face) is generally low (under 40%) for all compared tractography methods. Different tractography methods give conflicting results regarding the percentage of streamlines in each subdivision and the volume of the corresponding motor cortex, indicating that there is generally no clear relationship, and that reconstruction of CST somatotopy is still a large challenge. Overall, we conclude that while current tractography methods have made progress toward the well-known challenge of improving the reconstruction of the lateral projections of the CST, the overall problem of performing a comprehensive CST reconstruction, including clinically important projections in the lateral (hand and face areas) and medial portions (leg area), remains an important challenge for diffusion MRI tractography.

Whole-brain, gray, and white matter time-locked functional signal changes with simple tasks and model-free analysis

Recent studies have revealed the production of time-locked blood oxygenation level-dependent (BOLD) functional MRI (fMRI) signals throughout the entire brain in response to tasks, challenging the existence of sparse and localized brain functions and highlighting the pervasiveness of potential false negative fMRI findings. "Whole-brain" actually refers to gray matter, the only tissue traditionally studied with fMRI. However, several reports have demonstrated reliable detection of BOLD signals in white matter, which have previously been largely ignored. Using simple tasks and analyses, we demonstrate BOLD signal changes across the whole brain, in both white and gray matters, in similar manner to previous reports of whole brain studies. We investigated whether white matter displays time-locked BOLD signals across multiple structural pathways in response to a stimulus in a similar manner to the cortex. We find that both white and gray matter show time-locked activations across the whole brain, with a majority of both tissue types showing statistically significant signal changes for all task stimuli investigated. We observed a wide range of signal responses to tasks, with different regions showing different BOLD signal changes to the same task. Moreover, we find that each region may display different BOLD responses to different stimuli. Overall, we present compelling evidence that, just like all gray matter, essentially all white matter in the brain shows time-locked BOLD signal changes in response to multiple stimuli, challenging the idea of sparse functional localization and the prevailing wisdom of treating white matter BOLD signals as artifacts to be removed.

Statistical Learning Methods for Neuroimaging Data Analysis with Applications

The aim of this review is to provide a comprehensive survey of statistical challenges in neuroimaging data analysis, from neuroimaging techniques to large-scale neuroimaging studies and statistical learning methods. We briefly review eight popular neuroimaging techniques and their potential applications in neuroscience research and clinical translation. We delineate four themes of neuroimaging data and review major image processing analysis methods for processing neuroimaging data at the individual level. We briefly review four large-scale neuroimaging-related studies and a consortium on imaging genomics and discuss four themes of neuroimaging data analysis at the population level. We review nine major population-based statistical analysis methods and their associated statistical challenges and present recent progress in statistical methodology to address these challenges.

versaFlow: a versatile pipeline for resolution adapted diffusion MRI processing and its application to studying the variability of the PRIME-DE database

The lack of "gold standards" in Diffusion Weighted Imaging (DWI) makes validation cumbersome. To tackle this task, studies use translational analysis where results in humans are benchmarked against findings in other species. Non-Human Primates (NHP) are particularly interesting for this, as their cytoarchitecture is closely related to humans. However, tools used for processing and analysis must be adapted and finely tuned to work well on NHP images. Here, we propose versaFlow, a modular pipeline implemented in Nextflow, designed for robustness and scalability. The pipeline is tailored to in vivo NHP DWI at any spatial resolution; it allows for maintainability and customization. Processes and workflows are implemented using cutting-edge and state-of-the-art Magnetic Resonance Imaging (MRI) processing technologies and diffusion modeling algorithms, namely Diffusion Tensor Imaging (DTI), Constrained Spherical Deconvolution (CSD), and DIstribution of Anisotropic MicrOstructural eNvironments in Diffusion-compartment imaging (DIAMOND). Using versaFlow, we provide an in-depth study of the variability of diffusion metrics computed on 32 subjects from 3 sites of the Primate Data Exchange (PRIME-DE), which contains anatomical T1-weighted (T1w) and T2-weighted (T2w) images, functional MRI (fMRI), and DWI of NHP brains. This dataset includes images acquired over a range of resolutions, using single and multi-shell gradient samplings, on multiple scanner vendors. We perform a reproducibility study of the processing of versaFlow using the Aix-Marseilles site's data, to ensure that our implementation has minimal impact on the variability observed in subsequent analyses. We report very high reproducibility for the majority of metrics; only gamma distribution parameters of DIAMOND display less reproducible behaviors, due to the absence of a mechanism to enforce a random number seed in the software we used. This should be taken into consideration when future applications are performed. We show that the PRIME-DE diffusion data exhibits a great level of variability, similar or greater than results obtained in human studies. Its usage should be done carefully to prevent instilling uncertainty in statistical analyses. This hints at a need for sufficient harmonization in acquisition protocols and for the development of robust algorithms capable of managing the variability induced in imaging due to differences in scanner models and/or vendors.

Enhancing precision in human neuroscience

Human neuroscience has always been pushing the boundary of what is measurable. During the last decade, concerns about statistical power and replicability - in science in general, but also specifically in human neuroscience - have fueled an extensive debate. One important insight from this discourse is the need for larger samples, which naturally increases statistical power. An alternative is to increase the precision of measurements, which is the focus of this review. This option is often overlooked, even though statistical power benefits from increasing precision as much as from increasing sample size. Nonetheless, precision has always been at the heart of good scientific practice in human neuroscience, with researchers relying on lab traditions or rules of thumb to ensure sufficient precision for their studies. In this review, we encourage a more systematic approach to precision. We start by introducing measurement precision and its importance for well-powered studies in human neuroscience. Then, determinants for precision in a range of neuroscientific methods (MRI, M/EEG, EDA, Eye-Tracking, and Endocrinology) are elaborated. We end by discussing how a more systematic evaluation of precision and the application of respective insights can lead to an increase in reproducibility in human neuroscience.

Structural connectivity and its association with social connectedness in early adolescence

Adolescence is a critical period of social and neural development. Brain regions which process social information develop throughout adolescence as young people learn to navigate social environments. Studies investigating brain structural connectivity (indexed by white matter (WM) integrity), and social connectedness in adolescents have been limited until recently, with literature stemming mostly from adult samples, broad age ranges within adolescence or based on social network characteristics as opposed to social connectedness. This cross-sectional study of 12-year-olds (N = 73) explored the relationship between social connectedness (SCS) and structural connectivity in early adolescence, to gauge how this snapshot of WM development is associated with social behaviour. Whole brain voxel-wise diffusion tensor imaging was undertaken to determine correlations between SCS and fractional anisotropy (FA), radial (RD) and axial (AD) diffusivity of clusters within WM tracts. Significant negative relationships between FA and SCS scores were found in clusters within 11 WM tracts, with significant positive correlations between SCS and both RD and AD across clusters within 13 and 8 clusters, respectively. Clusters within the genu of the corpus callosum (CCgn) showed strong correlations for all three metrics, and regression models that included gender, age, and psychological distress, revealed SCS to be the only significant predictor of CCgn FA, RD and AD values. Overall, these findings suggest that those with lower social connectedness had a WM profile suggestive of reduced axonal density and/or coherence. Longitudinal research is needed to track such WM profiles during adolescent development and determine the associations with mental health and well-being outcomes.

Sex-specific brain microstructural reorganization in irritable bowel syndrome

ABSTRACT

Preliminary evidence suggests that there are sex differences in microstructural brain organization among individuals with irritable bowel syndrome (IBS). The aim of this study was to further investigate sex-dependent differences in brain microstructure and organization in a large sample of well-phenotyped participants with IBS compared with healthy controls. We hypothesized that female patients with IBS would show evidence for increased axonal strength and myelination within and between brain regions concerned with pain and sensory processing, when compared with males with IBS. We also hypothesized that female compared with male IBS subjects show greater levels of somatic awareness and sensory sensitivity consistent with multisystem sensory sensitivity. Diffusion tensor images and clinical assessments were obtained in 100 healthy controls (61 females) and 152 IBS (107 females) on a 3T Siemens Trio. Whole brain voxel-wise differences in fractional anisotropy, mean, radial and axial diffusivity, and track density as differences in somatic awareness and sensory sensitivity were assessed using the general linear model. Female compared with male IBS participants showed extensive microstructural alterations in sensorimotor, corticothalamic, and basal ganglia circuits involved in pain processing and integration of sensorimotor information. Together with the observed increases in symptom severity, somatic awareness, and sensory sensitivity, the findings support the hypotheses that the etiology and maintenance of symptoms in females with IBS may be driven by greater central sensitivity for multiple sensory stimuli.

Anatomically informed multi-level fiber tractography for targeted virtual dissection

OBJECTIVES

Diffusion-weighted MRI can assist preoperative planning by reconstructing the trajectory of eloquent fiber pathways, such as the corticospinal tract (CST). However, accurate reconstruction of the full extent of the CST remains challenging with existing tractography methods. We suggest a novel tractography algorithm exploiting unused fiber orientations to produce more complete and reliable results.

METHODS

Our novel approach, referred to as multi-level fiber tractography (MLFT), reconstructs fiber pathways by progressively considering previously unused fiber orientations at multiple levels of tract propagation. Anatomical priors are used to minimize the number of false-positive pathways. The MLFT method was evaluated on synthetic data and in vivo data by reconstructing the CST while compared to conventional tractography approaches.

RESULTS

The radial extent of MLFT reconstructions is comparable to that of probabilistic reconstruction: [Formula: see text] for the left and [Formula: see text] for the right hemisphere according to Wilcoxon test, while achieving significantly higher topography preservation compared to probabilistic tractography: [Formula: see text].

DISCUSSION

MLFT provides a novel way to reconstruct fiber pathways by adding the capability of including branching pathways in fiber tractography. Thanks to its robustness, feasible reconstruction extent and topography preservation, our approach may assist in clinical practice as well as in virtual dissection studies.

The structural connectivity of the human angular gyrus as revealed by microdissection and diffusion tractography

The angular gyrus (AG) has been described in numerous studies to be consistently activated in various functional tasks. The angular gyrus is a critical connector epicenter linking multiple functional networks due to its location in the posterior part of the inferior parietal cortex, namely at the junction between the parietal, temporal, and occipital lobes. It is thus crucial to identify the different pathways that anatomically connect this high-order association region to the rest of the brain. Our study revisits the three-dimensional architecture of the structural AG connectivity by combining state-of-the-art postmortem blunt microdissection with advanced in vivo diffusion tractography to comprehensively describe the association, projection, and commissural fibers that connect the human angular gyrus. AG appears as a posterior "angular stone" of associative connections belonging to mid- and long-range dorsal and ventral fibers of the superior and inferior longitudinal systems, respectively, to short-range parietal, occipital, and temporal fibers, including U-shaped fibers in the posterior transverse system. Thus, AG is at a pivotal dorso-ventral position reflecting its critical role in the different functional networks, particularly in language elaboration and spatial attention and awareness in the left and right hemispheres, respectively. We also reveal striatal, thalamic, and brainstem connections and a typical inter-hemispheric homotopic callosal connectivity supporting the suggested AG role in the integration of sensory input for modulating motor control and planning. The present description of AG's highly distributed wiring diagram may drastically improve intraoperative subcortical testing and post-operative neurologic outcomes related to surgery in and around the angular gyrus.

Fiber-specific structural properties relate to reading skills in children and adolescents

Recent studies suggest that the cross-sectional relationship between reading skills and white matter microstructure, as indexed by fractional anisotropy, is not as robust as previously thought. Fixel-based analyses yield fiber-specific micro- and macrostructural measures, overcoming several shortcomings of the traditional diffusion tensor model. We ran a whole-brain analysis investigating whether the product of fiber density and cross-section (FDC) related to single-word reading skills in a large, open, quality-controlled dataset of 983 children and adolescents ages 6-18. We also compared FDC between participants with (n = 102) and without (n = 570) reading disabilities. We found that FDC positively related to reading skills throughout the brain, especially in left temporoparietal and cerebellar white matter, but did not differ between reading proficiency groups. Exploratory analyses revealed that among metrics from other diffusion models - diffusion tensor imaging, diffusion kurtosis imaging, and neurite orientation dispersion and density imaging - only the orientation dispersion and neurite density indexes from NODDI were associated (inversely) with reading skills. The present findings further support the importance of left-hemisphere dorsal temporoparietal white matter tracts in reading. Additionally, these results suggest that future DWI studies of reading and dyslexia should be designed to benefit from advanced diffusion models, include cerebellar coverage, and consider continuous analyses that account for individual differences in reading skill.

White matter and sustained attention in children with attention/deficit-hyperactivity disorder: A longitudinal fixel-based analysis

Sustained attention is a cognitive function with known links to academic success and mental health disorders such as attention/deficit-hyperactivity disorder (ADHD). Several functional networks are critical to sustained attention, however the association between white matter maturation in tracts linking functional nodes and sustained attention in typical and atypical development is unknown. 309 diffusion-weighted imaging scans were acquired from 161 children and adolescents (80 ADHD, 81 control) at up to three timepoints over ages 9-14. A fixel-based analysis approach was used to calculate mean fiber density and fiber-bundle cross section in tracts of interest. Sustained attention was measured using omission errors and response time variability on the out-of-scanner sustained attention to response task. Linear mixed effects models examined associations of age, group and white matter metrics with sustained attention. Greater fiber density in the bilateral superior longitudinal fasciculus (SLF) I and right SLF II was associated with fewer attention errors in the control group only. In ADHD and control groups, greater fiber density in the left ILF and right thalamo-premotor pathway, as well as greater fiber cross-section in the left SLF I and II and right SLF III, was associated with better sustained attention. Relationships were consistent across the age span. Results suggest that greater axon diameter or number in the dorsal and middle SLF may facilitate sustained attention in neurotypical children but does not assist those with ADHD potentially due to disorder-related alterations in this region. Greater capacity for information transfer across the SLF was associated with attention maintenance in 9-14-year-olds regardless of diagnostic status, suggesting white matter macrostructure may also be important for attention maintenance. White matter and sustained attention associations were consistent across the longitudinal study, according with the stability of structural organization over this time. Future studies can investigate modifiability of white matter properties through ADHD medications.

Automatic segmentation of the core of the acoustic radiation in humans

Introduction

Acoustic radiation is one of the most important white matter fiber bundles of the human auditory system. However, segmenting the acoustic radiation is challenging due to its small size and proximity to several larger fiber bundles. TractSeg is a method that uses a neural network to segment some of the major fiber bundles in the brain. This study aims to train TractSeg to segment the core of acoustic radiation.

Methods

We propose a methodology to automatically extract the acoustic radiation from human connectome data, which is both of high quality and high resolution. The segmentation masks generated by TractSeg of nearby fiber bundles are used to steer the generation of valid streamlines through tractography. Only streamlines connecting the Heschl's gyrus and the medial geniculate nucleus were considered. These streamlines are then used to create masks of the core of the acoustic radiation that is used to train the neural network of TractSeg. The trained network is used to automatically segment the acoustic radiation from unseen images.

Results

The trained neural network successfully extracted anatomically plausible masks of the core of the acoustic radiation in human connectome data. We also applied the method to a dataset of 17 patients with unilateral congenital ear canal atresia and 17 age- and gender-paired controls acquired in a clinical setting. The method was able to extract 53/68 acoustic radiation in the dataset acquired with clinical settings. In 14/68 cases, the method generated fragments of the acoustic radiation and completely failed in a single case. The performance of the method on patients and controls was similar.

Discussion

In most cases, it is possible to segment the core of the acoustic radiations even in images acquired with clinical settings in a few seconds using a pre-trained neural network.

Leveraging manifold learning techniques to explore white matter anomalies: An application of the TractLearn pipeline in epilepsy

An accurate description of brain white matter anatomy in vivo remains a challenge. However, technical progress allows us to analyze structural variations in an increasingly sophisticated way. Current methods of processing diffusion MRI data now make it possible to correct some limiting biases. In addition, the development of statistical learning algorithms offers the opportunity to analyze the data from a new perspective. We applied newly developed tractography models to extract quantitative white matter parameters in a group of patients with chronic temporal lobe epilepsy. Furthermore, we implemented a statistical learning workflow optimized for the MRI diffusion data - the TractLearn pipeline - to model inter-individual variability and predict structural changes in patients. Finally, we interpreted white matter abnormalities in the context of several other parameters reflecting clinical status, as well as neuronal and cognitive functioning for these patients. Overall, we show the relevance of such a diffusion data processing pipeline for the evaluation of clinical populations. The "global to fine scale" funnel statistical approach proposed in this study also contributes to the understanding of neuroplasticity mechanisms involved in refractory epilepsy, thus enriching previous findings.

Anomalous and heterogeneous characteristics of the BOLD hemodynamic response function in white matter

Detailed knowledge of the BOLD hemodynamic response function (HRF) is crucial for accurate analyses and interpretation of functional MRI data. Considerable efforts have been made to characterize the HRF in gray matter (GM), but much less attention has been paid to BOLD effects in white matter (WM). However, several recent reports have demonstrated reliable detection and analyses of WM BOLD signals both after stimulation and in a resting state. WM and GM differ in composition, energy requirements, and blood flow, so their neurovascular couplings also may well be different. We aimed to derive a comprehensive characterization of the HRF in WM across a population, including accurate measurements of its shape and its variation along and between WM pathways, using resting-state fMRI acquisitions. Our results show that the HRF is significantly different between WM and GM. Features of the HRF, such as a prominent initial dip, show strong relationships with features of the tissue microstructure derived from diffusion imaging, and these relationships differ between WM and GM, consistent with BOLD signal fluctuations reflecting different energy demands and neurovascular couplings in tissues of different composition and function. We also show that the HRF varies in shape significantly along WM pathways and is different between different WM pathways, suggesting the temporal evolution of BOLD signals after an event vary in different parts of the WM. These features of the HRF in WM are especially relevant for interpretation of the biophysical basis of BOLD effects in WM.