Post mortem mapping of connectional anatomy for the validation of diffusion MRI

Translation of monosynaptic circuits underlying amygdala fMRI neurofeedback training

fMRI neurofeedback using autobiographical memory recall to upregulate the amygdala is associated with resting-state functional connectivity (rsFC) changes between the amygdala and the salience and default mode networks (SN and DMN, respectively). We hypothesize the existence of anatomical circuits underlying these rsFC changes. Using a cross-species brain parcellation, we identified in non-human primates locations homologous to the regions of interest (ROIs) from studies showing pre-to-post-neurofeedback changes in rsFC with the left amygdala. We injected bidirectional tracers in the basolateral, lateral, and central amygdala nuclei of adult macaques and used bright- and dark-field microscopy to identify cells and axon terminals in each ROI (SN: anterior cingulate, ventrolateral, and insular cortices; DMN: temporal pole, middle frontal gyrus, angular gyrus, precuneus, posterior cingulate cortex, parahippocampal gyrus, hippocampus, and thalamus). We also performed additional injections in specific ROIs to validate the results following amygdala injections and delineate potential disynaptic pathways. Finally, we used high-resolution diffusion MRI data from four post-mortem macaque brains and one in vivo human brain to translate our findings to the neuroimaging domain. Different amygdala nuclei had significant monosynaptic connections with all the SN and DMN ipsilateral ROIs. Amygdala connections with the DMN contralateral ROIs are disynaptic through the hippocampus and parahippocampal gyrus. Diffusion MRI in both species benefitted from using the ground-truth tracer data to validate its findings, as we identified false-negative ipsilateral and false-positive contralateral connectivity results. This study provides the foundation for future causal investigations of amygdala neurofeedback modulation of the SN and DMN through these anatomic connections.

Histology-guided MRI segmentation of brainstem nuclei critical to consciousness

While substantial progress has been made in mapping the connectivity of cortical networks responsible for conscious awareness, neuroimaging analysis of subcortical arousal networks that modulate arousal (i.e., wakefulness) has been limited by a lack of a robust segmentation procedures for brainstem arousal nuclei. Automated segmentation of brainstem arousal nuclei is an essential step toward elucidating the physiology of arousal in human consciousness and the pathophysiology of disorders of consciousness. We created a probabilistic atlas of brainstem arousal nuclei built on diffusion MRI scans of five ex vivo human brain specimens scanned at 750 μm isotropic resolution. Labels of arousal nuclei used to generate the probabilistic atlas were manually annotated with reference to nucleus-specific immunostaining in two of the five brain specimens. We then developed a Bayesian segmentation algorithm that utilizes the probabilistic atlas as a generative model and automatically identifies brainstem arousal nuclei in a resolution- and contrast-agnostic manner. The segmentation method displayed high accuracy in both healthy and lesioned in vivo T1 MRI scans and high test-retest reliability across both T1 and T2 MRI contrasts. Finally, we show that the segmentation algorithm can detect volumetric changes and differences in magnetic susceptibility within brainstem arousal nuclei in Alzheimer's disease and traumatic coma, respectively. We release the probabilistic atlas and Bayesian segmentation tool in FreeSurfer to advance the study of human consciousness and its disorders.

Diffusion Magnetic Resonance Imaging Tractography Guides Investigation of the Zona Incerta: A Novel Target for Deep Brain Stimulation

BACKGROUND

The zona incerta (ZI) is a subcortical structure primarily investigated in rodents that is implicated in various behaviors, ranging from motor control to survival-associated activities, partly due to its integration in multiple neural circuits. In the current study, we used diffusion magnetic resonance imaging tractography to segment the ZI and gain insight into its connectivity in various circuits in humans.

METHODS

We performed probabilistic tractography in 7T diffusion MRI on 178 participants from the Human Connectome Project to validate the ZI's anatomical subdivisions and their respective tracts. K-means clustering segmented the ZI based on each voxel's connectivity profile. We further characterized the connections of each ZI subregion using probabilistic tractography with each subregion as a seed.

RESULTS

We identified 2 dominant clusters that delineated the whole ZI into rostral and caudal subregions. The caudal ZI primarily connected with motor regions, while the rostral ZI received a topographic distribution of projections from prefrontal areas, notably the anterior cingulate and medial prefrontal cortices. We generated a probabilistic ZI atlas that was registered to a patient-participant's magnetic resonance imaging scan for placement of stereoencephalographic leads for electrophysiology-guided deep brain stimulation to treat their obsessive-compulsive disorder. Rostral ZI stimulation improved the patient's core symptoms (mean improvement 21%).

CONCLUSIONS

We present a tractography-based atlas of the rostral and caudal ZI subregions constructed using high-resolution diffusion magnetic resonance imaging from 178 healthy participants. Our work provides an anatomical foundation to explore the rostral ZI as a novel target for deep brain stimulation to treat refractory obsessive-compulsive disorder and other disorders associated with dysfunctional reward circuitry.

Establishing connectivity through microdissections of midbrain stimulation-related neural circuits

Comprehensive understanding of the neural circuits involving the ventral tegmental area is essential for elucidating the anatomofunctional mechanisms governing human behaviour, in addition to the therapeutic and adverse effects of deep brain stimulation for neuropsychiatric diseases. Although the ventral tegmental area has been targeted successfully with deep brain stimulation for different neuropsychiatric diseases, the axonal connectivity of the region is not fully understood. Here, using fibre microdissections in human cadaveric hemispheres, population-based high-definition fibre tractography and previously reported deep brain stimulation hotspots, we find that the ventral tegmental area participates in an intricate network involving the serotonergic pontine nuclei, basal ganglia, limbic system, basal forebrain and prefrontal cortex, which is implicated in the treatment of obsessive-compulsive disorder, major depressive disorder, Alzheimer's disease, cluster headaches and aggressive behaviours.

What has brain diffusion magnetic resonance imaging taught us about chronic primary pain: a narrative review

ABSTRACT

Chronic pain is a pervasive and debilitating condition with increasing implications for public health, affecting millions of individuals worldwide. Despite its high prevalence, the underlying neural mechanisms and pathophysiology remain only partly understood. Since its introduction 35 years ago, brain diffusion magnetic resonance imaging (MRI) has emerged as a powerful tool to investigate changes in white matter microstructure and connectivity associated with chronic pain. This review synthesizes findings from 58 articles that constitute the current research landscape, covering methods and key discoveries. We discuss the evidence supporting the role of altered white matter microstructure and connectivity in chronic primary pain conditions, highlighting the importance of studying multiple chronic pain syndromes to identify common neurobiological pathways. We also explore the prospective clinical utility of diffusion MRI, such as its role in identifying diagnostic, prognostic, and therapeutic biomarkers. Furthermore, we address shortcomings and challenges associated with brain diffusion MRI in chronic primary pain studies, emphasizing the need for the harmonization of data acquisition and analysis methods. We conclude by highlighting emerging approaches and prospective avenues in the field that may provide new insights into the pathophysiology of chronic pain and potential new therapeutic targets. Because of the limited current body of research and unidentified targeted therapeutic strategies, we are forced to conclude that further research is required. However, we believe that brain diffusion MRI presents a promising opportunity for enhancing our understanding of chronic pain and improving clinical outcomes.

Methodological considerations on diffusion MRI tractography in infants aged 0-2 years: a scoping review

Diffusion MRI (dMRI) enables studying the complex architectural organization of the brain's white matter (WM) through virtual reconstruction of WM fiber tracts (tractography). Despite the anticipated clinical importance of applying tractography to study structural connectivity and tract development during the critical period of rapid infant brain maturation, detailed descriptions on how to approach tractography in young infants are limited. Over the past two decades, tractography from infant dMRI has mainly been applied in research settings and focused on diffusion tensor imaging (DTI). Only few studies used techniques superior to DTI in terms of disentangling information on the brain's organizational complexity, including crossing fibers. While more advanced techniques may enhance our understanding of the intricate processes of normal and abnormal brain development and extensive knowledge has been gained from application on adult scans, their applicability in infants has remained underexplored. This may partially be due to the higher technical requirements versus the need to limit scan time in young infants. We review various previously described methodological practices for tractography in the infant brain (0-2 years-of-age) and provide recommendations to optimize advanced tractography approaches to enable more accurate reconstructions of the brain WM's complexity. IMPACT: Diffusion tensor imaging is the technique most frequently used for fiber tracking in the developing infant brain but is limited in capability to disentangle the complex white matter organization. Advanced tractography techniques allow for reconstruction of crossing fiber bundles to better reflect the brain's complex organization. Yet, they pose practical and technical challenges in the fast developing young infant's brain. Methods on how to approach advanced tractography in the young infant's brain have hardly been described. Based on a literature review, recommendations are provided to optimize tractography for the developing infant brain, aiming to advance early diagnosis and neuroprotective strategies.

Three-dimensional fiber orientation mapping of the human brain at micrometer resolution

The accurate measurement of three-dimensional (3D) fiber orientation in the brain is crucial for reconstructing fiber pathways and studying their involvement in neurological diseases. Comprehensive reconstruction of axonal tracts and small fascicles requires high-resolution technology beyond the ability of current in vivo imaging (e.g. diffusion magnetic resonance imaging). Optical imaging methods such as polarization-sensitive optical coherence tomography (PS-OCT) and polarization microscopy can quantify fiber orientation at micrometer resolution but have been limited to two-dimensional in-plane orientation or thin slices, preventing the comprehensive study of connectivity in 3D. In this work we present a novel method to quantify volumetric 3D orientation in full angular space with PS-OCT. We measure the polarization contrasts of the brain sample from two illumination angles of 0 and 15 degrees and apply a computational method that yields the 3D optic axis orientation and true birefringence. We further present 3D fiber orientation maps of entire coronal cerebrum sections and brainstem with 10 μm in-plane resolution, revealing unprecedented details of fiber configurations. We envision that our method will open a promising avenue towards large-scale 3D fiber axis mapping in the human brain as well as other complex fibrous tissues at microscopic level.

Micron-resolution fiber mapping in histology independent of sample preparation

Detailed knowledge of the brain's nerve fiber network is crucial for understanding its function in health and disease. However, mapping fibers with high resolution remains prohibitive in most histological sections because state-of-the-art techniques are incompatible with their preparation. Here, we present a micron-resolution light-scattering-based technique that reveals intricate fiber networks independent of sample preparation for extended fields of view. We uncover fiber structures in both label-free and stained, paraffin-embedded and deparaffinized, newly-prepared and archived, animal and human brain tissues - including whole-brain sections from the BigBrain atlas. We identify altered microstructures in demyelination and hippocampal neurodegeneration, and show key advantages over diffusion magnetic resonance imaging, polarization microscopy, and structure tensor analysis. We also reveal structures in non-brain tissues - including muscle, bone, and blood vessels. Our cost-effective, versatile technique enables studies of intricate fiber networks in any type of histological tissue section, offering a new dimension to neuroscientific and biomedical research.

Macaque Brainnetome Atlas: A multifaceted brain map with parcellation, connection, and histology

The rhesus macaque (Macaca mulatta) is a crucial experimental animal that shares many genetic, brain organizational, and behavioral characteristics with humans. A macaque brain atlas is fundamental to biomedical and evolutionary research. However, even though connectivity is vital for understanding brain functions, a connectivity-based whole-brain atlas of the macaque has not previously been made. In this study, we created a new whole-brain map, the Macaque Brainnetome Atlas (MacBNA), based on the anatomical connectivity profiles provided by high angular and spatial resolution ex vivo diffusion MRI data. The new atlas consists of 248 cortical and 56 subcortical regions as well as their structural and functional connections. The parcellation and the diffusion-based tractography were evaluated with invasive neuronal-tracing and Nissl-stained images. As a demonstrative application, the structural connectivity divergence between macaque and human brains was mapped using the Brainnetome atlases of those two species to uncover the genetic underpinnings of the evolutionary changes in brain structure. The resulting resource includes: (1) the thoroughly delineated Macaque Brainnetome Atlas (MacBNA), (2) regional connectivity profiles, (3) the postmortem high-resolution macaque diffusion and T2-weighted MRI dataset (Brainnetome-8), and (4) multi-contrast MRI, neuronal-tracing, and histological images collected from a single macaque. MacBNA can serve as a common reference frame for mapping multifaceted features across modalities and spatial scales and for integrative investigation and characterization of brain organization and function. Therefore, it will enrich the collaborative resource platform for nonhuman primates and facilitate translational and comparative neuroscience research.

Imaging of developing human brains with ex vivo PSOCT and dMRI

The human brain undergoes substantial developmental changes in the first five years of life. Particularly in the white matter, myelination of axons occurs near birth and continues at a rapid pace during the first 2 to 3 years. Diffusion MRI (dMRI) has revolutionized our understanding of developmental trajectories in white matter. However, the mm-resolution of in vivo techniques bears significant limitation in revealing the microstructure of the developing brain. Polarization sensitive optical coherence tomography (PSOCT) is a three-dimensional (3D) optical imaging technique that uses polarized light interferometry to target myelinated fiber tracts with micrometer resolution. Previous studies have shown that PSOCT contributes significantly to the elucidation of myelin content and quantification of fiber orientation in adult human brains. In this study, we utilized the PSOCT technique to study developing brains during the first 5 years of life in combination with ex vivo dMRI. The results showed that the optical properties of PSOCT quantitatively reveal the myelination process in young children. The imaging contrast of the optic axis orientation is a sensitive measure of fiber orientations in largely unmyelinated brains as young as 3-months-old. The micrometer resolution of PSOCT provides substantially enriched information about complex fiber networks and complements submillimeter dMRI. This new optical tool offers great potential to reveal the white matter structures in normal neurodevelopment and developmental disorders in unprecedented detail.

Structural connectivity matures along a sensorimotor-association connectional axis in youth

Childhood and adolescence are associated with protracted developmental remodeling of cortico-cortical structural connectivity. However, how heterochronous development in white matter structural connectivity spatially and temporally unfolds across the macroscale human connectome remains unknown. Leveraging non-invasive diffusion MRI data from both cross-sectional (N = 590) and longitudinal (baseline: N = 3,949; two-year follow-up: N = 3,155) developmental datasets, we found that structural connectivity development diverges along a pre-defined sensorimotor-association (S-A) connectional axis from ages 8.1 to 21.9 years. Specifically, we observed a continuum of developmental profiles that spans from an early childhood increase in connectivity strength in sensorimotor-sensorimotor connections to a late adolescent increase in association-association connectional strength. The S-A connectional axis also captured spatial variations in associations between structural connectivity and both higher-order cognition and general psychopathology. Together, our findings reveal a hierarchical axis in the development of structural connectivity across the human connectome.

Unveiling the axonal connectivity between the precuneus and temporal pole: Structural evidence from the cingulum pathways

Neuroimaging studies have consistently demonstrated concurrent activation of the human precuneus and temporal pole (TP), both during resting-state conditions and various higher-order cognitive functions. However, the precise underlying structural connectivity between these brain regions remains uncertain despite significant advancements in neuroscience research. In this study, we investigated the connectivity of the precuneus and TP by employing parcellation-based fiber micro-dissections in human brains and fiber tractography techniques in a sample of 1065 human subjects and a sample of 41 rhesus macaques. Our results demonstrate the connectivity between the posterior precuneus area POS2 and the areas 35, 36, and TG of the TP via the fifth subcomponent of the cingulum (CB-V) also known as parahippocampal cingulum. This finding contributes to our understanding of the connections within the posteromedial cortices, facilitating a more comprehensive integration of anatomy and function in both normal and pathological brain processes. PRACTITIONER POINTS: Our investigation delves into the intricate architecture and connectivity patterns of subregions within the precuneus and temporal pole, filling a crucial gap in our knowledge. We revealed a direct axonal connection between the posterior precuneus (POS2) and specific areas (35, 35, and TG) of the temporal pole. The direct connections are part of the CB-V pathway and exhibit a significant association with the cingulum, SRF, forceps major, and ILF. Population-based human tractography and rhesus macaque fiber tractography showed consistent results that support micro-dissection outcomes.

Volumetric and diffusion MRI abnormalities associated with dysarthria in multiple sclerosis

Up to half of all people with multiple sclerosis experience communication difficulties due to dysarthria, a disorder that impacts the motor aspects of speech production. Dysarthria in multiple sclerosis is linked to cerebellar dysfunction, disease severity and lesion load, but the neuroanatomical substrates of these symptoms remain unclear. In this study, 52 participants with multiple sclerosis and 14 age- and sex-matched healthy controls underwent structural and diffusion MRI, clinical assessment of disease severity and cerebellar dysfunction and a battery of motor speech tasks. Assessments of regional brain volume and white matter integrity, and their relationships with clinical and speech measures, were undertaken. White matter tracts of interest included the interhemispheric sensorimotor tract, cerebello-thalamo-cortical tract and arcuate fasciculus, based on their roles in motor and speech behaviours. Volumetric analyses were targeted to Broca's area, Wernicke's area, the corpus callosum, thalamus and cerebellum. Our results indicated that multiple sclerosis participants scored worse on all motor speech tasks. Fixel-based diffusion MRI analyses showed significant evidence of white matter tract atrophy in each tract of interest. Correlational analyses further indicated that higher speech naturalness-a perceptual measure of dysarthria-and lower reading rate were associated with axonal damage in the interhemispheric sensorimotor tract and left arcuate fasciculus in people with multiple sclerosis. Axonal damage in all tracts of interest also correlated with clinical scales sensitive to cerebellar dysfunction. Participants with multiple sclerosis had lower volumes of the thalamus and corpus callosum compared with controls, although no brain volumetrics correlated with measures of dysarthria. These findings indicate that axonal damage, particularly when measured using diffusion metrics, underpin dysarthria in multiple sclerosis.

A petavoxel fragment of human cerebral cortex reconstructed at nanoscale resolution

To fully understand how the human brain works, knowledge of its structure at high resolution is needed. Presented here is a computationally intensive reconstruction of the ultrastructure of a cubic millimeter of human temporal cortex that was surgically removed to gain access to an underlying epileptic focus. It contains about 57,000 cells, about 230 millimeters of blood vessels, and about 150 million synapses and comprises 1.4 petabytes. Our analysis showed that glia outnumber neurons 2:1, oligodendrocytes were the most common cell, deep layer excitatory neurons could be classified on the basis of dendritic orientation, and among thousands of weak connections to each neuron, there exist rare powerful axonal inputs of up to 50 synapses. Further studies using this resource may bring valuable insights into the mysteries of the human brain.

Evaluating backscattering polarized light imaging microstructural mapping capabilities through neural tissue and analogous phantom imaging

Significance

Knowledge of fiber microstructure and orientation in the brain is critical for many applications. Polarized light imaging (PLI) has been shown to have potential for better understanding neural fiber microstructure and directionality due to the anisotropy in myelin sheaths surrounding nerve fibers of the brain. Continuing to advance backscattering based PLI systems could provide a valuable avenue for in vivo neural imaging.

Aim

To assess the potential of backscattering PLI systems, the ability to resolve crossing fibers, and the sensitivity to fiber inclination and curvature are considered across different imaging wavelengths.

Approach

Investigation of these areas of relative uncertainty is undergone through imaging potential phantoms alongside analogous regions of interest in fixed ferret brain samples with a five-wavelength backscattering Mueller matrix polarimeter.

Results

Promising phantoms are discovered for which the retardance, diattenuation and depolarization mappings are derived from the Mueller matrix and studied to assess the sensitivity of this polarimeter configuration to fiber orientations and tissue structures.

Conclusions

Rich avenues for future study include further classifying this polarimeter's sensitivity to fiber inclination and fiber direction to accurately produce microstructural maps of neural tissue.

Over 30 Years of DiI Use for Human Neuroanatomical Tract Tracing: A Scoping Review

In the present study, we conducted a scoping review to provide an overview of the existing literature on the carbocyanine dye DiI, in human neuroanatomical tract tracing. The PubMed, Scopus, and Web of Science databases were systematically searched. We identified 61 studies published during the last three decades. While studies incorporated specimens across human life from the embryonic stage onwards, the majority of studies focused on adult human tissue. Studies that utilized peripheral nervous system (PNS) tissue were a minority, with the majority of studies focusing on the central nervous system (CNS). The most common topic of interest in previous tract tracing investigations was the connectivity of the visual pathway. DiI crystals were more commonly applied. Nevertheless, several studies utilized DiI in a paste or dissolved form. The maximum tracing distance and tracing speed achieved was, respectively, 70 mm and 1 mm/h. We identified studies that focused on optimizing tracing efficacy by varying parameters such as fixation, incubation temperature, dye re-application, or the application of electric fields. Additional studies aimed at broadening the scope of DiI use by assessing the utility of archival tissue and compatibility of tissue clearing in DiI applications. A combination of DiI tracing and immunohistochemistry in double-labeling studies have been shown to provide the means for assessing connectivity of phenotypically defined human CNS and PNS neuronal populations.

Pathophysiology in cortico-amygdala circuits and excessive aversion processing: the role of oligodendrocytes and myelination

Stress-related psychiatric illnesses, such as major depressive disorder, anxiety and post-traumatic stress disorder, present with alterations in emotional processing, including excessive processing of negative/aversive stimuli and events. The bidirectional human/primate brain circuit comprising anterior cingulate cortex and amygdala is of fundamental importance in processing emotional stimuli, and in rodents the medial prefrontal cortex-amygdala circuit is to some extent analogous in structure and function. Here, we assess the comparative evidence for: (i) Anterior cingulate/medial prefrontal cortex<->amygdala bidirectional neural circuits as major contributors to aversive stimulus processing; (ii) Structural and functional changes in anterior cingulate cortex<->amygdala circuit associated with excessive aversion processing in stress-related neuropsychiatric disorders, and in medial prefrontal cortex<->amygdala circuit in rodent models of chronic stress-induced increased aversion reactivity; and (iii) Altered status of oligodendrocytes and their oligodendrocyte lineage cells and myelination in anterior cingulate/medial prefrontal cortex<->amygdala circuits in stress-related neuropsychiatric disorders and stress models. The comparative evidence from humans and rodents is that their respective anterior cingulate/medial prefrontal cortex<->amygdala circuits are integral to adaptive aversion processing. However, at the sub-regional level, the anterior cingulate/medial prefrontal cortex structure-function analogy is incomplete, and differences as well as similarities need to be taken into account. Structure-function imaging studies demonstrate that these neural circuits are altered in both human stress-related neuropsychiatric disorders and rodent models of stress-induced increased aversion processing. In both cases, the changes include altered white matter integrity, albeit the current evidence indicates that this is decreased in humans and increased in rodent models. At the cellular-molecular level, in both humans and rodents, the current evidence is that stress disorders do present with changes in oligodendrocyte lineage, oligodendrocytes and/or myelin in these neural circuits, but these changes are often discordant between and even within species. Nonetheless, by integrating the current comparative evidence, this review provides a timely insight into this field and should function to inform future studies-human, monkey and rodent-to ascertain whether or not the oligodendrocyte lineage and myelination are causally involved in the pathophysiology of stress-related neuropsychiatric disorders.

A practical evaluation of measures derived from compressed sensing diffusion spectrum imaging

Diffusion Spectrum Imaging (DSI) using dense Cartesian sampling of q-space has been shown to provide important advantages for modeling complex white matter architecture. However, its adoption has been limited by the lengthy acquisition time required. Sparser sampling of q-space combined with compressed sensing (CS) reconstruction techniques has been proposed as a way to reduce the scan time of DSI acquisitions. However prior studies have mainly evaluated CS-DSI in post-mortem or non-human data. At present, the capacity for CS-DSI to provide accurate and reliable measures of white matter anatomy and microstructure in the living human brain remains unclear. We evaluated the accuracy and inter-scan reliability of 6 different CS-DSI schemes that provided up to 80% reductions in scan time compared to a full DSI scheme. We capitalized on a dataset of 26 participants who were scanned over eight independent sessions using a full DSI scheme. From this full DSI scheme, we subsampled images to create a range of CS-DSI images. This allowed us to compare the accuracy and inter-scan reliability of derived measures of white matter structure (bundle segmentation, voxel-wise scalar maps) produced by the CS-DSI and the full DSI schemes. We found that CS-DSI estimates of both bundle segmentations and voxel-wise scalars were nearly as accurate and reliable as those generated by the full DSI scheme. Moreover, we found that the accuracy and reliability of CS-DSI was higher in white matter bundles that were more reliably segmented by the full DSI scheme. As a final step, we replicated the accuracy of CS-DSI in a prospectively acquired dataset (n = 20, scanned once). Together, these results illustrate the utility of CS-DSI for reliably delineating in vivo white matter architecture in a fraction of the scan time, underscoring its promise for both clinical and research applications.

Differential functional organization of amygdala-medial prefrontal cortex networks in macaque and human

Over the course of evolution, the amygdala (AMG) and medial frontal cortex (mPFC) network, involved in behavioral adaptation, underwent structural changes in the old-world monkey and human lineages. Yet, whether and how the functional organization of this network differs remains poorly understood. Using resting-state functional magnetic resonance imagery, we show that the functional connectivity (FC) between AMG nuclei and mPFC regions differs between humans and awake macaques. In humans, the AMG-mPFC FC displays U-shaped pattern along the corpus callosum: a positive FC with the ventromedial prefrontal (vmPFC) and anterior cingulate cortex (ACC), a negative FC with the anterior mid-cingulate cortex (MCC), and a positive FC with the posterior MCC. Conversely, in macaques, the negative FC shifted more ventrally at the junction between the vmPFC and the ACC. The functional organization divergence of AMG-mPFC network between humans and macaques might help understanding behavioral adaptation abilities differences in their respective socio-ecological niches.

Eddy current-induced artifact correction in high b-value ex vivo human brain diffusion MRI with dynamic field monitoring

PURPOSE

To investigate whether spatiotemporal magnetic field monitoring can correct pronounced eddy current-induced artifacts incurred by strong diffusion-sensitizing gradients up to 300 mT/m used in high b-value diffusion-weighted (DW) EPI.

METHODS

A dynamic field camera equipped with 16 1 H NMR field probes was first used to characterize field perturbations caused by residual eddy currents from diffusion gradients waveforms in a 3D multi-shot EPI sequence on a 3T Connectom scanner for different gradient strengths (up to 300 mT/m), diffusion directions, and shots. The efficacy of dynamic field monitoring-based image reconstruction was demonstrated on high-gradient strength, submillimeter resolution whole-brain ex vivo diffusion MRI. A 3D multi-shot image reconstruction framework was developed that incorporated the nonlinear phase evolution measured with the dynamic field camera.

RESULTS

Phase perturbations in the readout induced by residual eddy currents from strong diffusion gradients are highly nonlinear in space and time, vary among diffusion directions, and interfere significantly with the image encoding gradients, changing the k-space trajectory. During the readout, phase modulations between odd and even EPI echoes become non-static and diffusion encoding direction-dependent. Superior reduction of ghosting and geometric distortion was achieved with dynamic field monitoring compared to ghosting reduction approaches such as navigator- and structured low-rank-based methods or MUSE followed by image-based distortion correction with the FSL tool "eddy."

CONCLUSION

Strong eddy current artifacts characteristic of high-gradient strength DW-EPI can be well corrected with dynamic field monitoring-based image reconstruction.

Advancements in Diffusion MRI Tractography for Neurosurgery

ABSTRACT

Diffusion magnetic resonance imaging tractography is a noninvasive technique that enables the visualization and quantification of white matter tracts within the brain. It is extensively used in preoperative planning for brain tumors, epilepsy, and functional neurosurgical procedures such as deep brain stimulation. Over the past 25 years, significant advancements have been made in imaging acquisition, fiber direction estimation, and tracking methods, resulting in considerable improvements in tractography accuracy. The technique enables the mapping of functionally critical pathways around surgical sites to avoid permanent functional disability. When the limitations are adequately acknowledged and considered, tractography can serve as a valuable tool to safeguard critical white matter tracts and provides insight regarding changes in normal white matter and structural connectivity of the whole brain beyond local lesions. In functional neurosurgical procedures such as deep brain stimulation, it plays a significant role in optimizing stimulation sites and parameters to maximize therapeutic efficacy and can be used as a direct target for therapy. These insights can aid in patient risk stratification and prognosis. This article aims to discuss state-of-the-art tractography methodologies and their applications in preoperative planning and highlight the challenges and new prospects for the use of tractography in daily clinical practice.

Use of Post-mortem Brain Tissue in Investigations of Obsessive- Compulsive Disorder: A Systematic Review

BACKGROUND

Post-mortem examination of the brain is a key strategy to increase our understanding of the neurobiology of mental disorders. While extensive post-mortem research has been undertaken on some mental disorders, others appear to have been relatively neglected.

OBJECTIVE

The objective of the study was to conduct a systematic review of post-mortem research on obsessive-compulsive disorder (OCD).

METHODS

A systematic review was performed in accordance with PRISMA guidelines to provide an overview of quantitative, qualitative, or mixed methods primary research studies on OCD. Search platforms included NCBI Pubmed, SCOPUS, and Web of Science.

RESULTS

A total of 52 publications were found, and after the removal of works not meeting the inclusion criteria, six (6) peer-reviewed publications remained. These post-mortem studies have provided data on DNA methylation, cellular and molecular alterations, and gene expression profiling in brain areas associated with OCD.

DISCUSSION AND CONCLUSION

Included studies highlight the potential value of post-mortem brains from well-characterized individuals with OCD and suggest the need for additional work in this area.

Quantification of perineural satellitosis in pretreatment glioblastoma with structural MRI and a diffusion tensor imaging template

Background

Survival outcomes for glioblastoma (GBM) patients remain unfavorable, and tumor recurrence is often observed. Understanding the radiological growth patterns of GBM could aid in improving outcomes. This study aimed to examine the relationship between contrast-enhancing tumor growth direction and white matter, using an image registration and deformation strategy.

Methods

In GBM patients 2 pretreatment scans (diagnostic and neuronavigation) were gathered retrospectively, and coregistered to a template and diffusion tensor imaging (DTI) atlas. The GBM lesions were segmented and coregistered to the same space. Growth vectors were derived and divided into vector populations parallel (Φ = 0-20°) and perpendicular (Φ = 70-90°) to white matter. To test for statistical significance between parallel and perpendicular groups, a paired samples Student's t-test was performed. O6-methylguanine-DNA methyltransferase (MGMT) methylation status and its correlation to growth rate were also tested using a one-way ANOVA test.

Results

For 78 GBM patients (mean age 61 years ± 13 SD, 32 men), the included GBM lesions showed a predominant preference for perineural satellitosis (P < .001), with a mean percentile growth of 30.8% (95% CI: 29.6-32.0%) parallel (0° < |Φ| < 20°) to white matter. Perpendicular tumor growth with respect to white matter microstructure (70° < |Φ| < 90°) showed to be 22.7% (95% CI: 21.3-24.1%) of total tumor growth direction.

Conclusions

The presented strategy showed that tumor growth direction in pretreatment GBM patients correlated with white matter architecture. Future studies with patient-specific DTI data are required to verify the accuracy of this method prospectively to identify its usefulness as a clinical metric in pre and posttreatment settings.

Multiscale label-free imaging of myelin in human brain tissue with polarization-sensitive optical coherence tomography and birefringence microscopy

The combination of polarization-sensitive optical coherence tomography (PS-OCT) and birefringence microscopy (BRM) enables multiscale assessment of myelinated axons in postmortem brain tissue, and these tools are promising for the study of brain connectivity and organization. We demonstrate label-free imaging of myelin structure across the mesoscopic and microscopic spatial scales by performing serial-sectioning PS-OCT of a block of human brain tissue and periodically sampling thin sections for high-resolution imaging with BRM. In co-registered birefringence parameter maps, we observe good correspondence and demonstrate that BRM enables detailed validation of myelin (hence, axonal) organization, thus complementing the volumetric information content of PS-OCT.

The anatomy of the four streams of the prefrontal cortex. Preliminary evidence from a population based high definition tractography study

The model of the four streams of the prefrontal cortex proposes 4 streams of information: motor through Brodmann area (BA) 8, emotion through BA 9, memory through BA 10, and emotional-related sensory through BA 11. Although there is a surge of functional data supporting these 4 streams within the PFC, the structural connectivity underlying these neural networks has not been fully clarified. Here we perform population-based high-definition tractography using an averaged template generated from data of 1,065 human healthy subjects acquired from the Human Connectome Project to further elucidate the structural organization of these regions. We report the structural connectivity of BA 8 with BA 6, BA 9 with the insula, BA 10 with the hippocampus, BA 11 with the temporal pole, and BA 11 with the amygdala. The 4 streams of the prefrontal cortex are subserved by a structural neural network encompassing fibers of the anterior part of the superior longitudinal fasciculus-I and II, corona radiata, cingulum, frontal aslant tract, and uncinate fasciculus. The identified neural network of the four streams of the PFC will allow the comprehensive analysis of these networks in normal and pathological brain function.

Quantitative imaging of three-dimensional fiber orientation in the human brain via two illumination angles using polarization-sensitive optical coherence tomography

The accurate measurement of three-dimensional (3D) fiber orientation in the brain is crucial for reconstructing fiber pathways and studying their involvement in neurological diseases. Optical imaging methods such as polarization-sensitive optical coherence tomography (PS-OCT) provide important tools to directly quantify fiber orientation at micrometer resolution. However, brain imaging based on the optic axis by PS-OCT so far has been limited to two-dimensional in-plane orientation, preventing the comprehensive study of connectivity in 3D. In this work, we present a novel method to obtain the 3D fiber orientation in full angular space with only two illumination angles. We measure the optic axis orientation and the apparent birefringence by PS-OCT from a normal and a 15 deg tilted illumination, and then apply a computational method yielding the 3D optic axis orientation and true birefringence. We verify that our method accurately recovers a large range of through-plane orientations from -85 deg to 85 deg with a high angular precision. We further present 3D fiber orientation maps of entire coronal sections of human cerebrum and brainstem with 10 μm in-plane resolution, revealing unprecedented details of fiber configurations. We envision that further development of our method will open a promising avenue towards large-scale 3D fiber axis mapping in the human brain and other complex fibrous tissues at microscopic level.

The spatial extent of anatomical connections within the thalamus varies across the cortical hierarchy in humans and macaques

Each cortical area has a distinct pattern of anatomical connections within the thalamus, a central subcortical structure composed of functionally and structurally distinct nuclei. Previous studies have suggested that certain cortical areas may have more extensive anatomical connections that target multiple thalamic nuclei, which potentially allows them to modulate distributed information flow. However, there is a lack of quantitative investigations into anatomical connectivity patterns within the thalamus. Consequently, it remains unknown if cortical areas exhibit systematic differences in the extent of their anatomical connections within the thalamus. To address this knowledge gap, we used diffusion magnetic resonance imaging (dMRI) to perform brain-wide probabilistic tractography for 828 healthy adults from the Human Connectome Project. We then developed a framework to quantify the spatial extent of each cortical area's anatomical connections within the thalamus. Additionally, we leveraged resting-state functional MRI, cortical myelin, and human neural gene expression data to test if the extent of anatomical connections within the thalamus varied along the cortical hierarchy. Our results revealed two distinct corticothalamic tractography motifs: 1) a sensorimotor cortical motif characterized by focal thalamic connections targeting posterolateral thalamus, associated with fast, feed-forward information flow; and 2) an associative cortical motif characterized by diffuse thalamic connections targeting anteromedial thalamus, associated with slow, feed-back information flow. These findings were consistent across human subjects and were also observed in macaques, indicating cross-species generalizability. Overall, our study demonstrates that sensorimotor and association cortical areas exhibit differences in the spatial extent of their anatomical connections within the thalamus, which may support functionally-distinct cortico-thalamic information flow.

Self-supervised segmentation and characterization of fiber bundles in anatomic tracing data

Anatomic tracing is the gold standard tool for delineating brain connections and for validating more recently developed imaging approaches such as diffusion MRI tractography. A key step in the analysis of data from tracer experiments is the careful, manual charting of fiber trajectories on histological sections. This is a very time-consuming process, which limits the amount of annotated tracer data that are available for validation studies. Thus, there is a need to accelerate this process by developing a method for computer-assisted segmentation. Such a method must be robust to the common artifacts in tracer data, including variations in the intensity of stained axons and background, as well as spatial distortions introduced by sectioning and mounting the tissue. The method should also achieve satisfactory performance using limited manually charted data for training. Here we propose the first deeplearning method, with a self-supervised loss function, for segmentation of fiber bundles on histological sections from macaque brains that have received tracer injections. We address the limited availability of manual labels with a semi-supervised training technique that takes advantage of unlabeled data to improve performance. We also introduce anatomic and across-section continuity constraints to improve accuracy. We show that our method can be trained on manually charted sections from a single case and segment unseen sections from different cases, with a true positive rate of ~0.80. We further demonstrate the utility of our method by quantifying the density of fiber bundles as they travel through different white-matter pathways. We show that fiber bundles originating in the same injection site have different levels of density when they travel through different pathways, a finding that can have implications for microstructure-informed tractography methods. The code for our method is available at https://github.com/v-sundaresan/fiberbundle_seg_tracing.

Controversies and progress on standardization of large-scale brain network nomenclature

Progress in scientific disciplines is accompanied by standardization of terminology. Network neuroscience, at the level of macroscale organization of the brain, is beginning to confront the challenges associated with developing a taxonomy of its fundamental explanatory constructs. The Workgroup for HArmonized Taxonomy of NETworks (WHATNET) was formed in 2020 as an Organization for Human Brain Mapping (OHBM)-endorsed best practices committee to provide recommendations on points of consensus, identify open questions, and highlight areas of ongoing debate in the service of moving the field toward standardized reporting of network neuroscience results. The committee conducted a survey to catalog current practices in large-scale brain network nomenclature. A few well-known network names (e.g., default mode network) dominated responses to the survey, and a number of illuminating points of disagreement emerged. We summarize survey results and provide initial considerations and recommendations from the workgroup. This perspective piece includes a selective review of challenges to this enterprise, including (1) network scale, resolution, and hierarchies; (2) interindividual variability of networks; (3) dynamics and nonstationarity of networks; (4) consideration of network affiliations of subcortical structures; and (5) consideration of multimodal information. We close with minimal reporting guidelines for the cognitive and network neuroscience communities to adopt.

Cerebellar structural, astrocytic, and neuronal abnormalities in the SMNΔ7 mouse model of spinal muscular atrophy

Spinalmuscular atrophy (SMA) is a neuromuscular disease that affects as many as 1 in 6000 individuals at birth, making it the leading genetic cause of infant mortality. A growing number of studies indicate that SMA is a multi-system disease. The cerebellum has received little attention even though it plays an important role in motor function and widespread pathology has been reported in the cerebella of SMA patients. In this study, we assessed SMA pathology in the cerebellum using structural and diffusion magnetic resonance imaging, immunohistochemistry, and electrophysiology with the SMNΔ7 mouse model. We found a significant disproportionate loss in cerebellar volume, decrease in afferent cerebellar tracts, selective lobule-specific degeneration of Purkinje cells, abnormal lobule foliation and astrocyte integrity, and a decrease in spontaneous firing of cerebellar output neurons in the SMA mice compared to controls. Our data suggest that defects in cerebellar structure and function due to decreased survival motor neuron (SMN) levels impair the functional cerebellar output affecting motor control, and that cerebellar pathology should be addressed to achieve comprehensive treatment and therapy for SMA patients.

Spatially heterogeneous structure-function coupling in haemodynamic and electromagnetic brain networks

The relationship between structural and functional connectivity in the brain is a key question in connectomics. Here we quantify patterns of structure-function coupling across the neocortex, by comparing structural connectivity estimated using diffusion MRI with functional connectivity estimated using both neurophysiological (MEG-based) and haemodynamic (fMRI-based) recordings. We find that structure-function coupling is heterogeneous across brain regions and frequency bands. The link between structural and functional connectivity is generally stronger in multiple MEG frequency bands compared to resting state fMRI. Structure-function coupling is greater in slower and intermediate frequency bands compared to faster frequency bands. We also find that structure-function coupling systematically follows the archetypal sensorimotor-association hierarchy, as well as patterns of laminar differentiation, peaking in granular layer IV. Finally, structure-function coupling is better explained using structure-informed inter-regional communication metrics than using structural connectivity alone. Collectively, these results place neurophysiological and haemodynamic structure-function relationships in a common frame of reference and provide a starting point for a multi-modal understanding of structure-function coupling in the brain.

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.

Multiple routes of communication within the amygdala-mPFC network: A comparative approach in humans and macaques

The network formed by the amygdala (AMG) and the medial Prefrontal Cortex (mPFC), at the interface between our internal and external environment, has been shown to support some important aspects of behavioral adaptation. Whether and how the anatomo-functional organization of this network evolved across primates remains unclear. Here, we compared AMG nuclei morphological characteristics and their functional connectivity with the mPFC in humans and macaques to identify potential homologies and differences between these species. Based on selected studies, we highlight two subsystems within the AMG-mPFC circuits, likely involved in distinct temporal dynamics of integration during behavioral adaptation. We also show that whereas the mPFC displays a large expansion but a preserved intrinsic anatomo-functional organization, the AMG displays a volume reduction and morphological changes related to specific nuclei. We discuss potential commonalities and differences in the dialogue between AMG nuclei and mPFC in humans and macaques based on available data.

An open resource combining multi-contrast MRI and microscopy in the macaque brain

Understanding brain structure and function often requires combining data across different modalities and scales to link microscale cellular structures to macroscale features of whole brain organisation. Here we introduce the BigMac dataset, a resource combining in vivo MRI, extensive postmortem MRI and multi-contrast microscopy for multimodal characterisation of a single whole macaque brain. The data spans modalities (MRI and microscopy), tissue states (in vivo and postmortem), and four orders of spatial magnitude, from microscopy images with micrometre or sub-micrometre resolution, to MRI signals on the order of millimetres. Crucially, the MRI and microscopy images are carefully co-registered together to facilitate quantitative multimodal analyses. Here we detail the acquisition, curation, and first release of the data, that together make BigMac a unique, openly-disseminated resource available to researchers worldwide. Further, we demonstrate example analyses and opportunities afforded by the data, including improvement of connectivity estimates from ultra-high angular resolution diffusion MRI, neuroanatomical insight provided by polarised light imaging and myelin-stained histology, and the joint analysis of MRI and microscopy data for reconstruction of the microscopy-inspired connectome. All data and code are made openly available.

Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering

Myelinated axons (nerve fibers) efficiently transmit signals throughout the brain via action potentials. Multiple methods that are sensitive to axon orientations, from microscopy to magnetic resonance imaging, aim to reconstruct the brain's structural connectome. As billions of nerve fibers traverse the brain with various possible geometries at each point, resolving fiber crossings is necessary to generate accurate structural connectivity maps. However, doing so with specificity is a challenging task because signals originating from oriented fibers can be influenced by brain (micro)structures unrelated to myelinated axons. X-ray scattering can specifically probe myelinated axons due to the periodicity of the myelin sheath, which yields distinct peaks in the scattering pattern. Here, we show that small-angle X-ray scattering (SAXS) can be used to detect myelinated, axon-specific fiber crossings. We first demonstrate the capability using strips of human corpus callosum to create artificial double- and triple-crossing fiber geometries, and we then apply the method in mouse, pig, vervet monkey, and human brains. We compare results to polarized light imaging (3D-PLI), tracer experiments, and to outputs from diffusion MRI that sometimes fails to detect crossings. Given its specificity, capability of 3-dimensional sampling and high resolution, SAXS could serve as a ground truth for validating fiber orientations derived using diffusion MRI as well as microscopy-based methods. STATEMENT OF SIGNIFICANCE: To study how the nerve fibers in our brain are interconnected, scientists need to visualize their trajectories, which often cross one another. Here, we show the unique capacity of small-angle X-ray scattering (SAXS) to study these fiber crossings without use of labeling, taking advantage of SAXS's specificity to myelin - the insulating sheath that is wrapped around nerve fibers. We use SAXS to detect double and triple crossing fibers and unveil intricate crossings in mouse, pig, vervet monkey, and human brains. This non-destructive method can uncover complex fiber trajectories and validate other less specific imaging methods (e.g., MRI or microscopy), towards accurate mapping of neuronal connectivity in the animal and human brain.

Using light and X-ray scattering to untangle complex neuronal orientations and validate diffusion MRI

Disentangling human brain connectivity requires an accurate description of nerve fiber trajectories, unveiled via detailed mapping of axonal orientations. However, this is challenging because axons can cross one another on a micrometer scale. Diffusion magnetic resonance imaging (dMRI) can be used to infer axonal connectivity because it is sensitive to axonal alignment, but it has limited spatial resolution and specificity. Scattered light imaging (SLI) and small-angle X-ray scattering (SAXS) reveal axonal orientations with microscopic resolution and high specificity, respectively. Here, we apply both scattering techniques on the same samples and cross-validate them, laying the groundwork for ground-truth axonal orientation imaging and validating dMRI. We evaluate brain regions that include unidirectional and crossing fibers in human and vervet monkey brain sections. SLI and SAXS quantitatively agree regarding in-plane fiber orientations including crossings, while dMRI agrees in the majority of voxels with small discrepancies. We further use SAXS and dMRI to confirm theoretical predictions regarding SLI determination of through-plane fiber orientations. Scattered light and X-ray imaging can provide quantitative micrometer 3D fiber orientations with high resolution and specificity, facilitating detailed investigations of complex fiber architecture in the animal and human brain.

Mapping Human Brain Pathways: Challenges and Opportunities in the Integration of Scales

The human brain is composed of a complex web of pathways. Diffusion magnetic resonance (MR) tractography is a neuroimaging technique that relies on the principle of diffusion to reconstruct brain pathways. Its tractography is broadly applicable to a range of problems as it is amenable for study in individuals of any age and from any species. However, it is well known that this technique can generate biologically implausible pathways, especially in regions of the brain where multiple fibers cross. This review highlights potential misconnections in two cortico-cortical association pathways with a focus on the aslant tract and inferior frontal occipital fasciculus. The lack of alternative methods to validate observations from diffusion MR tractography means there is a need to develop new integrative approaches to trace human brain pathways. This review discusses integrative approaches in neuroimaging, anatomical, and transcriptional variation as having much potential to trace the evolution of human brain pathways.

Fiber enhancement and 3D orientation analysis in label-free two-photon fluorescence microscopy

Fluorescence microscopy can be exploited for evaluating the brain's fiber architecture with unsurpassed spatial resolution in combination with different tissue preparation and staining protocols. Differently from state-of-the-art polarimetry-based neuroimaging modalities, the quantification of fiber tract orientations from fluorescence microscopy volume images entails the application of specific image processing techniques, such as Fourier or structure tensor analysis. These, however, may lead to unreliable outcomes as they do not isolate myelinated fibers from the surrounding tissue. In this work, we describe a novel image processing pipeline that enables the computation of accurate 3D fiber orientation maps from both grey and white matter regions, exploiting the selective multiscale enhancement of tubular structures of varying diameters provided by a 3D implementation of the Frangi filter. The developed software tool can efficiently generate orientation distribution function maps at arbitrary spatial scales which may support the histological validation of modern diffusion-weighted magnetic resonance imaging tractography. Despite being tested here on two-photon scanning fluorescence microscopy images, acquired from tissue samples treated with a label-free technique enhancing the autofluorescence of myelinated fibers, the presented pipeline was developed to be employed on all types of 3D fluorescence images and fiber staining.

Eddy current-induced artifacts correction in high gradient strength diffusion MRI with dynamic field monitoring: demonstration in ex vivo human brain imaging

Purpose

To demonstrate the advantages of spatiotemporal magnetic field monitoring to correct eddy current-induced artifacts (ghosting and geometric distortions) in high gradient strength diffusion MRI (dMRI).

Methods

A dynamic field camera with 16 NMR field probes was used to characterize eddy current fields induced from diffusion gradients for different gradients strengths (up to 300 mT/m), diffusion directions, and shots in a 3D multi-shot EPI sequence on a 3T Connectom scanner. The efficacy of dynamic field monitoring-based image reconstruction was demonstrated on high-resolution whole brain ex vivo dMRI. A 3D multi-shot image reconstruction framework was informed with the actual nonlinear phase evolution measured with the dynamic field camera, thereby accounting for high-order eddy currents fields on top of the image encoding gradients in the image formation model.

Results

Eddy current fields from diffusion gradients at high gradient strength in a 3T Connectom scanner are highly nonlinear in space and time, inducing high-order spatial phase modulations between odd/even echoes and shots that are not static during the readout. Superior reduction of ghosting and geometric distortion was achieved with dynamic field monitoring compared to ghosting approaches such as navigator- and structured low-rank-based methods or MUSE, followed by image-based distortion correction with eddy. Improved dMRI analysis is demonstrated with diffusion tensor imaging and high-angular resolution diffusion imaging.

Conclusion

Strong eddy current artifacts characteristic of high gradient strength dMRI can be well corrected with dynamic field monitoring-based image reconstruction, unlike the two-step approach consisting of ghosting correction followed by geometric distortion reduction with eddy.

High-fidelity, high-spatial-resolution diffusion magnetic resonance imaging of ex vivo whole human brain at ultra-high gradient strength with structured low-rank echo-planar imaging ghost correction

Diffusion magnetic resonance imaging (dMRI) of whole ex vivo human brain specimens enables three-dimensional (3D) mapping of structural connectivity at the mesoscopic scale, providing detailed evaluation of fiber architecture and tissue microstructure at a spatial resolution that is difficult to access in vivo. To account for the short T2 and low diffusivity of fixed tissue, ex vivo dMRI is often acquired using strong diffusion-sensitizing gradients and multishot/segmented 3D echo-planar imaging (EPI) sequences to achieve high spatial resolution. However, the combination of strong diffusion-sensitizing gradients and multishot/segmented EPI readout can result in pronounced ghosting artifacts incurred by nonlinear spatiotemporal variations in the magnetic field produced by eddy currents. Such ghosting artifacts cannot be corrected with conventional correction solutions and pose a significant roadblock to leveraging human MRI scanners with ultrahigh gradients for ex vivo whole-brain dMRI. Here, we show that ghosting-correction approaches that correct for either polarity-related ghosting or shot-to-shot variations in a separate manner are suboptimal for 3D multishot diffusion-weighted EPI experiments in fixed human brain specimens using strong diffusion-sensitizing gradients on the 3-T Connectom MRI scanner, resulting in orientationally biased dMRI estimates. We apply a recently developed advanced k-space reconstruction method based on structured low-rank matrix (SLM) modeling that handles both polarity-related ghosting and shot-to-shot variation simultaneously, to mitigate artifacts in high-angular resolution multishot dMRI data acquired in several fixed human brain specimens at 0.7-0.8-mm isotropic spatial resolution using b-values up to 10,000 s/mm2 and gradient strengths up to 280 mT/m. We demonstrate the improved mapping of diffusion tensor imaging and fiber orientation distribution functions in key neuroanatomical areas distributed across the whole brain using SLM-based EPI ghost correction compared with alternative techniques.

Prefrontal-habenular microstructural impairments in human cocaine and heroin addiction

The habenula (Hb) is central to adaptive reward- and aversion-driven behaviors, comprising a hub for higher-order processing networks involving the prefrontal cortex (PFC). Despite an established role in preclinical models of cocaine addiction, the translational significance of the Hb and its connectivity with the PFC in humans is unclear. Using diffusion tractography, we detailed PFC structural connectivity with the Hb and two control regions, quantifying tract-specific microstructural features in healthy and cocaine-addicted individuals. White matter was uniquely impaired in PFC-Hb projections in both short-term abstainers and current cocaine users. Abnormalities in this tract further generalized to an independent sample of heroin-addicted individuals and were associated, in an exploratory analysis, with earlier onset of drug use across the addiction subgroups, potentially serving as a predisposing marker amenable for early intervention. Importantly, these findings contextualize a plausible PFC-Hb circuit in the human brain, supporting preclinical evidence for its impairment in cocaine addiction.

Scale matters: The nested human connectome

A comprehensive description of how neurons and entire brain regions are interconnected is fundamental for a mechanistic understanding of brain function and dysfunction. Neuroimaging has shaped the way to approaching the human brain’s connectivity on the basis of diffusion magnetic resonance imaging and tractography. At the same time, polarization, fluorescence, and electron microscopy became available, which pushed spatial resolution and sensitivity to the axonal or even to the synaptic level. New methods are mandatory to inform and constrain whole-brain tractography by regional, high-resolution connectivity data and local fiber geometry. Machine learning and simulation can provide predictions where experimental data are missing. Future interoperable atlases require new concepts, including high-resolution templates and directionality, to represent variants of tractography solutions and estimates of their accuracy.

Insights from the IronTract challenge: Optimal methods for mapping brain pathways from multi-shell diffusion MRI

Limitations in the accuracy of brain pathways reconstructed by diffusion MRI (dMRI) tractography have received considerable attention. While the technical advances spearheaded by the Human Connectome Project (HCP) led to significant improvements in dMRI data quality, it remains unclear how these data should be analyzed to maximize tractography accuracy. Over a period of two years, we have engaged the dMRI community in the IronTract Challenge, which aims to answer this question by leveraging a unique dataset. Macaque brains that have received both tracer injections and ex vivo dMRI at high spatial and angular resolution allow a comprehensive, quantitative assessment of tractography accuracy on state-of-the-art dMRI acquisition schemes. We find that, when analysis methods are carefully optimized, the HCP scheme can achieve similar accuracy as a more time-consuming, Cartesian-grid scheme. Importantly, we show that simple pre- and post-processing strategies can improve the accuracy and robustness of many tractography methods. Finally, we find that fiber configurations that go beyond crossing (e.g., fanning, branching) are the most challenging for tractography. The IronTract Challenge remains open and we hope that it can serve as a valuable validation tool for both users and developers of dMRI analysis methods.

Refractive-index matching enhanced polarization sensitive optical coherence tomography quantification in human brain tissue

The importance of polarization-sensitive optical coherence tomography (PS-OCT) has been increasingly recognized in human brain imaging. Despite the recent progress of PS-OCT in revealing white matter architecture and orientation, quantification of fine-scale fiber tracts in the human brain cortex has been a challenging problem, due to a low birefringence in the gray matter. In this study, we investigated the effect of refractive index matching by 2,2'-thiodiethanol (TDE) immersion on the improvement of PS-OCT measurements in ex vivo human brain tissue. We show that we can obtain fiber orientation maps of U-fibers that underlie sulci, as well as cortical fibers in the gray matter, including radial fibers in gyri and distinct layers of fibers exhibiting laminar organization. Further analysis shows that index matching reduces the noise in axis orientation measurements by 56% and 39%, in white and gray matter, respectively. Index matching also enables precise measurements of apparent birefringence, which was underestimated in the white matter by 82% but overestimated in the gray matter by 16% prior to TDE immersion. Mathematical simulations show that the improvements are primarily attributed to the reduction in the tissue scattering coefficient, leading to an enhanced signal-to-noise ratio in deeper tissue regions, which could not be achieved by conventional noise reduction methods.