Histological validation of DW-MRI tractography in human postmortem tissue

The neurobiology of aesthetic chills: How bodily sensations shape emotional experiences

The phenomenon of aesthetic chills-shivers and goosebumps associated with either rewarding or threatening stimuli-offers a unique window into the brain basis of conscious reward because of their universal nature and simultaneous subjective and physical counterparts. Elucidating the neural mechanisms underlying aesthetic chills can reveal fundamental insights about emotion, consciousness, and the embodied mind. What is the precise timing and mechanism of bodily feedback in emotional experience? How are conscious feelings and motivations generated from interoceptive predictions? What is the role of uncertainty and precision signaling in shaping emotions? How does the brain distinguish and balance processing of rewards versus threats? We review neuroimaging evidence and highlight key questions for understanding how bodily sensations shape conscious feelings. This research stands to advance models of brain-body interactions shaping affect and may lead to novel nonpharmacological interventions for disorders of motivation and pleasure.

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.

The non-decussating and decussating trigeminothalamic tracts in humans: A combination of connectome-based tractography and histological validation

BACKGROUND

Functional anatomical research proposed the existence of a bilateral trigeminal ascending system although the anatomy trajectories of the trigeminothalamic connections cranial to the pons remain largely elusive. This study therefore aimed to clarify the anatomical distributions of the trigeminothalamic connections in humans.

METHODS

Advanced deterministic tractography to an averaged template of diffusion tensor imaging data from 1065 subjects from the Human Connectome Project was used. Seedings masks were placed in Montreal Neurological Institute standard space by use of the BigBrain histological dataset. Waypoint masks of the sensory thalamus was obtained from the Brainnetome Atlas.

RESULTS

Tractography results were validated by use of the BigBrain histological dataset and Polarized Light Imaging microscopy. The trigeminothalamic tract bifurcated into a decussating ventral and a non-decussating dorsal tract. The ventral and dorsal tracts ascended to the contralateral thalamus and ipsilateral thalamus and reflected the ventral trigeminothalamic tract and the dorsal trigeminothalamic tract, respectively. The projection of the ventral trigeminothalamic tract and the dorsal trigeminothalamic tract to both thalami confirm the existence of a bilateral trigeminothalamic system in humans.

CONCLUSIONS

Because our study is strictly anatomical, no further conclusions can be drawn with regard to physiological functionality. Future research should explore if the dorsal trigeminothalamic tract and the ventral trigeminothalamic tract actually transmit signals from noxious stimuli, this offers potential in understanding and possibly treating neuropathology in the orofacial region.

Using mesoscopic tract-tracing data to guide the estimation of fiber orientation distributions in the mouse brain from diffusion MRI

Diffusion MRI (dMRI) tractography is the only tool for non-invasive mapping of macroscopic structural connectivity over the entire brain. Although it has been successfully used to reconstruct large white matter tracts in the human and animal brains, the sensitivity and specificity of dMRI tractography remained limited. In particular, the fiber orientation distributions (FODs) estimated from dMRI signals, key to tractography, may deviate from histologically measured fiber orientation in crossing fibers and gray matter regions. In this study, we demonstrated that a deep learning network, trained using mesoscopic tract-tracing data from the Allen Mouse Brain Connectivity Atlas, was able to improve the estimation of FODs from mouse brain dMRI data. Tractography results based on the network generated FODs showed improved specificity while maintaining sensitivity comparable to results based on FOD estimated using a conventional spherical deconvolution method. Our result is a proof-of-concept of how mesoscale tract-tracing data can guide dMRI tractography and enhance our ability to characterize brain connectivity.

COnstrained Reference frame diffusion TEnsor Correlation Spectroscopic (CORTECS) MRI: A practical framework for high-resolution diffusion tensor distribution imaging

High-resolution imaging studies have consistently shown that in cortical tissue water diffuses preferentially along radial and tangential orientations with respect to the cortical surface, in agreement with histology. These dominant orientations do not change significantly even if the relative contributions from microscopic water pools to the net voxel signal vary across experiments that use different diffusion times, b-values, TEs, and TRs. With this in mind, we propose a practical new framework for imaging non-parametric diffusion tensor distributions (DTDs) by constraining the microscopic diffusion tensors of the DTD to be diagonalized using the same orthonormal reference frame of the mesoscopic voxel. In each voxel, the constrained DTD (cDTD) is completely determined by the correlation spectrum of the microscopic principal diffusivities associated with the axes of the voxel reference frame. Consequently, all cDTDs are inherently limited to the domain of positive definite tensors and can be reconstructed efficiently using Inverse Laplace Transform methods. Moreover, the cDTD reconstruction can be performed using only data acquired efficiently with single diffusion encoding, although it also supports datasets with multiple diffusion encoding. In tissues with a well-defined architecture, such as the cortex, we can further constrain the cDTD to contain only cylindrically symmetric diffusion tensors and measure the 2D correlation spectra of principal diffusivities along the radial and tangential orientation with respect to the cortical surface. To demonstrate this framework, we perform numerical simulations and analyze high-resolution dMRI data from a fixed macaque monkey brain. We estimate 2D cDTDs in the cortex and derive, in each voxel, the marginal distributions of the microscopic principal diffusivities, the corresponding distributions of the microscopic fractional anisotropies and mean diffusivities along with their 2D correlation spectra to quantify the cDTD shape-size characteristics. Signal components corresponding to specific bands in these cDTD-derived spectra show high specificity to cortical laminar structures observed with histology. Our framework drastically simplifies the measurement of non-parametric DTDs in high-resolution datasets with mesoscopic voxel sizes much smaller than the radius of curvature of the underlying anatomy, e.g., cortical surface, and can be applied retrospectively to analyze existing diffusion MRI data from fixed cortical tissues.

High-resolution cortical MAP-MRI reveals areal borders and laminar substructures observed with histological staining

The variations in cellular composition and tissue architecture measured with histology provide the biological basis for partitioning the brain into distinct cytoarchitectonic areas and for characterizing neuropathological tissue alterations. Clearly, there is an urgent need to develop whole-brain neuroradiological methods that can assess cortical cyto- and myeloarchitectonic features non-invasively. Mean apparent propagator (MAP) MRI is a clinically feasible diffusion MRI method that quantifies efficiently and comprehensively the net microscopic displacements of water molecules diffusing in tissues. We investigate the sensitivity of high-resolution MAP-MRI to detecting areal and laminar variations in cortical cytoarchitecture and compare our results with observations from corresponding histological sections in the entire brain of a rhesus macaque monkey. High-resolution images of MAP-derived parameters, in particular the propagator anisotropy (PA), non-gaussianity (NG), and the return-to-axis probability (RTAP) reveal cortical area-specific lamination patterns in good agreement with the corresponding histological stained sections. In a few regions, the MAP parameters provide superior contrast to the five histological stains used in this study, delineating more clearly boundaries and transition regions between cortical areas and laminar substructures. Throughout the cortex, various MAP parameters can be used to delineate transition regions between specific cortical areas observed with histology and to refine areal boundaries estimated using atlas registration-based cortical parcellation. Using surface-based analysis of MAP parameters we quantify the cortical depth dependence of diffusion propagators in multiple regions-of-interest in a consistent and rigorous manner that is largely independent of the cortical folding geometry. The ability to assess cortical cytoarchitectonic features efficiently and non-invasively, its clinical feasibility, and translatability make high-resolution MAP-MRI a promising 3D imaging tool for studying whole-brain cortical organization, characterizing abnormal cortical development, improving early diagnosis of neurodegenerative diseases, identifying targets for biopsies, and complementing neuropathological investigations.

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.

Testing the suitability of neuroanatomical tracing method in human fetuses with long years of postmortem delay

PURPOSE

Human tissues in gross anatomical archives with long years of postmortem delays are considered suboptimal relative to recently fixed materials for neuroanatomical tracing studies, yet efficacy of neuroanatomical tracing on archival fetal tissues largely unexplored. We aimed to explore the suitability of human archival tissue in neuroanatomical tracing with lipophilic carbocyanine dyes.

METHODS

We used crystal and paste forms 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI) and analogues for neuroanatomical tracing on different peripheral nerves in 15-18-year archival old formalin-fixed human fetuses. We employed bright-field, fluorescent and confocal microscopy to visualize the peripheric nerve traces, spinal cord and vibratome cut sections. Fluorescent signal of the dyes on epineurium and on axonal membranes were visualized under fluorescence and confocal microscopes and performance of the dye diffusion was assessed by semi-quantitative image analysis.

RESULTS

We followed up seven lipophilic dye embeddings in 16-28 gestational week-old human fetuses (n = 4) with 16.75 ± 1.29-year postmortem delay. The mean distance of distally moved carbocyanine dye diffusion measured on epineurium was detected as 25.11 ± 9.1 mm.

CONCLUSION

Based on the results of 13 distinct studies performed neuroanatomical tracing with human tissues in the immediate postmortem hours or days, average traced distance was 16.32 ± 15.95 mm, and a 95% confidence interval lower limit of 4.9 mm and upper limit of 27.73 mm. The tracing distances we observed in our current study fall entirely within this confidence interval. To our awareness, this is the first report to demonstrate that specific neuroanatomical tracing presented in axonal membrane level on peripheral nerves is possible on gross anatomical repositories.

A critical review of connectome validation studies

Diffusion MRI tractography is the most widely used macroscale method for mapping connectomes in vivo. However, tractography is prone to various errors and biases, and thus tractography-derived connectomes require careful validation. Here, we critically review studies that have developed or utilized phantoms and tracer maps to validate tractography-derived connectomes, either quantitatively or qualitatively. We identify key factors impacting connectome reconstruction accuracy, including streamline seeding, propagation and filtering methods, and consider the strengths and limitations of state-of-the-art connectome phantoms and associated validation studies. These studies demonstrate the inherent limitations of current fiber orientation models and tractography algorithms and their impact on connectome reconstruction accuracy. Reconstructing connectomes with both high sensitivity and high specificity is challenging, given that some tractography methods can generate an abundance of spurious connections, while others can overlook genuine fiber bundles. We argue that streamline filtering can minimize spurious connections and potentially improve the biological plausibility of connectomes derived from tractography. We find that algorithmic choices such as the tractography seeding methodology, angular threshold, and streamline propagation method can substantially impact connectome reconstruction accuracy. Hence, careful application of tractography is necessary to reconstruct accurate connectomes. Improvements in diffusion MRI acquisition techniques will not necessarily overcome current tractography limitations without accompanying modeling and algorithmic advances.

The functional characterization of callosal connections

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The functional characterization of callosal connections is informed by anatomical data.

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Callosal connections play a conditional driving role depending on the brain state and behavioral demands.

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Callosal connections play a modulatory function, in addition to a driving role.

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The corpus callosum participates in learning and interhemispheric transfer of sensorimotor habits.

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The corpus callosum contributes to language processing and cognitive functions.

The brain operates through the synaptic interaction of distant neurons within flexible, often heterogeneous, distributed systems. Histological studies have detailed the connections between distant neurons, but their functional characterization deserves further exploration. Studies performed on the corpus callosum in animals and humans are unique in that they capitalize on results obtained from several neuroscience disciplines. Such data inspire a new interpretation of the function of callosal connections and delineate a novel road map, thus paving the way toward a general theory of cortico-cortical connectivity. Here we suggest that callosal axons can drive their post-synaptic targets preferentially when coupled to other inputs endowing the cortical network with a high degree of conditionality. This might depend on several factors, such as their pattern of convergence-divergence, the excitatory and inhibitory operation mode, the range of conduction velocities, the variety of homotopic and heterotopic projections and, finally, the state-dependency of their firing. We propose that, in addition to direct stimulation of post-synaptic targets, callosal axons often play a conditional driving or modulatory role, which depends on task contingencies, as documented by several recent studies.

Synchrotron X-ray micro-CT as a validation dataset for diffusion MRI in whole mouse brain

PURPOSE

To introduce synchrotron X-ray microcomputed tomography (microCT) and demonstrate its use as a natively isotropic, nondestructive, 3D validation modality for diffusion MRI in whole, fixed mouse brain.

METHODS

Postmortem diffusion MRI and microCT data were acquired of the same whole mouse brain. Diffusion data were processed using constrained spherical deconvolution. Synchrotron data were acquired at an isotropic voxel size of 1.17 μm. Structure tensor analysis was used to calculate fiber orientation distribution functions from the microCT data. A pipeline was developed to spatially register the 2 datasets in order to perform qualitative comparisons of fiber geometries represented by fiber orientation distribution functions. Fiber orientations from both modalities were used to perform whole-brain deterministic tractography to demonstrate validation of long-range white matter pathways.

RESULTS

Fiber orientation distribution functions were able to be extracted throughout the entire microCT dataset, with spatial registration to diffusion MRI simplified due to the whole brain extent of the microCT data. Fiber orientations and tract pathways showed good agreement between modalities.

CONCLUSION

Synchrotron microCT is a potentially valuable new tool for future multi-scale diffusion MRI validation studies, providing comparable value to optical histology validation methods while addressing some key limitations in data acquisition and ease of processing.

The Complex Hodological Architecture of the Macaque Dorsal Intraparietal Areas as Emerging from Neural Tracers and DW-MRI Tractography

In macaque monkeys, dorsal intraparietal areas are involved in several daily visuomotor actions. However, their border and sources of cortical afferents remain loosely defined. Combining retrograde histologic tracing and MRI diffusion-based tractography, we found a complex hodology of the dorsal bank of the intraparietal sulcus (db-IPS), which can be subdivided into a rostral intraparietal area PEip, projecting to the spinal cord, and a caudal medial intraparietal area MIP lacking such projections. Both include an anterior and a posterior sector, emerging from their ipsilateral, gradient-like connectivity profiles. As tractography estimations, we used the cross-sectional area of the white matter bundles connecting each area with other parietal and frontal regions, after selecting regions of interest (ROIs) corresponding to the injection sites of neural tracers. For most connections, we found a significant correlation between the proportions of cells projecting to all sectors of PEip and MIP along the continuum of the db-IPS and tractography. The latter also revealed “false positive” but plausible connections awaiting histologic validation.

Dedicated container for postmortem human brain ultra-high field magnetic resonance imaging

BACKGROUND

The emerging field of ultra-high field MRI (UHF-MRI, 7 Tesla and higher) provides the opportunity to image human brains at a higher resolution and with higher signal-to-noise ratios compared to the more widely available 1.5 and 3T scanners. Scanning postmortem tissue additionally allows for greatly increased scan times and fewer movement issues leading to improvements in image quality. However, typical postmortem neuroimaging routines involve placing the tissue within plastic bags that leave room for susceptibility artifacts from tissue-air interfaces, inadequate submersion, and leakage issues. To address these challenges in postmortem imaging, a custom-built nonferromagnetic container was developed that allows whole brain hemispheres to be scanned at sub-millimeter resolution within typical head-coils.

METHOD

The custom-built polymethylmethacrylaat container consists of a cylinder with a hemispheric side and a lid with valves on the adjacent side. This shape fits within common MR head-coils and allows whole hemispheres to be submerged and vacuum sealed within it reducing imaging artifacts that would otherwise arise at air-tissue boundaries. Two hemisphere samples were scanned on a Siemens 9.4T Magnetom MRI scanner. High resolution T2* weighted data was obtained with a custom 3D gradient echo (GRE) sequence and diffusion-weighted imaging (DWI) scans were obtained with a 3D kT-dSTEAM sequence along 48 directions.

RESULTS

The custom-built container proved to submerge and contain tissue samples effectively and showed no interferences with MR scanning acquisition. The 3D GRE sequence provided high resolution isotropic T2* weighted data at 250 μm which showed a clear visualization of gray and white matter structures. DWI scans allowed for dense reconstruction of structural white matter connections via tractography.

CONCLUSION

Using this custom-built container worked towards achieving high quality MR images of postmortem brain material. This procedure can have advantages over traditional schemes including utilization of a standardized protocol and the reduced likelihood of leakage. This methodology could be adjusted and used to improve typical postmortem imaging routines.

Comparison of diffusion MRI and CLARITY fiber orientation estimates in both gray and white matter regions of human and primate brain

Diffusion MRI (dMRI) represents one of the few methods for mapping brain fiber orientations non-invasively. Unfortunately, dMRI fiber mapping is an indirect method that relies on inference from measured diffusion patterns. Comparing dMRI results with other modalities is a way to improve the interpretation of dMRI data and help advance dMRI technologies. Here, we present methods for comparing dMRI fiber orientation estimates with optical imaging of fluorescently labeled neurofilaments and vasculature in 3D human and primate brain tissue cuboids cleared using CLARITY. The recent advancements in tissue clearing provide a new opportunity to histologically map fibers projecting in 3D, which represents a captivating complement to dMRI measurements. In this work, we demonstrate the capability to directly compare dMRI and CLARITY in the same human brain tissue and assess multiple approaches for extracting fiber orientation estimates from CLARITY data. We estimate the three-dimensional neuronal fiber and vasculature orientations from neurofilament and vasculature stained CLARITY images by calculating the tertiary eigenvector of structure tensors. We then extend CLARITY orientation estimates to an orientation distribution function (ODF) formalism by summing multiple sub-voxel structure tensor orientation estimates. In a sample containing part of the human thalamus, there is a mean angular difference of 19o±15o between the primary eigenvectors of the dMRI tensors and the tertiary eigenvectors from the CLARITY neurofilament stain. We also demonstrate evidence that vascular compartments do not affect the dMRI orientation estimates by showing an apparent lack of correspondence (mean angular difference = 49o±23o) between the orientation of the dMRI tensors and the structure tensors in the vasculature stained CLARITY images. In a macaque brain dataset, we examine how the CLARITY feature extraction depends on the chosen feature extraction parameters. By varying the volume of tissue over which the structure tensor estimates are derived, we show that orientation estimates are noisier with more spurious ODF peaks for sub-voxels below 30 µm3 and that, for our data, the optimal gray matter sub-voxel size is between 62.5 µm3 and 125 µm3. The example experiments presented here represent an important advancement towards robust multi-modal MRI-CLARITY comparisons.

7 Tesla MRI Followed by Histological 3D Reconstructions in Whole-Brain Specimens

Post mortem magnetic resonance imaging (MRI) studies on the human brain are of great interest for the validation of in vivo MRI. It facilitates a link between functional and anatomical information available from MRI in vivo and neuroanatomical knowledge available from histology/immunocytochemistry. However, linking in vivo and post mortem MRI to microscopy techniques poses substantial challenges. Fixation artifacts and tissue deformation of extracted brains, as well as co registration of 2D histology to 3D MRI volumes complicate direct comparison between modalities. Moreover, post mortem brain tissue does not have the same physical properties as in vivo tissue, and therefore MRI approaches need to be adjusted accordingly. Here, we present a pipeline in which whole-brain human post mortem in situ MRI is combined with subsequent tissue processing of the whole human brain, providing a 3-dimensional reconstruction via blockface imaging. To this end, we adapted tissue processing procedures to allow both post mortem MRI and subsequent histological and immunocytochemical processing. For MRI, tissue was packed in a susceptibility matched solution, tailored to fit the dimensions of the MRI coil. Additionally, MRI sequence parameters were adjusted to accommodate T1 and T2^∗ shortening, and scan time was extended, thereby benefiting the signal-to-noise-ratio that can be achieved using extensive averaging without motion artifacts. After MRI, the brain was extracted from the skull and subsequently cut while performing optimized blockface imaging, thereby allowing three-dimensional reconstructions. Tissues were processed for Nissl and silver staining, and co-registered with the blockface images. The combination of these techniques allows direct comparisons across modalities.

Mapping the trigeminal root entry zone and its pontine fibre distribution patterns

Introduction

Recently, an additional trigeminothalamic tract – the dorsal trigeminothalamic tract – has been described in human brainstems by our group next to the known ventral trigeminothalamic tract. As various elements of the trigeminal system are known to be organised in a somatotopic fashion, the question arose whether the fibres within the trigeminal root show specific distributions patterns in their contribution to the ventral trigeminothalamic tract and dorsal trigeminothalamic tract specifically.

Methods

This study investigated the arrangement of the fibres in the trigeminal root by combining various imaging methods in the pons of 11 post-mortem specimens. The pons were investigated by polarised light imaging (PLI) (n = 4; to quantify fibre orientation; 100 µm interslice distance), histochemical staining methods (n = 3; to visualise the internal myeloarchitecture; 60 µm) and ultra-high field, post-mortem magnetic resonance imaging (MRI) (n = 4; for tractography; 500 µm interslice distance).

Results

This study shows that the fibres, from the point where the trigeminal root enters the brainstem, are distinctly arranged by their contribution to the ventral trigeminothalamic tract and dorsal trigeminothalamic tract. This finding is supported by both post-mortem, ultra-high dMRI and different light microscopy techniques.

Conclusion

The data from this study suggest that the fibres in the superior half of the root contribute mainly to the ventral trigeminothalamic tract, whereas the fibres in the inferior half mainly contribute to the dorsal trigeminothalamic tract. Such a somatotopic organisation could possibly create new insights into the anatomical origin of trigeminal neuralgia and the clinical relevance of this somatotopic organisation should therefore be further explored.

Reduced white-matter integrity and lower speed of information processing in adolescents with mild and moderate neonatal hypoxic-ischaemic encephalopathy

INTRODUCTION

Studies have shown that adolescents with moderate hypoxic-ischaemic encephalopathy (HIE) may have specific cognitive deficits, especially reduced speed of information processing. The aim of our study was to confirm these earlier findings find out whether the degree of impairment in speed of information processing correlates with the degree of white-matter impairment as measured by diffusion tensor imaging (DTI).

METHODS

Thirty-three participants (mean age 18y 5mo, SD 12mo; 19 male) with mild or moderate HIE and 32 neurotypical adolescents (mean age 17y 10mo, SD 12mo, 18 male) completed a comprehensive neuropsychological battery measuring short-term memory, inhibition, speed of information processing, long-term visual and verbal memory. Fourteen participants also underwent structural MRI and DTI scans.

RESULTS

After controlling for age, gender and maternal education we found a significant effect of HIE on speed of information processing (F_{(2, 64)} = 3.51, p < .037, η² = 0.115), but not on other neuropsychological domains. Using tract-based spatial statistics we were also able to confirm a correlation between the degree of impairment in this cognitive domain and fractional anisotropy in several white-matter tracts.

CONCLUSIONS

The long-term cognitive outcome of moderate HIE includes reduced speed of information processing and is in part mediated by reduced integrity of major white-matter tracts.

How Human Is Human Connectional Neuroanatomy?

The structure of the human brain has been studied extensively. Despite all the knowledge accrued, direct information about connections, from origin to termination, in the human brain is extremely limited. Yet there is a widespread misperception that human connectional neuroanatomy is well-established and validated. In this article, we consider what is known directly about human structural and connectional neuroanatomy. Information on neuroanatomical connections in the human brain is derived largely from studies in non-human experimental models in which the entire connectional pathway, including origins, course, and terminations, is directly visualized. Techniques to examine structural connectivity in the human brain are progressing rapidly; nevertheless, our present understanding of such connectivity is limited largely to data derived from homological comparisons, particularly with non-human primates. We take the position that an in-depth and more precise understanding of human connectional neuroanatomy will be obtained by a systematic application of this homological approach.

Visualizing the trigeminovagal complex in the human medulla by combining ex-vivo ultra-high resolution structural MRI and polarized light imaging microscopy

A trigeminovagal complex, as described in some animals, could help to explain the effect of vagus nerve stimulation as a treatment for headache disorders. However, the existence of a trigeminovagal complex in humans remains unclear. This study, therefore investigated the existence of the trigeminovagal complex in humans. One post-mortem human brainstem was scanned at 11.7T to obtain structural (T1-weighted) and diffusion magnetic resonance images ((d)MR images). Post-processing of dMRI data provided track density imaging (TDI) maps to investigate white matter at a smaller resolution than the imaging resolution. To evaluate the reconstructed tracts, the MR-scanned brainstem and three additional brainstems were sectioned for polarized light imaging (PLI) microscopy. T1-weighted images showed hyperintense vagus medullar striae, coursing towards the dorsomedial aspect of the medulla. dMRI-, TDI- and PLI-images showed these striae to intersect the trigeminal spinal tract (sp5) in the lateral medulla. In addition, PLI images showed that a minority of vagus fibers separated from the vagus trajectory and joined the trigeminal spinal nucleus (Sp5) and the sp5. The course of the vagus tract in the rostral medulla was demonstrated in this study. This study shows that the trigeminal- and vagus systems interconnect anatomically at the level of the rostral medulla where the vagus fibers intersect with the Sp5 and sp5. Physiological and clinical utility of this newly identified interconnection is a topic for further research.

Diagnosis and prognosis of Alzheimer's disease using brain morphometry and white matter connectomes

Accurate, reliable prediction of risk for Alzheimer's disease (AD) is essential for early, disease-modifying therapeutics. Multimodal MRI, such as structural and diffusion MRI, is likely to contain complementary information of neurodegenerative processes in AD. Here we tested the utility of the multimodal MRI (T1-weighted structure and diffusion MRI), combined with high-throughput brain phenotyping-morphometry and structural connectomics-and machine learning, as a diagnostic tool for AD. We used, firstly, a clinical cohort at a dementia clinic (National Health Insurance Service-Ilsan Hospital [NHIS-IH]; N = 211; 110 AD, 64 mild cognitive impairment [MCI], and 37 cognitively normal with subjective memory complaints [SMC]) to test the diagnostic models; and, secondly, Alzheimer's Disease Neuroimaging Initiative (ADNI)-2 to test the generalizability. Our machine learning models trained on the morphometric and connectome estimates (number of features = 34,646) showed optimal classification accuracy (AD/SMC: 97% accuracy, MCI/SMC: 83% accuracy; AD/MCI: 97% accuracy) in NHIS-IH cohort, outperforming a benchmark model (FLAIR-based white matter hyperintensity volumes). In ADNI-2 data, the combined connectome and morphometry model showed similar or superior accuracies (AD/HC: 96%; MCI/HC: 70%; AD/MCI: 75% accuracy) compared with the CSF biomarker model (t-tau, p-tau, and Amyloid β, and ratios). In predicting MCI to AD progression in a smaller cohort of ADNI-2 (n = 60), the morphometry model showed similar performance with 69% accuracy compared with CSF biomarker model with 70% accuracy. Our comparisons of the classifiers trained on structural MRI, diffusion MRI, FLAIR, and CSF biomarkers showed the promising utility of the white matter structural connectomes in classifying AD and MCI in addition to the widely used structural MRI-based morphometry, when combined with machine learning.

Decoding the microstructural correlate of diffusion MRI

Diffusion imaging has evolved considerably over the past decade. While it provides valuable information about the structural connectivity at the macro- and mesoscopic scale, bridging the gap to the microstructure at the level of single nerve fibers poses an enormous challenge. This is particularly true for the human brain with its large size, its large white-matter volume and availability of histological techniques for studying human whole-brain sections and subsequent 3D reconstruction. Classic post-mortem techniques for studying the fiber architecture of the brain, such as myeloarchitectonic staining or dye tracing, are complemented by novel histological approaches, such as 3D polarized light imaging or optical coherence tomography, enabling unique insight into the fiber architecture from large fiber bundles within deep white matter to single nerve fibers in the cortex. The present review discusses the benefits and challenges of these latest developments in comparison with the classic techniques, with particular focus on the mutual exchange between in vivo and post-mortem diffusion imaging and post-mortem microstructural approaches for understanding the wiring of the brain across different scales.

LEARNING 3D WHITE MATTER MICROSTRUCTURE FROM 2D HISTOLOGY

Histological analysis is typically the gold standard for validating measures of tissue microstructure derived from magnetic resonance imaging (MRI) contrasts. However, most histological investigations are inherently 2-dimensional (2D), due to increased field-of-view, higher in-plane resolutions, ease of acquisition, decreased costs, and a large number of available contrasts compared to 3-dimensional (3D) analysis. Because of this, it would be of great interest to be able to learn the 3D tissue microstructure from 2D histology. In this study, we use diffusion MRI (dMRI) of a squirrel monkey brain and corresponding myelin stained sections in combination with a convolution neural network to learn the relationship between the 3D diffusion estimated axonal fiber orientation distributions and the 2D myelin stain. We find that we are able to estimate the 3D fiber distribution with moderate to high angular agreement with the ground truth (median angular correlation coefficients of 0.48 across the unseen slices). This network could be used to validate dMRI neuronal structural measurements in 3D, even if only 2D histology is available for validation. Generalization is possible to transfer this network to human stained sections to infer the 3D fiber distribution at resolutions currently unachievable with dMRI, which would allow diffusion fiber tractography at unprecedented resolutions. We envision the use of similar networks to learn other 3D microstructural measures from an array of potential common 2D histology contrasts.

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

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

Post-Mortem MRI and Histopathology in Neurologic Disease: A Translational Approach

In this review, combined post-mortem brain magnetic resonance imaging (MRI) and histology studies are highlighted, illustrating the relevance of translational approaches to define novel MRI signatures of neuropathological lesions in neuroinflammatory and neurodegenerative disorders. Initial studies combining post-mortem MRI and histology have validated various MRI sequences, assessing their sensitivity and specificity as diagnostic biomarkers in neurologic disease. More recent studies have focused on defining new radiological (bio)markers and implementing them in the clinical (research) setting. By combining neurological and neuroanatomical expertise with radiological development and pathological validation, a cycle emerges that allows for the discovery of novel MRI biomarkers to be implemented in vivo. Examples of this cycle are presented for multiple sclerosis, Alzheimer's disease, Parkinson's disease, and traumatic brain injury. Some applications have been shown to be successful, while others require further validation. In conclusion, there is much to explore with post-mortem MRI and histology studies, which can eventually be of high relevance for clinical practice.

The choice of embedding media affects image quality, tissue R2 * , and susceptibility behaviors in post-mortem brain MR microscopy at 7.0T

PURPOSE

The quality and precision of post-mortem MRI microscopy may vary depending on the embedding medium used. To investigate this, our study evaluated the impact of 5 widely used media on: (1) image quality, (2) contrast of high spatial resolution gradient-echo (T₁ and T₂ ^* -weighted) MR images, (3) effective transverse relaxation rate (R₂ ^* ), and (4) quantitative susceptibility measurements (QSM) of post-mortem brain specimens.

METHODS

Five formaldehyde-fixed brain slices were scanned using 7.0T MRI in: (1) formaldehyde solution (formalin), (2) phosphate-buffered saline (PBS), (3) deuterium oxide (D₂ O), (4) perfluoropolyether (Galden), and (5) agarose gel. SNR and contrast-to-noise ratii (SNR/CNR) were calculated for cortex/white matter (WM) and basal ganglia/WM regions. In addition, median R₂ ^* and QSM values were extracted from caudate nucleus, putamen, globus pallidus, WM, and cortical regions.

RESULTS

PBS, Galden, and agarose returned higher SNR/CNR compared to formalin and D₂ O. Formalin fixation, and its use as embedding medium for scanning, increased tissue R₂ ^* . Imaging with agarose, D₂ O, and Galden returned lower R₂ ^* values than PBS (and formalin). No major QSM offsets were observed, although spatial variance was increased (with respect to R₂ ^* behaviors) for formalin and agarose.

CONCLUSIONS

Embedding media affect gradient-echo image quality, R₂ ^* , and QSM in differing ways. In this study, PBS embedding was identified as the most stable experimental setup, although by a small margin. Agarose and Galden were preferred to formalin or D₂ O embedding. Formalin significantly increased R₂ ^* causing noisier data and increased QSM variance.

Optimization of macaque brain DMRI connectome by neuron tracing and myelin stain data

Accurate assessment of connectional anatomy of primate brains can be an important avenue to better understand the structural and functional organization of brains. To this end, numerous connectome projects have been initiated to create a comprehensive map of the connectional anatomy over a large spatial expanse. Tractography based on diffusion MRI (dMRI) data has been used as a tool by many connectome projects in that it is widely used to visualize axonal pathways and reveal microstructural features on living brains. However, the measures obtained from dMRI are indirect inference of microstructures. This intrinsic limitation reduces the reliability of dMRI in constructing connectomes for brains. In this work, we proposed a framework to increase the accuracy of constructing a dMRI-based connectome on macaque brains by integrating meso-scale connective information from tract-tracing data and micro-scale axonal orientation information from myelin stain data. Our results suggest that this integrative framework could advance the mapping accuracy of dMRI based connections and axonal pathways, and demonstrate the prospect of the proposed framework in constructing a large-scale connectome on living primate brains.

Ex vivo visualization of the trigeminal pathways in the human brainstem using 11.7T diffusion MRI combined with microscopy polarized light imaging

Classic anatomical atlases depict a contralateral hemispheral representation of each side of the face. Recently, however, a bilateral projection of each hemiface was hypothesized, based on animal studies that showed the coexistence of an additional trigeminothalamic tract sprouting from the trigeminal principal sensory nucleus that ascends ipsilaterally. This study aims to provide an anatomical substrate for the hypothesized bilateral projection. Three post-mortem human brainstems were scanned for anatomical and diffusion magnetic resonance imaging at 11.7T. The trigeminal tracts were delineated in each brainstem using track density imaging (TDI) and tractography. To evaluate the reconstructed tracts, the same brainstems were sectioned for polarized light imaging (PLI). Anatomical 11.7T MRI shows a dispersion of the trigeminal tract (tt) into a ventral and dorsal portion. This bifurcation was also seen on the TDI maps, tractography results and PLI images of all three specimens. Referring to a similar anatomic feature in primate brains, the dorsal and ventral tracts were named the dorsal and ventral trigeminothalamic tract (dtt and vtt), respectively. This study shows that both the dtt and vtt are present in humans, indicating that each hemiface has a bilateral projection, although the functional relevance of these tracts cannot be determined by the present anatomical study. If both tracts convey noxious stimuli, this could open up new insights into and treatments for orofacial pain in patients.

When tractography meets tracer injections: a systematic study of trends and variation sources of diffusion-based connectivity

Tractography is a powerful technique capable of non-invasively reconstructing the structural connections in the brain using diffusion MRI images, but the validation of tractograms is challenging due to lack of ground truth. Owing to recent developments in mapping the mouse brain connectome, high-resolution tracer injection-based axonal projection maps have been created and quickly adopted for the validation of tractography. Previous studies using tracer injections mainly focused on investigating the match in projections and optimal tractography protocols. Being a complicated technique, however, tractography relies on multiple stages of operations and parameters. These factors introduce large variabilities in tractograms, hindering the optimization of protocols and making the interpretation of results difficult. Based on this observation, in contrast to previous studies, in this work we focused on quantifying and ranking the amount of performance variation introduced by these factors. For this purpose, we performed over a million tractography experiments and studied the variability across different subjects, injections, anatomical constraints and tractography parameters. By using N-way ANOVA analysis, we show that all tractography parameters are significant and importantly performance variations with respect to the differences in subjects are comparable to the variations due to tractography parameters, which strongly underlines the importance of fully documenting the tractography protocols in scientific experiments. We also quantitatively show that inclusion of anatomical constraints is the most significant factor for improving tractography performance. Although this critical factor helps reduce false positives, our analysis indicates that anatomy-informed tractography still fails to capture a large portion of axonal projections.

A comparison of three fiber tract delineation methods and their impact on white matter analysis

Diffusion magnetic resonance imaging (dMRI) is an important method for studying white matter connectivity in the brain in vivo in both healthy and clinical populations. Improvements in dMRI tractography algorithms, which reconstruct macroscopic three-dimensional white matter fiber pathways, have allowed for methodological advances in the study of white matter; however, insufficient attention has been paid to comparing post-tractography methods that extract white matter fiber tracts of interest from whole-brain tractography. Here we conduct a comparison of three representative and conceptually distinct approaches to fiber tract delineation: 1) a manual multiple region of interest-based approach, 2) an atlas-based approach, and 3) a groupwise fiber clustering approach, by employing methods that exemplify these approaches to delineate the arcuate fasciculus, the middle longitudinal fasciculus, and the uncinate fasciculus in 10 healthy male subjects. We enable qualitative comparisons across methods, conduct quantitative evaluations of tract volume, tract length, mean fractional anisotropy, and true positive and true negative rates, and report measures of intra-method and inter-method agreement. We discuss methodological similarities and differences between the three approaches and the major advantages and drawbacks of each, and review research and clinical contexts for which each method may be most apposite. Emphasis is given to the means by which different white matter fiber tract delineation approaches may systematically produce variable results, despite utilizing the same input tractography and reliance on similar anatomical knowledge.

Tests of cortical parcellation based on white matter connectivity using diffusion tensor imaging

The cerebral cortex is conventionally divided into a number of domains based on cytoarchitectural features. Diffusion tensor imaging (DTI) enables noninvasive parcellation of the cortex based on white matter connectivity patterns. However, the correspondence between DTI-connectivity-based and cytoarchitectural parcellation has not been systematically established. In this study, we compared histological parcellation of New World monkey neocortex to DTI- connectivity-based classification and clustering in the same brains. First, we used supervised classification to parcellate parieto-frontal cortex based on DTI tractograms and the cytoarchitectural prior (obtained using Nissl staining). We performed both within and across sample classification, showing reasonable classification performance in both conditions. Second, we used unsupervised clustering to parcellate the cortex and compared the clusters to the cytoarchitectonic standard. We then explored the similarities and differences with several post-hoc analyses, highlighting underlying principles that drive the DTI-connectivity-based parcellation. The differences in parcellation between DTI-connectivity and Nissl histology probably represent both DTI's bias toward easily-tracked bundles and true differences between cytoarchitectural and connectivity defined domains. DTI tractograms appear to cluster more according to functional networks, rather than mapping directly onto cytoarchitectonic domains. Our results show that caution should be used when DTI-tractography classification, based on data from another brain, is used as a surrogate for cytoarchitectural parcellation.

Cortical parcellation based on structural connectivity: A case for generative models

One of the major challenges in systems neuroscience is to identify brain networks and unravel their significance for brain function -this has led to the concept of the 'connectome'. Connectomes are currently extensively studied in large-scale international efforts at multiple scales, and follow different definitions with respect to their connections as well as their elements. Perhaps the most promising avenue for defining the elements of connectomes originates from the notion that individual brain areas maintain distinct (long-range) connection profiles. These connectivity patterns determine the areas' functional properties and also allow for their anatomical delineation and mapping. This rationale has motivated the concept of connectivity-based cortex parcellation. In the past ten years, non-invasive mapping of human brain connectivity has led to immense advances in the development of parcellation techniques and their applications. Unfortunately, many of these approaches primarily aim for confirmation of well-known, existing architectonic maps and, to that end, unsuitably incorporate prior knowledge and frequently build on circular argumentation. Often, current approaches also tend to disregard the specific apertures of connectivity measurements, as well as the anatomical specificities of cortical areas, such as spatial compactness, regional heterogeneity, inter-subject variability, the multi-scaling nature of connectivity information, and potential hierarchical organisation. From a methodological perspective, however, a useful framework that regards all of these aspects in an unbiased way is technically demanding. In this commentary, we first outline the concept of connectivity-based cortex parcellation and discuss its prospects and limitations in particular with respect to structural connectivity. To improve reliability and efficiency, we then strongly advocate for connectivity-based cortex parcellation as a modelling approach; that is, an approximation of the data based on (model) parameter inference. As such, a parcellation algorithm can be formally tested for robustness -the precision of its predictions can be quantified and statistics about potential generalization of the results can be derived. Such a framework also allows the question of model constraints to be reformulated in terms of hypothesis testing through model selection and offers a formative way to integrate anatomical knowledge in terms of prior distributions.

Connectivity-based parcellation of the nucleus accumbens into core and shell portions for stereotactic target localization and alterations in each NAc subdivision in mTLE patients

The nucleus accumbens (NAc), an important target of deep brain stimulation for some neuropsychiatric disorders, is thought to be involved in epileptogenesis, especially the shell portion. However, little is known about the exact parcellation within the NAc, and its structural abnormalities or connections alterations of each NAc subdivision in temporal lobe epilepsy (TLE) patients. Here, we used diffusion probabilistic tractography to subdivide the NAc into core and shell portions in individual TLE patients to guide stereotactic localization of NAc shell. The structural and connection abnormalities in each NAc subdivision in the groups were then estimated. We successfully segmented the NAc in 24 of 25 controls, 14 of 16 left TLE patients, and 14 of 18 right TLE patients. Both left and right TLE patients exhibited significantly decreased fractional anisotropy (FA) and increased radial diffusivity (RD) in the shell, while there was no significant alteration in the core. Moreover, relatively distinct structural connectivity of each NAc subdivision was demonstrated. More extensive connection abnormalities were detected in the NAc shell in TLE patients. Our results indicate that neuronal degeneration and damage caused by seizure mainly exists in NAc shell and provide anatomical evidence to support the role of NAc shell in epileptogenesis. Remarkably, those NAc shell tracts with increased connectivities in TLE patients were found decreased in FA, which indicates disruption of fiber integrity. This finding suggests the regeneration of aberrant connections, a compensatory and repair process ascribed to recurrent seizures that constitutes part of the characteristic changes in the epileptic network.

The challenge of mapping the human connectome based on diffusion tractography

Tractography based on non-invasive diffusion imaging is central to the study of human brain connectivity. To date, the approach has not been systematically validated in ground truth studies. Based on a simulated human brain data set with ground truth tracts, we organized an open international tractography challenge, which resulted in 96 distinct submissions from 20 research groups. Here, we report the encouraging finding that most state-of-the-art algorithms produce tractograms containing 90% of the ground truth bundles (to at least some extent). However, the same tractograms contain many more invalid than valid bundles, and half of these invalid bundles occur systematically across research groups. Taken together, our results demonstrate and confirm fundamental ambiguities inherent in tract reconstruction based on orientation information alone, which need to be considered when interpreting tractography and connectivity results. Our approach provides a novel framework for estimating reliability of tractography and encourages innovation to address its current limitations.

Though tractography is widely used, it has not been systematically validated. Here, authors report results from 20 groups showing that many tractography algorithms produce both valid and invalid bundles.

Multidimensional encoding of brain connectomes

The ability to map brain networks in living individuals is fundamental in efforts to chart the relation between human behavior, health and disease. Advances in network neuroscience may benefit from developing new frameworks for mapping brain connectomes. We present a framework to encode structural brain connectomes and diffusion-weighted magnetic resonance (dMRI) data using multidimensional arrays. The framework integrates the relation between connectome nodes, edges, white matter fascicles and diffusion data. We demonstrate the utility of the framework for in vivo white matter mapping and anatomical computing by evaluating 1,490 connectomes, thirteen tractography methods, and three data sets. The framework dramatically reduces storage requirements for connectome evaluation methods, with up to 40x compression factors. Evaluation of multiple, diverse datasets demonstrates the importance of spatial resolution in dMRI. We measured large increases in connectome resolution as function of data spatial resolution (up to 52%). Moreover, we demonstrate that the framework allows performing anatomical manipulations on white matter tracts for statistical inference and to study the white matter geometrical organization. Finally, we provide open-source software implementing the method and data to reproduce the results.

Age-related changes in structural connectivity are improved using subject-specific thresholding

BACKGROUND

Deterministic diffusion tractography obtained from high angular resolution diffusion imaging (HARDI) requires user-defined quantitative anisotropy (QA) thresholds. Most studies employ a common threshold across all subjects even though there is a strong degree of individual variation within groups. We sought to explore whether it would be beneficial to use individual thresholds in order to accommodate individual variance. To do this, we conducted two independent experiments.

METHOD

First, tractography of the arcuate fasciculus and network connectivity measures were examined in a sample of 14 healthy participants. Second, we assessed the effects of QA threshold on group differences in network connectivity measures between healthy young (n=19) and old (n=14) individuals.

RESULTS

The results of both experiments were significantly influenced by QA threshold. Common thresholds set too high failed to produce sufficient reconstructions in most subjects, thus decreasing the likelihood of detecting meaningful group differences. On the other hand, common thresholds set too low resulted in spurious reconstructions, providing deleterious results.

COMPARISON WITH EXISTING METHODS

Subject specific thresholds acquired using our QA threshold selection method (QATS) appeared to provide the most meaningful networks while ensuring that data from all subjects contributed to the analyses.

CONCLUSIONS

Together, these results support the use of a subject-specific threshold to ensure that data from all subjects are included in the analyses being conducted.

Influence of fractional anisotropy thresholds on diffusion tensor imaging tractography of the periprostatic neurovascular bundle and selected pelvic tissues: do visualized tracts really represent nerves?

Background Diffusion tensor imaging (DTI) tractography has recently been shown to successfully visualize periprostatic tracts allegedly representing the neurovascular bundle. Purpose To examine the impact of different fractional anisotropy (FA) thresholds on the results of DTI tractography in the male pelvis as well as to evaluate the resulting specificity for nerve tracts. Material and Methods Ten healthy male volunteers were examined at 3 Tesla. DTI tractography was performed based on seed points placed circularly around the prostate, in the rectoprostatic angle, the peripheral zone of the prostate, the sciatic nerve, and in addition the urinary bladder using FA thresholds of 0.20, 0.05, and 0.01. DTI tract number and DTI tract length measured with different FA thresholds were compared. ANOVA with repeated measures was used for statistics. Results DTI tract number and tract length were significantly dependent on FA thresholds. While a FA threshold of 0.20 visualized the typical distribution of DTI tracts in the sciatic nerve, a FA threshold of ≤0.05 was necessary to yield results visually mimicking the distribution of nerve tracts in the NVB. However, with such low FA thresholds even in the filled urinary bladder DTI tracts could be visualized. With FA thresholds of 0.20, the number and length of periprostatic DTI tracts did not differ from those measured within the prostate. Conclusion DTI tractography can be used to visualize DTI tracts periprostatically. However, one may doubt that these DTI tracts represent nerve tracts and that the periprostatic neurovascular bundle can be evaluated in a meaningful way with the current methods available.

High resolution anatomical and quantitative MRI of the entire human occipital lobe ex vivo at 9.4T

Several magnetic resonance imaging (MRI) contrasts are sensitive to myelin content in gray matter in vivo which has ignited ambitions of MRI-based in vivo cortical histology. Ultra-high field (UHF) MRI, at fields of 7 T and beyond, is crucial to provide the resolution and contrast needed to sample contrasts over the depth of the cortex and get closer to layer resolved imaging. Ex vivo MRI of human post mortem samples is an important stepping stone to investigate MRI contrast in the cortex, validate it against histology techniques applied in situ to the same tissue, and investigate the resolutions needed to translate ex vivo findings to in vivo UHF MRI. Here, we investigate key technology to extend such UHF studies to large human brain samples while maintaining high resolution, which allows investigation of the layered architecture of several cortical areas over their entire 3D extent and their complete borders where architecture changes. A 16 channel cylindrical phased array radiofrequency (RF) receive coil was constructed to image a large post mortem occipital lobe sample (~80×80×80 mm³) in a wide-bore 9.4 T human scanner with the aim of achieving high-resolution anatomical and quantitative MR images. Compared with a human head coil at 9.4 T, the maximum Signal-to-Noise ratio (SNR) was increased by a factor of about five in the peripheral cortex. Although the transmit profile with a circularly polarized transmit mode at 9.4 T is relatively inhomogeneous over the large sample, this challenge was successfully resolved with parallel transmit using the kT-points method. Using this setup, we achieved 60μm anatomical images for the entire occipital lobe showing increased spatial definition of cortical details compared to lower resolutions. In addition, we were able to achieve sufficient control over SNR, B₀ and B₁ homogeneity and multi-contrast sampling to perform quantitative T₂* mapping over the same volume at 200 μm. Markov Chain Monte Carlo sampling provided maximum posterior estimates of quantitative T₂* and their uncertainty, allowing delineation of the stria of Gennari over the entire length and width of the calcarine sulcus. We discuss how custom RF receive coil arrays built to specific large post mortem sample sizes can provide a platform for UHF cortical layer-specific quantitative MRI over large fields of view.

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Custom-built 16 channel 9.4 T RF-coil to image large post mortem samples at high resolution.

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Parallel transmit techniques allow homogenization of B₁⁺ for 3D GRE imaging at UHF.

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60 μm anatomical MRI of the entire human occipital lobe.

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200 μm isotropic quantitative T₂^* mapping of the entire human occipital lobe.

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A platform for future UHF cortical layer specific qMRI over large FoVs.

Automatic Segmentation of Human Cortical Layer-Complexes and Architectural Areas Using Ex vivo Diffusion MRI and Its Validation

Recently, several magnetic resonance imaging contrast mechanisms have been shown to distinguish cortical substructure corresponding to selected cortical layers. Here, we investigate cortical layer and area differentiation by automatized unsupervised clustering of high-resolution diffusion MRI data. Several groups of adjacent layers could be distinguished in human primary motor and premotor cortex. We then used the signature of diffusion MRI signals along cortical depth as a criterion to detect area boundaries and find borders at which the signature changes abruptly. We validate our clustering results by histological analysis of the same tissue. These results confirm earlier studies which show that diffusion MRI can probe layer-specific intracortical fiber organization and, moreover, suggests that it contains enough information to automatically classify architecturally distinct cortical areas. We discuss the strengths and weaknesses of the automatic clustering approach and its appeal for MR-based cortical histology.

Cerebello-cerebral connectivity in the developing brain

Disrupted cerebellar development and injury is associated with impairments in both motor and non-motor domains. Methods to non-invasively characterize cerebellar afferent and efferent connections during early development are lacking. The aim of this study was to assess the feasibility of delineating cortico-ponto-cerebellar (CPC) and cerebello-thalamo-cortical (CTC) white matter tracts during brain development using high angular resolution diffusion imaging (HARDI). HARDI data were obtained in 24 infants born between 24⁺⁶ and 39 weeks gestational age (median 33⁺⁴ weeks) and scanned between 29⁺¹ and 44 weeks postmenstrual age (PMA) (median 37⁺¹ weeks). Probabilistic tractography of CPC and CTC fibers was performed using constrained spherical deconvolution. Connections between cerebellum and contralateral cerebral hemisphere were identified in all infants studied. Fractional anisotropy (FA) values of CTC and CPC pathways increased with increasing PMA at scan (p < 0.001). The supratentorial regions connecting to contralateral cerebellum in most subjects, irrespective of PMA at scan, included the precentral cortex, superior frontal cortex, supplementary motor area, insula, postcentral cortex, precuneus, and paracentral lobule. This study demonstrates the feasibility of assessing CTC and CPC white matter connectivity in vivo during the early stages of development. The ability to assess cerebellar connectivity during this critical developmental period may help improve our understanding of the role of the cerebellum in a wide range of neuromotor and neurocognitive disorders.

Frontostriatal anatomical connections predict age- and difficulty-related differences in reinforcement learning

Reinforcement learning (RL) is supported by a network of striatal and frontal cortical structures that are connected through white-matter fiber bundles. With age, the integrity of these white-matter connections declines. The role of structural frontostriatal connectivity in individual and age-related differences in RL is unclear, although local white-matter density and diffusivity have been linked to individual differences in RL. Here we show that frontostriatal tract counts in young human adults (aged 18-28), as assessed noninvasively with diffusion-weighted magnetic resonance imaging and probabilistic tractography, positively predicted individual differences in RL when learning was difficult (70% valid feedback). In older adults (aged 63-87), in contrast, learning under both easy (90% valid feedback) and difficult conditions was predicted by tract counts in the same frontostriatal network. Furthermore, network-level analyses showed a double dissociation between the task-relevant networks in young and older adults, suggesting that older adults relied on different frontostriatal networks than young adults to obtain the same task performance. These results highlight the importance of successful information integration across striatal and frontal regions during RL, especially with variable outcomes.

Advances in MRI-based computational neuroanatomy: from morphometry to in-vivo histology

PURPOSE OF REVIEW

Current computational neuroanatomy based on MRI focuses on morphological measures of the brain. We present recent methodological developments in quantitative MRI (qMRI) that provide standardized measures of the brain, which go beyond morphology. We show how biophysical modelling of qMRI data can provide quantitative histological measures of brain tissue, leading to the emerging field of in-vivo histology using MRI (hMRI).

RECENT FINDINGS

qMRI has greatly improved the sensitivity and specificity of computational neuroanatomy studies. qMRI metrics can also be used as direct indicators of the mechanisms driving observed morphological findings. For hMRI, biophysical models of the MRI signal are being developed to directly access histological information such as cortical myelination, axonal diameters or axonal g-ratio in white matter. Emerging results indicate promising prospects for the combined study of brain microstructure and function.

SUMMARY

Non-invasive brain tissue characterization using qMRI or hMRI has significant implications for both research and clinics. Both approaches improve comparability across sites and time points, facilitating multicentre/longitudinal studies and standardized diagnostics. hMRI is expected to shed new light on the relationship between brain microstructure, function and behaviour, both in health and disease, and become an indispensable addition to computational neuroanatomy.

Comparison of 3D orientation distribution functions measured with confocal microscopy and diffusion MRI

The ability of diffusion MRI (dMRI) fiber tractography to non-invasively map three-dimensional (3D) anatomical networks in the human brain has made it a valuable tool in both clinical and research settings. However, there are many assumptions inherent to any tractography algorithm that can limit the accuracy of the reconstructed fiber tracts. Among them is the assumption that the diffusion-weighted images accurately reflect the underlying fiber orientation distribution (FOD) in the MRI voxel. Consequently, validating dMRI's ability to assess the underlying fiber orientation in each voxel is critical for its use as a biomedical tool. Here, using post-mortem histology and confocal microscopy, we present a method to perform histological validation of orientation functions in 3D, which has previously been limited to two-dimensional analysis of tissue sections. We demonstrate the ability to extract the 3D FOD from confocal z-stacks, and quantify the agreement between the MRI estimates of orientation information obtained using constrained spherical deconvolution (CSD) and the true geometry of the fibers. We find an orientation error of approximately 6° in voxels containing nearly parallel fibers, and 10-11° in crossing fiber regions, and note that CSD was unable to resolve fibers crossing at angles below 60° in our dataset. This is the first time that the 3D white matter orientation distribution is calculated from histology and compared to dMRI. Thus, this technique serves as a gold standard for dMRI validation studies - providing the ability to determine the extent to which the dMRI signal is consistent with the histological FOD, and to establish how well different dMRI models can predict the ground truth FOD.

A survey of current trends in diffusion MRI for structural brain connectivity

In this paper, we review the state of the art in diffusion magnetic resonance imaging (dMRI) and we present current trends in modelling the brain's tissue microstructure and the human connectome. dMRI is today the only tool that can probe the brain's axonal architecture in vivo and non-invasively, and has grown in leaps and bounds in the last two decades since its conception. A plethora of models with increasing complexity and better accuracy have been proposed to characterise the integrity of the cerebral tissue, to understand its microstructure and to infer its connectivity. Here, we discuss a wide range of the most popular, important and well-established local microstructure models and biomarkers that have been proposed from these models. Finally, we briefly present the state of the art in tractography techniques that allow us to understand the architecture of the brain's connectivity.

Strengths and weaknesses of state of the art fiber tractography pipelines--A comprehensive in-vivo and phantom evaluation study using Tractometer

Many different tractography approaches and corresponding isolated evaluation attempts have been presented over the last years, but a comparative and quantitative evaluation of tractography algorithms still remains a challenge, particularly in-vivo. The recently presented evaluation framework Tractometer is the first attempt to approach this challenge in a quantitative, comparative, persistent and open-access way. Tractometer is currently based on the evaluation of several global connectivity and tract-overlap metrics on hardware phantom data. The work presented in this paper focuses on extending Tractometer with a metric that enables the assessment of the local consistency of tractograms with the underlying image data that is not only applicable to phantom dataset but allows the quantitative and purely data-driven evaluation of in-vivo tractography. We furthermore present an extensive reference-based evaluation study of 25,000 tractograms obtained on phantom and in-vivo datasets using the presented local metric as well as all the methods already established in Tractometer. The experiments showed that the presented local metric successfully reflects the behavior of in-vivo tractography under different conditions and that it is consistent with the results of previous studies. Additionally our experiments enabled a multitude of conclusions with implications for fiber tractography in general, including recommendations regarding optimal choice of a local modeling technique, tractography algorithm, and parameterization, confirming and complementing the results of earlier studies.

Contralateral cerebello-thalamo-cortical pathways with prominent involvement of associative areas in humans in vivo

In addition to motor functions, it has become clear that in humans the cerebellum plays a significant role in cognition too, through connections with associative areas in the cerebral cortex. Classical anatomy indicates that neo-cerebellar regions are connected with the contralateral cerebral cortex through the dentate nucleus, superior cerebellar peduncle, red nucleus and ventrolateral anterior nucleus of the thalamus. The anatomical existence of these connections has been demonstrated using virus retrograde transport techniques in monkeys and rats ex vivo. In this study, using advanced diffusion MRI tractography we show that it is possible to calculate streamlines to reconstruct the pathway connecting the cerebellar cortex with contralateral cerebral cortex in humans in vivo. Corresponding areas of the cerebellar and cerebral cortex encompassed similar proportion (about 80%) of the tract, suggesting that the majority of streamlines passing through the superior cerebellar peduncle connect the cerebellar hemispheres through the ventrolateral thalamus with contralateral associative areas. This result demonstrates that this kind of tractography is a useful tool to map connections between the cerebellum and the cerebral cortex and moreover could be used to support specific theories about the abnormal communication along these pathways in cognitive dysfunctions in pathologies ranging from dyslexia to autism.

In vivo mapping of macroscopic neuronal projections in the mouse hippocampus using high-resolution diffusion MRI

Recent developments in diffusion magnetic resonance imaging (MRI) make it a promising tool for non-invasive mapping of the spatial organization of axonal and dendritic networks in gray matter regions of the brain. Given the complex cellular environments, in which these networks reside, evidence on the capability of diffusion MRI-based tractography to study these networks is still lacking. In this study, we used a localized diffusion MRI approach to acquire high spatial and angular resolution images of the live mouse hippocampus. The diffusion MRI and tractography results were compared with histology and the Allen mouse brain connectivity atlas using a multi-step image registration pipeline. The results demonstrated that in vivo diffusion MRI data at 0.1mm isotropic resolution revealed the organization of axonal and dendritic networks in the hippocampus and the tractography results shared remarkable similarity with the viral tracer data in term of their spatial projection patterns. Quantitative analysis showed significant correlations between tractography- and tracer-based projection density measurements in the mouse hippocampus. These findings suggest that high-resolution diffusion MRI and tractography can reveal macroscopic neuronal projections in the mouse hippocampus and are important for future development of advanced tractography methods.

Dentatorubrothalamic tract localization with postmortem MR diffusion tractography compared to histological 3D reconstruction

Diffusion-weighted imaging (DWI) tractography is a technique with great potential to characterize the in vivo anatomical position and integrity of white matter tracts. Tractography, however, remains an estimation of white matter tracts, and false-positive and false-negative rates are not available. The goal of the present study was to compare postmortem tractography of the dentatorubrothalamic tract (DRTT) by its 3D histological reconstruction, to estimate the reliability of the tractography algorithm in this specific tract. Recent studies have shown that the cerebellum is involved in cognitive, language and emotional functions besides its role in motor control. However, the exact working mechanism of the cerebellum is still to be elucidated. As the DRTT is the main output tract it is of special interest for the neuroscience and clinical community. A postmortem human brain specimen was scanned on a 7T MRI scanner using a diffusion-weighted steady-state free precession sequence. Tractography was performed with PROBTRACKX. The specimen was subsequently serially sectioned and stained for myelin using a modified Heidenhain–Woelke staining. Image registration permitted the 3D reconstruction of the histological sections and comparison with MRI. The spatial concordance between the two modalities was evaluated using ROC analysis and a similarity index (SI). ROC curves showed a high sensitivity and specificity in general. Highest measures were observed in the superior cerebellar peduncle with an SI of 0.72. Less overlap was found in the decussation of the DRTT at the level of the mesencephalon. The study demonstrates high spatial accuracy of postmortem probabilistic tractography of the DRTT when compared to a 3D histological reconstruction. This gives hopeful prospect for studying structure–function correlations in patients with cerebellar disorders using tractography of the DRTT.