Super-resolution track-density imaging studies of mouse brain: Comparison to histology

An Open Resource: MR and light sheet microscopy stereotaxic atlas of the mouse brain

We have combined MR histology and light sheet microscopy (LSM) of five postmortem C57BL/6J mouse brains in a stereotaxic space based on micro-CT yielding a multimodal 3D atlas with the highest spatial and contrast resolution yet reported. Brains were imaged in situ with multi gradient echo (mGRE) and diffusion tensor imaging (DTI) at 15 μm resolution (∼ 2.4 million times that of clinical MRI). Scalar images derived from the average DTI and mGRE provide unprecedented contrast in 14 complementary 3D volumes, each highlighting distinct histologic features. The same tissues scanned with LSM and registered into the stereotaxic space provide 17 different molecular cell type stains. The common coordinate framework labels (CCFv3) complete the multimodal atlas. The atlas has been used to correct distortions in the Allen Brain Atlas and harmonize it with Franklin Paxinos. It provides a unique resource for stereotaxic labeling of mouse brain images from many sources.

Impact of inner ear malformation and cochlear nerve deficiency on the development of auditory-language network in children with profound sensorineural hearing loss

Profound congenital sensorineural hearing loss (SNHL) prevents children from developing spoken language. Cochlear implantation and auditory brainstem implantation can provide partial hearing sensation, but language development outcomes can vary, particularly for patients with inner ear malformations and/or cochlear nerve deficiency (IEM&CND). Currently, the peripheral auditory structure is evaluated through visual inspection of clinical imaging, but this method is insufficient for surgical planning and prognosis. The central auditory pathway is also challenging to examine in vivo due to its delicate subcortical structures. Previous attempts to locate subcortical auditory nuclei using fMRI responses to sounds are not applicable to patients with profound hearing loss as no auditory brainstem responses can be detected in these individuals, making it impossible to capture corresponding blood oxygen signals in fMRI. In this study, we developed a new pipeline for mapping the auditory pathway using structural and diffusional MRI. We used a fixel-based approach to investigate the structural development of the auditory-language network for profound SNHL children with normal peripheral structure and those with IEM&CND under 6 years old. Our findings indicate that the language pathway is more sensitive to peripheral auditory condition than the central auditory pathway, highlighting the importance of early intervention for profound SNHL children to provide timely speech inputs. We also propose a comprehensive pre-surgical evaluation extending from the cochlea to the auditory-language network, showing significant correlations between age, gender, Cn.VIII median contrast value, and the language network with post-implant qualitative outcomes.

Ex vivo 100 μm isotropic diffusion MRI-based tractography of connectivity changes in the end-stage R6/2 mouse model of Huntington's disease

Background

Huntington's disease is a progressive neurodegenerative disorder. Brain atrophy, as measured by volumetric magnetic resonance imaging (MRI), is a downstream consequence of neurodegeneration, but microstructural changes within brain tissue are expected to precede this volumetric decline. The tissue microstructure can be assayed non-invasively using diffusion MRI, which also allows a tractographic analysis of brain connectivity.

Methods

We here used ex vivo diffusion MRI (11.7 T) to measure microstructural changes in different brain regions of end-stage (14 weeks of age) wild type and R6/2 mice (male and female) modeling Huntington's disease. To probe the microstructure of different brain regions, reduce partial volume effects and measure connectivity between different regions, a 100 μm isotropic voxel resolution was acquired.

Results

Although fractional anisotropy did not reveal any difference between wild-type controls and R6/2 mice, mean, axial, and radial diffusivity were increased in female R6/2 mice and decreased in male R6/2 mice. Whole brain streamlines were only reduced in male R6/2 mice, but streamline density was increased. Region-to-region tractography indicated reductions in connectivity between the cortex, hippocampus, and thalamus with the striatum, as well as within the basal ganglia (striatum-globus pallidus-subthalamic nucleus-substantia nigra-thalamus).

Conclusions

Biological sex and left/right hemisphere affected tractographic results, potentially reflecting different stages of disease progression. This proof-of-principle study indicates that diffusion MRI and tractography potentially provide novel biomarkers that connect volumetric changes across different brain regions. In a translation setting, these measurements constitute a novel tool to assess the therapeutic impact of interventions such as neuroprotective agents in transgenic models, as well as patients with Huntington's disease.

Superficial white matter across development, young adulthood, and aging: volume, thickness, and relationship with cortical features

Superficial white matter (SWM) represents a significantly understudied part of the human brain, despite comprising a large portion of brain volume and making up a majority of cortico-cortical white matter connections. Using multiple, high-quality datasets with large sample sizes (N = 2421, age range 5-100) in combination with methodological advances in tractography, we quantified features of SWM volume and thickness across the brain and across development, young adulthood, and aging. We had four primary aims: (1) characterize SWM thickness across brain regions (2) describe associations between SWM volume and age (3) describe associations between SWM thickness and age, and (4) quantify relationships between SWM thickness and cortical features. Our main findings are that (1) SWM thickness varies across the brain, with patterns robust across individuals and across the population at the region-level and vertex-level; (2) SWM volume shows unique volumetric trajectories with age that are distinct from gray matter and other white matter trajectories; (3) SWM thickness shows nonlinear cross-sectional changes across the lifespan that vary across regions; and (4) SWM thickness is associated with features of cortical thickness and curvature. For the first time, we show that SWM volume follows a similar trend as overall white matter volume, peaking at a similar time in adolescence, leveling off throughout adulthood, and decreasing with age thereafter. Notably, the relative fraction of total brain volume of SWM continuously increases with age, and consequently takes up a larger proportion of total white matter volume, unlike the other tissue types that decrease with respect to total brain volume. This study represents the first characterization of SWM features across the large portion of the lifespan and provides the background for characterizing normal aging and insight into the mechanisms associated with SWM development and decline.

Integrating multimodality magnetic resonance imaging to the Allen Mouse Brain Common Coordinate Framework

High-resolution magnetic resonance imaging (MRI) affords unique image contrasts to nondestructively probe the tissue microstructure; validation of MRI findings with conventional histology is essential to better understand the MRI contrasts. However, the dramatic difference in the spatial resolution and image contrast of these two techniques impedes accurate comparison between MRI metrics and traditional histology. To better validate various MRI metrics, we acquired whole mouse brain multigradient recalled-echo and multishell diffusion MRI datasets at 25-μm isotropic resolution. The recently developed Allen Mouse Brain Common Coordinate Framework (CCFv3) provides opportunities to integrate multimodal and multiscale datasets of the whole mouse brain in a common three-dimensional (3D) space. The T2*, quantitative susceptibility mapping, diffusion tensor imaging, and neurite orientation dispersion and density imaging parameters were compared with both serial two-photon tomography images and 3D Nissl staining images in the CCFv3 at the same spatial resolution. The correlation between MRI and Nissl staining strongly depends on different metrics and different regions of the brain. Integrating different imaging modalities to the same space may substantially improve our understanding of the complexity of the brain at different scales.

Merged magnetic resonance and light sheet microscopy of the whole mouse brain

We have developed workflows to align 3D magnetic resonance histology (MRH) of the mouse brain with light sheet microscopy (LSM) and 3D delineations of the same specimen. We start with MRH of the brain in the skull with gradient echo and diffusion tensor imaging (DTI) at 15 μm isotropic resolution which is ~ 1,000 times higher than that of most preclinical MRI. Connectomes are generated with superresolution tract density images of ~5 μm. Brains are cleared, stained for selected proteins, and imaged by LSM at 1.8 μm/pixel. LSM data are registered into the reference MRH space with labels derived from the ABA common coordinate framework. The result is a high-dimensional integrated volume with registration (HiDiver) with alignment precision better than 50 µm. Throughput is sufficiently high that HiDiver is being used in quantitative studies of the impact of gene variants and aging on mouse brain cytoarchitecture and connectomics.

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.

Microstructural mapping of dentate gyrus pathology in Alzheimer's disease: A 16.4 Tesla MRI study

The dentate gyrus (DG) is an integral portion of the hippocampal formation, and it is composed of three layers. Quantitative magnetic resonance (MR) imaging has the capability to map brain tissue microstructural properties which can be exploited to investigate neurodegeneration in Alzheimer's disease (AD). However, assessing subtle pathological changes within layers requires high resolution imaging and histological validation. In this study, we utilized a 16.4 Tesla scanner to acquire ex vivo multi-parameter quantitative MRI measures in human specimens across the layers of the DG. Using quantitative diffusion tensor imaging (DTI) and multi-parameter MR measurements acquired from AD (N = 4) and cognitively normal control (N = 6) tissues, we performed correlation analyses with histological measurements. Here, we found that quantitative MRI measures were significantly correlated with neurofilament and phosphorylated Tau density, suggesting sensitivity to layer-specific changes in the DG of AD tissues.

In vivo probabilistic atlas of white matter tracts of the human subthalamic area combining track density imaging and optimized diffusion tractography

The human subthalamic area is a region of high anatomical complexity, tightly packed with tiny fiber bundles. Some of them, including the pallidothalamic, cerebello-thalamic, and mammillothalamic tracts, are relevant targets in functional neurosurgery for various brain diseases. Diffusion-weighted imaging-based tractography has been suggested as a useful tool to map white matter pathways in the human brain in vivo and non-invasively, though the reconstruction of these specific fiber bundles is challenging due to their small dimensions and complex anatomy. To the best of our knowledge, a population-based, in vivo probabilistic atlas of subthalamic white matter tracts is still missing. In the present work, we devised an optimized tractography protocol for reproducible reconstruction of the tracts of subthalamic area in a large data sample from the Human Connectome Project repository. First, we leveraged the super-resolution properties and high anatomical detail provided by short tracks track-density imaging (stTDI) to identify the white matter bundles of the subthalamic area on a group-level template. Tracts identification on the stTDI template was also aided by visualization of histological sections of human specimens. Then, we employed this anatomical information to drive tractography at the subject-level, optimizing tracking parameters to maximize between-subject and within-subject similarities as well as anatomical accuracy. Finally, we gathered subject level tracts reconstructed with optimized tractography into a large-scale, normative population atlas. We suggest that this atlas could be useful in both clinical anatomy and functional neurosurgery settings, to improve our understanding of the complex morphology of this important brain region.

Seed-induced Aβ deposits in the corpus callosum disrupt white matter integrity in a mouse model of Alzheimer’s disease

Neuropathologically, Alzheimer’s disease (AD) is characterized by the accumulation of amyloid-beta peptide (Aβ) and subsequent formation of the so-called Aβ plaques. Along with neuronal loss, previous studies report white matter anomalies and corpus callosum (CC) atrophy in AD patients. Notably, perturbations in the white matter can be observed years before expected disease onset, suggesting that early stages of disease progression play a role in AD-associated loss of myelin integrity. Through seed-induced deposition of Aβ, we are able to examine alterations of central nervous system (CNS) integrity during the initial stages of plaque formation. In this study, we investigate the impact of Aβ seeding in the CC utilizing various imaging techniques as well as quantitative gene expression analysis and demonstrate that Aβ deposits result in an imbalance of glial cells in the CC. We found increased amounts of phagocytic microglia and reactive astrocytes, while oligodendrocyte progenitor cell (OPC) numbers were reduced. Moreover, white matter aberrations adjacent to the Aβ seeding were observed together with an overall decline in callosal myelination. This data indicate that the initial stages of plaque formation induce oligodendrocyte dysfunction, which might ultimately lead to myelin loss.

Resolution and b value dependent Structural Connectome in ex vivo Mouse Brain

Diffusion magnetic resonance imaging has been widely used in both clinical and preclinical studies to characterize tissue microstructure and structural connectivity. The diffusion MRI protocol for the Human Connectome Project (HCP) has been developed and optimized to obtain high-quality, high-resolution diffusion MRI (dMRI) datasets. However, such efforts have not been fully explored in preclinical studies, especially for rodents. In this study, high quality dMRI datasets of mouse brains were acquired at 9.4T system from two vendors. In particular, we acquired a high-spatial resolution dMRI dataset (25 μm isotropic with 126 diffusion encoding directions), which we believe to be the highest spatial resolution yet obtained; and a high-angular resolution dMRI dataset (50 μm isotropic with 384 diffusion encoding directions), which we believe to be the highest angular resolution compared to the dMRI datasets at the microscopic resolution. We systematically investigated the effects of three important parameters that affect the final outcome of the connectome: b value (1000s/mm² to 8000 s/mm²), angular resolution (10 to 126), and spatial resolution (25 μm to 200 μm). The stability of tractography and connectome increase with the angular resolution, where more than 50 angles is necessary to achieve consistent results. The connectome and quantitative parameters derived from graph theory exhibit a linear relationship to the b value (R² > 0.99); a single-shell acquisition with b value of 3000 s/mm² shows comparable results to the multi-shell high angular resolution dataset. The dice coefficient decreases and both false positive rate and false negative rate gradually increase with coarser spatial resolution. Our study provides guidelines and foundations for exploration of tradeoffs among acquisition parameters for the structural connectome in ex vivo mouse brain.

Monitoring Neuronal Network Disturbances of Brain Diseases: A Preclinical MRI Approach in the Rodent Brain

Functional and structural neuronal networks, as recorded by resting-state functional MRI and diffusion MRI-based tractography, gain increasing attention as data driven whole brain imaging methods not limited to the foci of the primary pathology or the known key affected regions but permitting to characterize the entire network response of the brain after disease or injury. Their connectome contents thus provide information on distal brain areas, directly or indirectly affected by and interacting with the primary pathological event or affected regions. From such information, a better understanding of the dynamics of disease progression is expected. Furthermore, observation of the brain's spontaneous or treatment-induced improvement will contribute to unravel the underlying mechanisms of plasticity and recovery across the whole-brain networks. In the present review, we discuss the values of functional and structural network information derived from systematic and controlled experimentation using clinically relevant animal models. We focus on rodent models of the cerebral diseases with high impact on social burdens, namely, neurodegeneration, and stroke.

In vivo 3D Reconstruction of the Human Pallidothalamic and Nigrothalamic Pathways With Super-Resolution 7T MR Track Density Imaging and Fiber Tractography

The output network of the basal ganglia plays an important role in motor, associative, and limbic processing and is generally characterized by the pallidothalamic and nigrothalamic pathways. However, these connections in the human brain remain difficult to elucidate because of the resolution limit of current neuroimaging techniques. The present study aimed to investigate the mesoscopic nature of these connections between the thalamus, substantia nigra pars reticulata, and globus pallidus internal segment using 7 Tesla (7T) magnetic resonance imaging (MRI). In this study, track-density imaging (TDI) of the whole human brain was employed to overcome the limitations of observing the pallidothalamic and nigrothalamic tracts. Owing to the super-resolution of the TD images, the substructures of the SN, as well as the associated tracts, were identified. This study demonstrates that 7T MRI and MR tractography can be used to visualize anatomical details, as well as 3D reconstruction, of the output projections of the basal ganglia.

A multicontrast MR atlas of the Wistar rat brain

We describe a multi-contrast, multi-dimensional atlas of the Wistar rat acquired at microscopic spatial resolution using magnetic resonance histology (MRH). Diffusion weighted images, and associated scalar images were acquired of a single specimen with a fully sampled Fourier reconstruction, 61 angles and b=3000 s/mm2 yielding 50 um isotropic spatial resolution. The higher angular sampling allows use of the GQI algorithm improving the angular invariance of the scalar images and yielding an orientation distribution function to assist in delineating subtle boundaries where there are crossing fibers  and track density images providing insight into local fiber architecture.  A multigradient echo image of the same specimen was acquired at 25 um isotropic spatial resolution. A quantitative susceptibility map enhances fiber architecture relative to the magnitude images.  An accompanying multi-specimen atlas (n=6) was acquired with compressed sensing with the same diffusion protocol as used for the single specimen atlas.  An average was created using diffeomorphic mapping. Scalar volumes from the diffusion data, a T2* weighted volume, a quantitative susceptibility map, and a track density volume, all registered to the same space provide multiple contrasts to assist in anatomic delineation. The new template  provides significantly increased contrast in the scalar DTI images when compared to previous atlases. A compact interactive viewer based on 3D Slicer is provided to facilitate comparison among the contrasts in the multiple volumes. The single volume and average atlas with multiple 3D volumes provide an improved template for anatomic interrogation of the Wistar rat brain. The improved contrast to noise in the scalar DTI images and the addition of other volumes (eg. QA,QSM,TDI ) will facilitate automated label registration for MR histology and preclinical imaging.

Experimental Imaging Study of Encephalomalacia Fluid-Attenuated Inversion Recovery (FLAIR) Hyperintense Lesions in Posttraumatic Epilepsy

This study introduced new MRI techniques such as neurite orientation dispersion and density imaging (NODDI); NODDI applies a three-compartment tissue model to multishell DWI data that allows the examination of both the intra- and extracellular properties of white matter tissue. This, in turn, enables us to distinguish the two key aspects of axonal pathology-the packing density of axons in the white matter and the spatial organization of axons (orientation dispersion (OD)). NODDI is used to detect possible abnormalities of posttraumatic encephalomalacia fluid-attenuated inversion recovery (FLAIR) hyperintense lesions in neurite density and dispersion. Methods. 26 epilepsy patients associated with FLAIR hyperintensity around the trauma encephalomalacia region were in the epilepsy group. 18 posttraumatic patients with a FLAIR hyperintense encephalomalacia region were in the nonepilepsy group. Neurite density and dispersion affection in FLAIR hyperintense lesions around encephalomalacia were measured by NODDI using intracellular volume fraction (ICVF), and we compare these findings with conventional diffusion MRI parameters, namely, fractional anisotropy (FA) and apparent diffusion coefficient (ADC). Differences were compared between the epilepsy and nonepilepsy groups, as well as in the FLAIR hyperintense part and in the FLAIR hypointense part to try to find neurite density and dispersion differences in these parts. Results. ICVF of FLAIR hyperintense lesions in the epilepsy group was significantly higher than that in the nonepilepsy group (P < 0.001). ICVF reveals more information of FLAIR(+) and FLAIR(-) parts of encephalomalacia than OD and FA and ADC. Conclusion. The FLAIR hyperintense part around encephalomalacia in the epilepsy group showed higher ICVF, indicating that this part may have more neurite density and dispersion and may be contributing to epilepsy. NODDI indicated high neurite density with the intensity of myelin in the FLAIR hyperintense lesion. Therefore, NODDI likely shows that neurite density may be a more sensitive marker of pathology than FA.

In Vivo Super-Resolution Track-Density Imaging for Thalamic Nuclei Identification

The development of novel techniques for the in vivo, non-invasive visualization and identification of thalamic nuclei has represented a major challenge for human neuroimaging research in the last decades. Thalamic nuclei have important implications in various key aspects of brain physiology and many of them show selective alterations in various neurologic and psychiatric disorders. In addition, both surgical stimulation and ablation of specific thalamic nuclei have been proven to be useful for the treatment of different neuropsychiatric diseases. The present work aimed at describing a novel protocol for histologically guided delineation of thalamic nuclei based on short-tracks track-density imaging (stTDI), which is an advanced imaging technique exploiting high angular resolution diffusion tractography to obtain super-resolved white matter maps. We demonstrated that this approach can identify up to 13 distinct thalamic nuclei bilaterally with very high inter-subject (ICC: 0.996, 95% CI: 0.993-0.998) and inter-rater (ICC:0.981; 95% CI:0.963-0.989) reliability, and that both subject-based and group-level thalamic parcellation show a fair share of similarity to a recent standard-space histological thalamic atlas. Finally, we showed that stTDI-derived thalamic maps can be successfully employed to study structural and functional connectivity of the thalamus and may have potential implications both for basic and translational research, as well as for presurgical planning purposes.

A 48-channel receive array coil for mesoscopic diffusion-weighted MRI of ex vivo human brain on the 3 T connectome scanner

In vivo diffusion-weighted magnetic resonance imaging is limited in signal-to-noise-ratio (SNR) and acquisition time, which constrains spatial resolution to the macroscale regime. Ex vivo imaging, which allows for arbitrarily long scan times, is critical for exploring human brain structure in the mesoscale regime without loss of SNR. Standard head array coils designed for patients are sub-optimal for imaging ex vivo whole brain specimens. The goal of this work was to design and construct a 48-channel ex vivo whole brain array coil for high-resolution and high b-value diffusion-weighted imaging on a 3T Connectome scanner. The coil was validated with bench measurements and characterized by imaging metrics on an agar brain phantom and an ex vivo human brain sample. The two-segment coil former was constructed for a close fit to a whole human brain, with small receive elements distributed over the entire brain. Imaging tests including SNR and G-factor maps were compared to a 64-channel head coil designed for in vivo use. There was a 2.9-fold increase in SNR in the peripheral cortex and a 1.3-fold gain in the center when compared to the 64-channel head coil. The 48-channel ex vivo whole brain coil also decreases noise amplification in highly parallel imaging, allowing acceleration factors of approximately one unit higher for a given noise amplification level. The acquired diffusion-weighted images in a whole ex vivo brain specimen demonstrate the applicability and advantage of the developed coil for high-resolution and high b-value diffusion-weighted ex vivo brain MRI studies.

Mapping the living mouse brain neural architecture: strain-specific patterns of brain structural and functional connectivity

Mapping brain structural and functional connectivity (FC) became an essential approach in neuroscience as network properties can underlie behavioral phenotypes. In mouse models, revealing strain-related patterns of brain wiring is crucial, since these animals are used to answer questions related to neurological or neuropsychiatric disorders. C57BL/6 and BALB/cJ strains are two of the primary "genetic backgrounds" for modeling brain disease and testing therapeutic approaches. However, extensive literature describes basal differences in the behavioral, neuroanatomical and neurochemical profiles of the two strains, which raises questions on whether the observed effects are pathology specific or depend on the genetic background of each strain. Here, we performed a systematic comparative exploration of brain structure and function of C57BL/6 and BALB/cJ mice using Magnetic Resonance Imaging (MRI). We combined deformation-based morphometry (DBM), diffusion MRI and high-resolution fiber mapping (hrFM) along with resting-state functional MRI (rs-fMRI) and demonstrated brain-wide differences in the morphology and "connectome" features of the two strains. Essential inter-strain differences were depicted regarding the size and the fiber density (FD) within frontal cortices, along cortico-striatal, thalamic and midbrain pathways as well as genu and splenium of corpus callosum. Structural dissimilarities were accompanied by specific FC patterns, emphasizing strain differences in frontal and basal forebrain functional networks as well as hubness characteristics. Rs-fMRI data further indicated differences of reward-aversion circuitry and default mode network (DMN) patterns. The inter-hemispherical FC showed flexibility and strain-specific adjustment of their patterns in agreement with the structural characteristics.

Analysis of homozygous and heterozygous Csf1r knockout in the rat as a model for understanding microglial function in brain development and the impacts of human CSF1R mutations

Mutations in the human CSF1R gene have been associated with dominant and recessive forms of neurodegenerative disease. Here we describe the impacts of Csf1r mutation in the rat on development of the brain. Diffusion imaging indicated small reductions in major fiber tracts that may be associated in part with ventricular enlargement. RNA-seq profiling revealed a set of 105 microglial markers depleted in all brain regions of the Csf1rko rats. There was no evidence of region or sex-specific expression of microglia-associated transcripts. Other than the microglial signature, Csf1rko had no effect on any neuronal or region-specific transcript cluster. Expression of markers of oligodendrocytes, astrocytes, dopaminergic neurons and Purkinje cells was minimally affected. However, there were defects in dendritic arborization of doublecortin-positive neurogenic precursors and expression of poly-sialylated neural cell adhesion molecule (PS-NCAM) in the dentate gyrus of the hippocampus. Heterozygous Csf1rko rats had no detectable brain phenotype. We conclude that most brain developmental processes occur normally in the absence of microglia and that CSF1R haploinsufficiency is unlikely to cause leukoencephalopathy.

White matter changes following experimental pediatric traumatic brain injury: an advanced diffusion-weighted imaging investigation

Pediatric traumatic brain injury (pTBI) is a major community health concern. Due to ongoing maturation, injury to the brain at a young age can have devastating consequences in later life. However, how pTBI affects brain development, including white matter maturation, is still poorly understood. Here, we used advanced diffusion weighted imaging (DWI) to assess chronic white matter changes after experimental pTBI. Mice at post-natal day 21 sustained a TBI using the controlled cortical impact model and magnetic resonance imaging (MRI) was performed at 6 months post-injury using a 4.7 T Bruker scanner. Four diffusion shells with 81 directions and b-values of 1000, 3000, 5000, and 7000s/mm² were acquired and analyzed using MRtrix3 software. Advanced DWI metrics, including fiber density, fiber cross-section and a combined fiber density and cross-section measure, were investigated together with three track-weighted images (TWI): the average pathlength map, mean curvature and the track density image. These advanced metrics were compared to traditional diffusion tensor imaging (DTI) metrics which indicated that TBI injured mice had reduced fractional anisotropy and increased radial diffusivity in the white matter when compared to age-matched sham controls. Consistent with previous findings, fiber density and TWI metrics appeared to be more sensitive to white matter changes than DTI metrics, revealing widespread reductions in fiber density and TWI metrics in pTBI mice compared to sham controls. These results provide additional support for the use of advanced DWI metrics in assessing white matter degeneration following injury and highlight the chronic outcomes that can follow pTBI.

Variability and heritability of mouse brain structure: Microscopic MRI atlases and connectomes for diverse strains

Genome-wide association studies have demonstrated significant links between human brain structure and common DNA variants. Similar studies with rodents have been challenging because of smaller brain volumes. Using high field MRI (9.4 T) and compressed sensing, we have achieved microscopic resolution and sufficiently high throughput for rodent population studies. We generated whole brain structural MRI and diffusion connectomes for four diverse isogenic lines of mice (C57BL/6J, DBA/2J, CAST/EiJ, and BTBR) at spatial resolution 20,000 times higher than human connectomes. We measured narrow sense heritability (h2) I.e. the fraction of variance explained by strains in a simple ANOVA model for volumes and scalar diffusion metrics, and estimates of residual technical error for 166 regions in each hemisphere and connectivity between the regions. Volumes of discrete brain regions had the highest mean heritability (0.71 ± 0.23 SD, n = 332), followed by fractional anisotropy (0.54 ± 0.26), radial diffusivity (0.34 ± 0.022), and axial diffusivity (0.28 ± 0.19). Connection profiles were statistically different in 280 of 322 nodes across all four strains. Nearly 150 of the connection profiles were statistically different between the C57BL/6J, DBA/2J, and CAST/EiJ lines. Microscopic whole brain MRI/DTI has allowed us to identify significant heritable phenotypes in brain volume, scalar DTI metrics, and quantitative connectomes.

Cytoarchitecture of the mouse brain by high resolution diffusion magnetic resonance imaging

MRI has been widely used to probe the neuroanatomy of the mouse brain, directly correlating MRI findings to histology is still challenging due to the limited spatial resolution and various image contrasts derived from water relaxation or diffusion properties. Magnetic resonance histology has the potential to become an indispensable research tool to mitigate such challenges. In the present study, we acquired high spatial resolution MRI datasets, including diffusion MRI (dMRI) at 25 ​μm isotropic resolution and quantitative susceptibility mapping (QSM) at 21.5 ​μm isotropic resolution to validate with conventional mouse brain histology. Diffusion weighted images (DWIs) show better delineation of cortical layers and glomeruli in the olfactory bulb than fractional anisotropy (FA) maps. However, among all the image contrasts, including quantitative susceptibility mapping (QSM), T1/T2∗ images and DTI metrics, FA maps highlight unique laminar architecture in sub-regions of the hippocampus, including the strata of the dentate gyrus and CA fields of the hippocampus. The mean diffusivity (MD) and axial diffusivity (AD) yield higher correlation with DAPI (0.62 and 0.71) and NeuN (0.78 and 0.74) than with NF-160 (-0.34 and -0.49). The correlations between FA and DAPI, NeuN, and NF-160 are 0.31, -0.01, and -0.49, respectively. Our findings demonstrate that MRI at microscopic resolution deliver a three-dimensional, non-invasive and non-destructive platform for characterization of fine structural detail in both gray matter and white matter of the mouse brain.

Toward an MRI-Based Mesoscale Connectome of the Squid Brain

Using high-resolution diffusion magnetic resonance imaging (dMRI) and a suite of old and new staining techniques, the beginnings of a multi-scale connectome map of the squid brain is erected. The first of its kind for a cephalopod, this includes the confirmation of 281 known connections with the addition of 145 previously undescribed pathways. These and other features suggest a suite of functional attributes, including (1) retinotopic organization through the optic lobes and into other brain areas well beyond that previously recognized, (2) a level of complexity and sub-division in the basal lobe supporting ideas of convergence with the vertebrate basal ganglia, and (3) differential lobe-dependent growth rates that mirror complexity and transitions in ontogeny.

Upregulation of Cisd2 attenuates Alzheimer's-related neuronal loss in mice

CDGSH iron-sulfur domain-containing protein 2 (Cisd2), a protein that declines in an age-dependent manner, mediates lifespan in mammals. Cisd2 deficiency causes accelerated aging and shortened lifespan, whereas persistent expression of Cisd2 promotes longevity in mice. Alzheimer's disease (AD) is the most prevalent form of senile dementia and is without an effective therapeutic strategy. We investigated whether Cisd2 upregulation is able to ameliorate amyloid β (Aβ) toxicity and prevent neuronal loss using an AD mouse model. Our study makes three major discoveries. First, using the AD mouse model (APP/PS1 double transgenic mice), the dosage of Cisd2 appears to modulate the severity of AD phenotypes. Cisd2 overexpression (∼two-fold) significantly promoted survival and alleviated the pathological defects associated with AD. Conversely, Cisd2 deficiency accelerated AD pathogenesis. Secondly, Cisd2 overexpression protected against Aβ-mediated mitochondrial damage and attenuated loss of neurons and neuronal progenitor cells. Finally, an increase in Cisd2 shifted the expression profiles of a panel of genes that are dysregulated by AD toward the patterns observed in wild-type mice. These findings highlight Cisd2-based therapies as a potential disease-modifying strategy for AD. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Analysis of Propagation of Slow Rhythmic Activity Induced in Ex Vivo Rat Brain Slices

Slow wave oscillation is a synchronous oscillatory mechanism that is a characteristic wave type of the cerebral cortex during physiological deep sleep or anesthesia. It may play an important role in cortical analysis of sensory input. Our goal was (1) to develop optimal conditions for the induction of this slow rhythmic activity in adult rat cortical slices, (2) to identify connections through which the activity propagates between coupled cortical regions, and (3) to study the pattern of horizontal and vertical flow of activity developed spontaneously in cortical slices. Experiments were performed on intact or differently incised rat cortical slices. According to our results, spontaneous cortical activity develops reliably in slightly modified artificial cerebrospinal fluid, first in the entorhinal cortical region of horizontally cut slices and then it spreads directly to the perirhinal (PRh) cortex. The activity readily generated in layer 2/3 of the entorhinal cortex then quickly spreads vertically to upper layer 2-3 in the same area and to the neighboring regions, that is, to the PRh cortex. Synchronization of activity in neighboring cortical areas occurs through both callosal connections and layer 2-3 intrinsic network, which are important in the propagation of spontaneous, inherent cortical slow wave activity.

Diffusion tensor tractography in children with sensory processing disorder: Potentials for devising machine learning classifiers

The "sensory processing disorder" (SPD) refers to brain's inability to organize sensory input for appropriate use. In this study, we determined the diffusion tensor imaging (DTI) microstructural and connectivity correlates of SPD, and apply machine learning algorithms for identification of children with SPD based on DTI/tractography metrics. A total of 44 children with SPD and 41 typically developing children (TDC) were prospectively recruited and scanned. In addition to fractional anisotropy (FA), mean diffusivity (MD), and radial diffusivity (RD), we applied probabilistic tractography to generate edge density (ED) and track density (TD) from DTI maps. For identification of children with SPD, accurate classification rates from a combination of DTI microstructural (FA, MD, AD, and RD), connectivity (TD) and connectomic (ED) metrics with different machine learning algorithms - including naïve Bayes, random forest, support vector machine, and neural networks - were determined. In voxel-wise analysis, children with SPD had lower FA, ED, and TD but higher MD and RD compared to TDC - predominantly in posterior white matter tracts including posterior corona radiata, posterior thalamic radiation, and posterior body and splenium of corpus callosum. In stepwise penalized logistic regression, the only independent variable distinguishing children with SPD from TDC was the average TD in the splenium (p < 0.001). Among different combinations of machine learning algorithms and DTI/connectivity metrics, random forest models using tract-based TD yielded the highest accuracy in classification of SPD - 77.5% accuracy, 73.8% sensitivity, and 81.6% specificity. Our findings demonstrate impaired microstructural and connectivity/connectomic integrity in children with SPD, predominantly in posterior white matter tracts, and with reduced TD of the splenium of corpus callosum as the most distinctive pattern. Applying machine learning algorithms, these connectivity metrics can be used to devise novel imaging biomarkers for neurodevelopmental disorders.

Diffusion MRI fiber tractography of the brain

The ability of fiber tractography to delineate non-invasively the white matter fiber pathways of the brain raises possibilities for clinical applications and offers enormous potential for neuroscience. In the last decade, fiber tracking has become the method of choice to investigate quantitative MRI parameters in specific bundles of white matter. For neurosurgeons, it is quickly becoming an invaluable tool for the planning of surgery, allowing for visualization and localization of important white matter pathways before and even during surgery. Fiber tracking has also claimed a central role in the field of "connectomics," a technique that builds and studies comprehensive maps of the complex network of connections within the brain, and to which significant resources have been allocated worldwide. Despite its unique abilities and exciting applications, fiber tracking is not without controversy, in particular when it comes to its interpretation. As neuroscientists are eager to study the brain's connectivity, the quantification of tractography-derived "connection strengths" between distant brain regions is becoming increasingly popular. However, this practice is often frowned upon by fiber-tracking experts. In light of this controversy, this paper provides an overview of the key concepts of tractography, the technical considerations at play, and the different types of tractography algorithm, as well as the common misconceptions and mistakes that surround them. We also highlight the ongoing challenges related to fiber tracking. While recent methodological developments have vastly increased the biological accuracy of fiber tractograms, one should be aware that, even with state-of-the-art techniques, many issues that severely bias the resulting structural "connectomes" remain unresolved.

The Superoanterior Fasciculus (SAF): A Novel White Matter Pathway in the Human Brain?

Fiber tractography (FT) using diffusion magnetic resonance imaging (dMRI) is widely used for investigating microstructural properties of white matter (WM) fiber-bundles and for mapping structural connections of the human brain. While studying the architectural configuration of the brain's circuitry with FT is not without controversy, recent progress in acquisition, processing, modeling, analysis, and visualization of dMRI data pushes forward the reliability in reconstructing WM pathways. Despite being aware of the well-known pitfalls in analyzing dMRI data and several other limitations of FT discussed in recent literature, we present the superoanterior fasciculus (SAF), a novel bilateral fiber tract in the frontal region of the human brain that-to the best of our knowledge-has not been documented. The SAF has a similar shape to the anterior part of the cingulum bundle, but it is located more frontally. To minimize the possibility that these FT findings are based on acquisition or processing artifacts, different dMRI data sets and processing pipelines have been used to describe the SAF. Furthermore, we evaluated the configuration of the SAF with complementary methods, such as polarized light imaging (PLI) and human brain dissections. The FT results of the SAF demonstrate a long pathway, consistent across individuals, while the human dissections indicate fiber pathways connecting the postero-dorsal with the antero-dorsal cortices of the frontal lobe.

Structural brain anomalies in patients with FOXG1 syndrome and in Foxg1+/- mice

Objective

FOXG1 syndrome is a rare neurodevelopmental disorder associated with heterozygous FOXG1 variants or chromosomal microaberrations in 14q12. The study aimed at assessing the scope of structural cerebral anomalies revealed by neuroimaging to delineate the genotype and neuroimaging phenotype associations.

Methods

We compiled 34 patients with a heterozygous (likely) pathogenic FOXG1 variant. Qualitative assessment of cerebral anomalies was performed by standardized re-analysis of all 34 MRI data sets. Statistical analysis of genetic, clinical and neuroimaging data were performed. We quantified clinical and neuroimaging phenotypes using severity scores. Telencephalic phenotypes of adult Foxg1+/- mice were examined using immunohistological stainings followed by quantitative evaluation of structural anomalies.

Results

Characteristic neuroimaging features included corpus callosum anomalies (82%), thickening of the fornix (74%), simplified gyral pattern (56%), enlargement of inner CSF spaces (44%), hypoplasia of basal ganglia (38%), and hypoplasia of frontal lobes (29%). We observed a marked, filiform thinning of the rostrum as recurrent highly typical pattern of corpus callosum anomaly in combination with distinct thickening of the fornix as a characteristic feature. Thickening of the fornices was not reported previously in FOXG1 syndrome. Simplified gyral pattern occurred significantly more frequently in patients with early truncating variants. Higher clinical severity scores were significantly associated with higher neuroimaging severity scores. Modeling of Foxg1 heterozygosity in mouse brain recapitulated the associated abnormal cerebral morphology phenotypes, including the striking enlargement of the fornix.

Interpretation

Combination of specific corpus callosum anomalies with simplified gyral pattern and hyperplasia of the fornices is highly characteristic for FOXG1 syndrome.

Heterozygosity for Nuclear Factor One X in mice models features of Malan syndrome

BACKGROUND

Nuclear Factor One X (NFIX) haploinsufficiency in humans results in Malan syndrome, a disorder characterized by overgrowth, macrocephaly and intellectual disability. Although clinical assessments have determined the underlying symptomology of Malan syndrome, the fundamental mechanisms contributing to the enlarged head circumference and intellectual disability in these patients remains undefined.

METHODS

Here, we used Nfix heterozygous mice as a model to investigate these aspects of Malan syndrome. Volumetric magnetic resonance imaging (MRI) was used to calculate the volumes of 20 brain sub regions. Diffusion tensor MRI was used to perform tractography-based analyses of the corpus callosum, hippocampal commissure, and anterior commissure, as well as structural connectome mapping of the whole brain. Immunohistochemistry examined the neocortical cellular populations. Two behavioral assays were performed, including the active place avoidance task to assess spatial navigation and learning and memory function, and the 3-chambered sociability task to examine social behaviour.

FINDINGS

Adult Nfix+/- mice exhibit significantly increased brain volume (megalencephaly) compared to wildtypes, with the cerebral cortex showing the highest increase. Moreover, all three forebrain commissures, in particular the anterior commissure, revealed significantly reduced fractional anisotropy, axial and radial diffusivity, and tract density intensity. Structural connectome analyses revealed aberrant connectivity between many crucial brain regions. Finally, Nfix+/- mice exhibit behavioral deficits that model intellectual disability.

INTERPRETATION

Collectively, these data provide a significant conceptual advance in our understanding of Malan syndrome by suggesting that megalencephaly underlies the enlarged head size of these patients, and that disrupted cortical connectivity may contribute to the intellectual disability these patients exhibit. FUND: Australian Research Council (ARC) Discovery Project Grants, ARC Fellowship, NYSTEM and Australian Postgraduate Fellowships.

Post mortem high resolution diffusion MRI for large specimen imaging at 11.7 T with 3D segmented echo-planar imaging

BACKGROUND

Diffusion weighted imaging (DWI) is the only in vivo technique allowing for the mapping of tissue fiber architecture. Post mortem DWI is an increasingly popular method, since longer acquisition times (compared to in vivo) allow higher spatial and angular resolutions to be achieved. However, DWI protocols must be adapted to post mortem tissue (e.g., tuning acquisition parameters to account for changes in T1/T2). New method: In this work, we developed a framework to obtain high quality diffusion weighted images on post mortem large samples by using a combination of fast imaging with 3D diffusion-weighted segmented EPI (3D-DW seg-EPI), Gadolinium soaking and data denoising. Analyses including tractography were used to check the quality of the acquired data, including a comparison with 3D-DW SE acquisitions. Comparison with existing method: Effects on diffusion data of each of the components of the framework were tested: 3D-DW seg-EPI versus 3D-DW SE EPI; with and without data denoising; with and without Gd-soaking.

CONCLUSIONS

Our study demonstrated the feasibility of analysing anatomical connectivity using diffusion imaging of a post mortem macaque brain with a 3D-DW seg-EPI sequence acquired at ultra-high field. The combination of high angular and spatial resolution DWI with Gd-soaking and denoising provided data allowing us to perform diffusion tractography with results very similar to those obtained with a 3D-DW SE acquisition (with shorter acquisition times: 222 h versus 37 h for 3D-DW seg-EPI).

Track density imaging in progressive supranuclear palsy: A pilot study

Progressive supranuclear palsy (PSP) is a neurodegenerative disorder characterized by white matter (WM) changes in different supra- and infratentorial brain structures. We used track density imaging (TDI) to characterize WM microstructural alterations in patients with PSP-Richardson's Syndrome (PSP-RS). Moreover, we investigated the diagnostic utility of TDI in distinguishing patients with PSP-RS from those with Parkinson's disease and healthy controls (HC). Twenty PSP-RS patients, 21 PD patients, and 23 HC underwent a 3 T MRI diffusion-weighted (DW) imaging. Then, we combined constrained spherical deconvolution and WM probabilistic tractography to reconstruct track density maps by calculating the number of WM streamlines traversing each voxel. Voxel-wise analysis was performed to assess group differences in track density maps. A support vector machine (SVM) approach was also used to evaluate the performance of TDI for discriminating between groups. Relative to PD patients, decreases in track density in PSP-RS patients were found in brainstem, cerebellum, thalamus, corpus callosum, and corticospinal tract. Similar findings were obtained between PSP-RS patients and HC. No differences in TDI were observed between PD and HC. SVM approach based on whole-brain analysis differentiated PD patients from PSP-RS with an area under the curve (AUC) of 0.82. The AUC reached a value of 0.98 considering only the voxels belonging to the superior cerebellar peduncle. This study shows that TDI may represent a useful approach for characterizing WM alterations in PSP-RS patients. Moreover, track density decrease in PSP could be considered a new feature for the differentiation of patients with PSP-RS from those with PD.

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.

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.

Facial nerve tractography: A new tool for the detection of perineural spread in parotid cancers

OBJECTIVES

To determine whether facial nerve MR tractography is useful in detecting PeriNeural Spread in parotid cancers.

METHODS

Forty-five participants were enrolled. Thirty patients with surgically managed parotid tumors (15 malignant, 15 benign) were compared with 15 healthy volunteers. All of them had undergone 3T-MRI with diffusion acquisition and post-processing constrained spherical deconvolution-based tractography. Parameters of diffusion-weighted sequences were b-value 1,000 s/mm², 32 directions. Two radiologists performed a blinded visual reading of tractographic maps and graded the facial nerve average pathlength and fractional anisotropy (FA). We also compared diagnostic accuracy of tractography with morphological MRI sequences to detect PeriNeural Spread. Non-parametric methods were used.

RESULTS

Average pathlength was significantly higher in cases with PeriNeural Spread (39.86 mm [Quartile1: 36.27; Quartile3: 51.19]) versus cases without (16.23 mm [12.90; 24.90]), p<0.001. The threshold above which there was a significant association with PeriNeural Spread was set at 27.36 mm (Se: 100%; Sp: 84%; AUC: 0.96, 95% CI 0.904-1). There were no significant differences in FA between groups. Tractography map visual analyses directly displayed PeriNeural Spread in distal neural ramifications with sensitivity of 75%, versus 50% using morphological sequences.

CONCLUSIONS

Tractography could be used to identify facial nerve PeriNeural Spread by parotid cancers.

KEY POINTS

• Tractography could detect facial nerve PeriNeural Spread in parotid cancers. • The average pathlength parameter is increased in case of PeriNeural Spread. • Tractography could map PeriNeural Spread more precisely than conventional imaging.

Age is reflected in the Fractal Dimensionality of MRI Diffusion Based Tractography

Fractal analysis is a widely used tool to analyze the geometrical complexity of biological structures. The geometry of natural objects such as plants, clouds, cellular structures, blood vessel, and many others cannot be described sufficiently with Euclidian geometric properties, but can be represented by a parameter called the fractal dimension. Here we show that a specific estimate of fractal dimension, the correlation dimension, is able to describe changes in the structural complexity of the human brain, based on data from magnetic resonance diffusion imaging. White matter nerve fiber bundles, represented by tractograms, were analyzed with regards to geometrical complexity, using fractal geometry. The well-known age-related change of white matter tissue was used to verify changes by means of fractal dimension. Structural changes in the brain were successfully be observed and quantified by fractal dimension and compared with changes in fractional anisotropy.

Track-weighted imaging for neuroretina: Evaluations in healthy volunteers and ischemic optic neuropathy

BACKGROUND

The use of MRI-tractography to explore the human neuroretina is yet to be reported. Track-weighted imaging (TWI) was recently introduced as a qualitative tractography-based method with high anatomical contrast.

PURPOSE

To explore the human retina in healthy volunteers and patients with anterior ischemic optic neuropathy (AION) using TWI reconstructions.

STUDY TYPE

Prospective.

POPULATION

Twenty AION patients compared with 20 healthy volunteers.

FIELD STRENGTH/SEQUENCE

3.0T MRI diffusion-weighted imaging (DWI) with b-value of 1000 s/mm2 and 60 diffusion-weighting noncollinear directions.

ASSESSMENT

We performed constrained spherical deconvolution from the diffusion-weighted signal and volumetric tractography method, whereby 10 million streamlines are initiated from seed points randomly distributed throughout the orbital area. We then reconstructed TWI maps with isotropic voxel size of 300 μm.

STATISTICAL TESTS

We tested the effect of the number of diffusion-weighting directions, ocular laterality, and ocular dominance on healthy retinal fascicles distribution. We then performed factorial analysis of variance to test the effects of the presence/absence of the fascicles on the visual field defect in patients.

RESULTS

In healthy volunteers, we found more temporal fascicle in right eyes (P = 0.001), more superior fascicles in dominant eyes (P = 0.014), and fewer fascicles with tractography maps based on 30 directions than those based on 45 directions (P = 9 × 10-8 ) and 60 directions (P = 6 × 10-7 ). Eight out of 20 AION patients presented with complete absence of neuroretinal fascicle, side of the disease, which was correlated with visual field mean deviation at the 6-month visit [F(1,17) = 6.97, P = 0.016]. Seven patients presented with a temporal fascicle in the injured eye; this fascicle presence was linked to visual field mean deviation at the 6-month visit [F(1,17) = 8.43, P = 0.009].

DATA CONCLUSION

In AION patients, the presence of the temporal neuroretinal fascicle in the affected eye provides an objective outcome radiological sign correlated with visual performance.

LEVEL OF EVIDENCE

2 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018.

Super-Resolution Track-Density Imaging Reveals Fine Anatomical Features in Tree Shrew Primary Visual Cortex and Hippocampus

Diffusion-weighted magnetic resonance imaging (dMRI) is widely used to study white and gray matter (GM) micro-organization and structural connectivity in the brain. Super-resolution track-density imaging (TDI) is an image reconstruction method for dMRI data, which is capable of providing spatial resolution beyond the acquired data, as well as novel and meaningful anatomical contrast that cannot be obtained with conventional reconstruction methods. TDI has been used to reveal anatomical features in human and animal brains. In this study, we used short track TDI (stTDI), a variation of TDI with enhanced contrast for GM structures, to reconstruct direction-encoded color maps of fixed tree shrew brain. The results were compared with those obtained with the traditional diffusion tensor imaging (DTI) method. We demonstrated that fine microstructures in the tree shrew brain, such as Baillarger bands in the primary visual cortex and the longitudinal component of the mossy fibers within the hippocampal CA3 subfield, were observable with stTDI, but not with DTI reconstructions from the same dMRI data. The possible mechanisms underlying the enhanced GM contrast are discussed.

Greater occipital nerve MR tractography: Feasibility and anatomical considerations

BACKGROUND AND PURPOSE

To assess the feasibility of greater occipital nerve (GON) tractography using a fully automated tractography technique on the whole-neck volume, in comparison with anatomical knowledge.

METHODS

Healthy subjects were consecutively included in this study if they had no history or symptoms of headache or brain disorder. A 3T MRI scanner with a 32 channel head coil was used. The following parameters for Diffusion Weighed (DWI) were used: b value of 1000 s/mm², 32 directions, acquired voxel size: 2 mm isotropic. High-Order tractography with the Constrained Spherical Deconvolution (CSD) model was generated. Track-Weighted Imaging (TWI) maps were generated with MRTrix. Two radiologists performed blind evaluations of the GON pathways on TWI maps.

RESULTS

A total of 20 healthy subjects were included (12 males and eight females, mean age 53.8 years old). In comparison with anatomical atlas, GON complete visualization (from C1-C2 origin to muscular emergence) was possible in 18 out of 20 healthy subjects. In two cases, GON was not visible in the cervical spine foramen.

CONCLUSION

Tractography through TWI is a feasible technique to accurately depict GON. This technique may appear as a promising technique for therapeutic management of patients with occipital neuralgia.

Whole mouse brain imaging using optical coherence tomography: reconstruction, normalization, segmentation, and comparison with diffusion MRI

An automated massive histology setup combined with an optical coherence tomography (OCT) microscope was used to image a total of [Formula: see text] whole mouse brains. Each acquisition generated a dataset of thousands of OCT volumetric tiles at a sampling resolution of [Formula: see text]. This paper describes techniques for reconstruction and segmentation of the sliced brains. In addition to the measured OCT optical reflectivity, a single scattering photon model was used to compute the attenuation coefficients within each tissue slice. Average mouse brain templates were generated for both the OCT reflectivity and attenuation contrasts and were used with an [Formula: see text]-tissue segmentation algorithm. To better understand the brain tissue OCT contrast origin, one of the mouse brains was acquired using dMRI and coregistered to its corresponding assembled brain. Our results indicate that the optical reflectivity in a fiber bundle varies with its orientation, its fiber density, and the number of fiber orientations it contains. The OCT mouse brain template generation and coregistration to dMRI data demonstrate the potential of this massive histology technique to pursue cross-sectional, multimodal, and multisubject investigations of small animal brains.

Whole-Brain High-Resolution Structural Connectome: Inter-Subject Validation and Application to the Anatomical Segmentation of the Striatum

The present study describes extraction of high-resolution structural connectome (HRSC) in 99 healthy subjects, acquired and made available by the Human Connectome Project. Single subject connectomes were then registered to the common surface space to allow assessment of inter-individual reproducibility of this novel technique using a leave-one-out approach. The anatomic relevance of the surface-based connectome was examined via a clustering algorithm, which identified anatomic subdivisions within the striatum. The connectivity of these striatal subdivisions were then mapped on the cortical and other subcortical surfaces. Findings demonstrate that HRSC analysis is robust across individuals and accurately models the actual underlying brain networks related to the striatum. This suggests that this method has the potential to model and characterize the healthy whole-brain structural network at high anatomic resolution.

Within brain area tractography suggests local modularity using high resolution connectomics

Previous structural brain connectivity studies have mainly focussed on the macroscopic scale of around 1,000 or fewer brain areas (network nodes). However, it has recently been demonstrated that high resolution structural connectomes of around 50,000 nodes can be generated reproducibly. In this study, we infer high resolution brain connectivity matrices using diffusion imaging data from the Human Connectome Project. With such high resolution we are able to analyse networks within brain areas in a single subject. We show that the global network has a scale invariant topological organisation, which means there is a hierarchical organisation of the modular architecture. Specifically, modules within brain areas are spatially localised. We find that long range connections terminate between specific modules, whilst short range connections via highly curved association fibers terminate within modules. We suggest that spatial locations of white matter modules overlap with cytoarchitecturally distinct grey matter areas and may serve as the structural basis for function specialisation within brain areas. Future studies might elucidate how brain diseases change this modular architecture within brain areas.

Improvement in White Matter Tract Reconstruction with Constrained Spherical Deconvolution and Track Density Mapping in Low Angular Resolution Data: A Pediatric Study and Literature Review

INTRODUCTION

Diffusion-weighted magnetic resonance imaging (DW-MRI) allows noninvasive investigation of brain structure in vivo. Diffusion tensor imaging (DTI) is a frequently used application of DW-MRI that assumes a single main diffusion direction per voxel, and is therefore not well suited for reconstructing crossing fiber tracts. Among the solutions developed to overcome this problem, constrained spherical deconvolution with probabilistic tractography (CSD-PT) has provided superior quality results in clinical settings on adult subjects; however, it requires particular acquisition parameters and long sequences, which may limit clinical usage in the pediatric age group. The aim of this work was to compare the results of DTI with those of track density imaging (TDI) maps and CSD-PT on data from neonates and children, acquired with low angular resolution and low b-value diffusion sequences commonly used in pediatric clinical MRI examinations.

MATERIALS AND METHODS

We analyzed DW-MRI studies of 50 children (eight neonates aged 3-28 days, 20 infants aged 1-8 months, and 22 children aged 2-17 years) acquired on a 1.5 T Philips scanner using 34 gradient directions and a b-value of 1,000 s/mm². Other sequence parameters included 60 axial slices; acquisition matrix, 128 × 128; average scan time, 5:34 min; voxel size, 1.75 mm × 1.75 mm × 2 mm; one b = 0 image. For each subject, we computed principal eigenvector (EV) maps and directionally encoded color TDI maps (DEC-TDI maps) from whole-brain tractograms obtained with CSD-PT; the cerebellar-thalamic, corticopontocerebellar, and corticospinal tracts were reconstructed using both CSD-PT and DTI. Results were compared by two neuroradiologists using a 5-point qualitative score.

RESULTS

The DEC-TDI maps obtained presented higher anatomical detail than EV maps, as assessed by visual inspection. In all subjects, white matter (WM) tracts were successfully reconstructed using both tractography methodologies. The mean qualitative scores of all tracts obtained with CSD-PT were significantly higher than those obtained with DTI (p-value < 0.05 for all comparisons).

CONCLUSION

CSD-PT can be successfully applied to DW-MRI studies acquired at 1.5 T with acquisition parameters adapted for pediatric subjects, thus providing TDI maps with greater anatomical detail. This methodology yields satisfactory results for clinical purposes in the pediatric age group.

Track density imaging of hypertrophic olivary degeneration from multiple sclerosis plaque

A 32-year-old female with relapsing–remitting multiple sclerosis (MS) presented with severe new onset ataxia and diplopia. MRI showed a new inflammatory MS lesion that involved the right dorsal pons and extended into the adjacent superior cerebellar peduncle. The patient improved with aggressive immunotherapy; however, repeat MRI 3 months later revealed a new non-enhancing lesion in the left inferior medullary olive. The differential diagnosis for this new lesion included an MS lesion vs hypertrophic olivary degeneration, with infarct or neoplasm as the less likely considerations. We used track density imaging, which provides unprecedented anatomic details based on probabilistic tractography streamlines, to demonstrate apparent changes in the integrity of the dentato–rubro–olivary pathway (Guillain–Mollaret triangle) that were consistent with the diagnosis of hypertrophic olivary degeneration from the antecedent MS lesion involving the right superior cerebellar peduncle. Further medical therapy was avoided, and follow-up MRI 1 year later showed interval involution of the left olivary lesion. This case demonstrates the potential clinical utility of using track density imaging to detect lesion-induced alterations in brainstem connectivity and characterize neurodegeneration in patients.

Label-free photoacoustic tomography of whole mouse brain structures ex vivo

Capitalizing on endogenous hemoglobin contrast, photoacoustic-computed tomography (PACT), a deep-tissue high-resolution imaging modality, has drawn increasing interest in neuroimaging. However, most existing studies are limited to functional imaging on the cortical surface and the deep brain structural imaging capability of PACT has never been demonstrated. Here, we explicitly studied the limiting factors of deep brain PACT imaging. We found that the skull distorted the acoustic signal and blood suppressed the structural contrast from other chromophores. When the two effects are mitigated, PACT can potentially provide high-resolution label-free imaging of structures in the entire mouse brain. With [Formula: see text] in-plane resolution, we can clearly identify major structures of the brain, which complements magnetic resonance microscopy for imaging small-animal brain structures. Spectral PACT studies indicate that structural contrasts mainly originate from cytochrome distribution and that the presence of lipid sharpens the image contrast; brain histology results provide further validation. The feasibility of imaging the structure of the brain in vivo is also discussed. Our results demonstrate that PACT is a promising modality for both structural and functional brain imaging.

Multimodal 7T Imaging of Thalamic Nuclei for Preclinical Deep Brain Stimulation Applications

Precise neurosurgical targeting of electrode arrays within the brain is essential to the successful treatment of a range of brain disorders with deep brain stimulation (DBS) therapy. Here, we describe a set of computational tools to generate in vivo, subject-specific atlases of individual thalamic nuclei thus improving the ability to visualize thalamic targets for preclinical DBS applications on a subject-specific basis. A sequential nonlinear atlas warping technique and a Bayesian estimation technique for probabilistic crossing fiber tractography were applied to high field (7T) susceptibility-weighted and diffusion-weighted imaging, respectively, in seven rhesus macaques. Image contrast, including contrast within thalamus from the susceptibility-weighted images, informed the atlas warping process and guided the seed point placement for fiber tractography. The susceptibility-weighted imaging resulted in relative hyperintensity of the intralaminar nuclei and relative hypointensity in the medial dorsal nucleus, pulvinar, and the medial/ventral border of the ventral posterior nuclei, providing context to demarcate borders of the ventral nuclei of thalamus, which are often targeted for DBS applications. Additionally, ascending fiber tractography of the medial lemniscus, superior cerebellar peduncle, and pallidofugal pathways into thalamus provided structural demarcation of the ventral nuclei of thalamus. The thalamic substructure boundaries were validated through in vivo electrophysiological recordings and post-mortem blockface tissue sectioning. Together, these imaging tools for visualizing and segmenting thalamus have the potential to improve the neurosurgical targeting of DBS implants and enhance the selection of stimulation settings through more accurate computational models of DBS.