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Diffusion-weighted MRI is our most promising method for estimating microscopic tissue morphology in vivo. The signal acquisition is based on scanner-generated external magnetic gradients. However, it will also be affected by susceptibility-induced internal magnetic gradients caused by interactions between the tissue and the static magnetic field of the scanner. With 3D in silico experiments, we show how internal gradients cause morphology-, compartment-, and orientation-dependence of spin-echo and pulsed-gradient spin-echo experiments in myelinated axons. These effects surpass those observed with previous 2D modelling corresponding to straight cylinders. For an ex vivo monkey brain, we observe the orientation-dependence generated only when including non-circular cross-sections in the in silico morphological configurations, and find orientation-dependent deviation of up to 17% for diffusion tensor metrics. Interestingly, we find that the orientation-dependence not only biases the signal across different brain regions, but also carries a sensitivity to the morphology of axonal cross-sections which is not attainable by the idealised theoretical diffusion-weighted MRI signal., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Brain white matter is a dynamic environment that continuously adapts and reorganizes in response to stimuli and pathological changes. Glial cells, especially, play a key role in tissue repair, inflammation modulation, and neural recovery. The movements of glial cells and changes in their concentrations can influence the surrounding axon morphology. We introduce the White Matter Generator (WMG) tool to enable the study of how axon morphology is influenced through such dynamical processes, and how this, in turn, influences the diffusion-weighted MRI signal. This is made possible by allowing interactive changes to the configuration of the phantom generation throughout the optimization process. The phantoms can consist of myelinated axons, unmyelinated axons, and cell clusters, separated by extra-cellular space. Due to morphological flexibility and computational advantages during the optimization, the tool uses ellipsoids as building blocks for all structures; chains of ellipsoids for axons, and individual ellipsoids for cell clusters. After optimization, the ellipsoid representation can be converted to a mesh representation which can be employed in Monte-Carlo diffusion simulations. This offers an effective method for evaluating tissue microstructure models for diffusion-weighted MRI in controlled bio-mimicking white matter environments. Hence, the WMG offers valuable insights into white matter's adaptive nature and implications for diffusion-weighted MRI microstructure models, and thereby holds the potential to advance clinical diagnosis, treatment, and rehabilitation strategies for various neurological disorders and injuries., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Winther, Peulicke, Andersson, Kjer, Bærentzen and Dyrby.)

Purpose: This study aims to evaluate two distinct approaches for fiber radius estimation using diffusion-relaxation MRI data acquired in biomimetic microfiber phantoms that mimic hollow axons. The methods considered are the spherical mean power-law approach and a T 2 -based pore size estimation technique., Theory and Methods: A general diffusion-relaxation theoretical model for the spherical mean signal from water molecules within a distribution of cylinders with varying radii was introduced, encompassing the evaluated models as particular cases. Additionally, a new numerical approach was presented for estimating effective radii (i.e., MRI-visible mean radii) from the ground truth radii distributions, not reliant on previous theoretical approximations and adaptable to various acquisition sequences. The ground truth radii were obtained from scanning electron microscope images., Results: Both methods show a linear relationship between effective radii estimated from MRI data and ground-truth radii distributions, although some discrepancies were observed. The spherical mean power-law method overestimated fiber radii. Conversely, the T 2 -based method exhibited higher sensitivity to smaller fiber radii, but faced limitations in accurately estimating the radius in one particular phantom, possibly because of material-specific relaxation changes., Conclusion: The study demonstrates the feasibility of both techniques to predict pore sizes of hollow microfibers. The T 2 -based technique, unlike the spherical mean power-law method, does not demand ultra-high diffusion gradients, but requires calibration with known radius distributions. This research contributes to the ongoing development and evaluation of neuroimaging techniques for fiber radius estimation, highlights the advantages and limitations of both methods, and provides datasets for reproducible research., (© 2024 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals LLC on behalf of International Society for Magnetic Resonance in Medicine.)

Axon radius is a potential biomarker for brain diseases and a crucial tissue microstructure parameter that determines the speed of action potentials. Diffusion MRI (dMRI) allows non-invasive estimation of axon radius, but accurately estimating the radius of axons in the human brain is challenging. Most axons in the brain have a radius below one micrometer, which falls below the sensitivity limit of dMRI signals even when using the most advanced human MRI scanners. Therefore, new MRI methods that are sensitive to small axon radii are needed. In this proof-of-concept investigation, we examine whether a surface-based axonal relaxation process could mediate a relationship between intra-axonal T 2 and T 1 times and inner axon radius, as measured using postmortem histology. A unique in vivo human diffusion-T 1 -T 2 relaxation dataset was acquired on a 3T MRI scanner with ultra-strong diffusion gradients, using a strong diffusion-weighting (i.e., b = 6,000 s/mm 2 ) and multiple inversion and echo times. A second reduced diffusion-T 2 dataset was collected at various echo times to evaluate the model further. The intra-axonal relaxation times were estimated by fitting a diffusion-relaxation model to the orientation-averaged spherical mean signals. Our analysis revealed that the proposed surface-based relaxation model effectively explains the relationship between the estimated relaxation times and the histological axon radius measured in various corpus callosum regions. Using these histological values, we developed a novel calibration approach to predict axon radius in other areas of the corpus callosum. Notably, the predicted radii and those determined from histological measurements were in close agreement., Competing Interests: MB was an employee of Hays plc and a consultant for F. Hoffmann-La Roche Ltd. SM was an employee and shareholder of F. Hoffmann-La Roche Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Barakovic, Pizzolato, Tax, Rudrapatna, Magon, Dyrby, Granziera, Thiran, Jones and Canales-Rodríguez.)

We enable the estimation of the per-axon axial diffusivity from single encoding, strongly diffusion-weighted, pulsed gradient spin echo data. Additionally, we improve the estimation of the per-axon radial diffusivity compared to estimates based on spherical averaging. The use of strong diffusion weightings in magnetic resonance imaging (MRI) allows to approximate the signal in white matter as the sum of the contributions from only axons. At the same time, spherical averaging leads to a major simplification of the modeling by removing the need to explicitly account for the unknown distribution of axonal orientations. However, the spherically averaged signal acquired at strong diffusion weightings is not sensitive to the axial diffusivity, which cannot therefore be estimated although needed for modeling axons - especially in the context of multi-compartmental modeling. We introduce a new general method for the estimation of both the axial and radial axonal diffusivities at strong diffusion weightings based on kernel zonal modeling. The method could lead to estimates that are free from partial volume bias with gray matter or other isotropic compartments. The method is tested on publicly available data from the MGH Adult Diffusion Human Connectome project. We report reference values of axonal diffusivities based on 34 subjects, and derive estimates of axonal radii from only two shells. The estimation problem is also addressed from the angle of the required data preprocessing, the presence of biases related to modeling assumptions, current limitations, and future possibilities., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Marco Pizzolato reports financial support was provided by EUFramework Programme for Research and Innovation Marie Sklodowska-Curie Actions. Erick Jorge Canales-Rodríguez reports financial support was provided by Swiss National Science Foundation. Mariam Andersson reports financial support was provided by Capital Region of Denmark. Tim B. Dyrby reports financial support was provided by the European Research Council., (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)

Magnetic resonance imaging (MRI) and light-sheet fluorescence microscopy (LSFM) are technologies that enable non-disruptive 3-dimensional imaging of whole mouse brains. A combination of complementary information from both modalities is desirable for studying neuroscience in general, disease progression and drug efficacy. Although both technologies rely on atlas mapping for quantitative analyses, the translation of LSFM recorded data to MRI templates has been complicated by the morphological changes inflicted by tissue clearing and the enormous size of the raw data sets. Consequently, there is an unmet need for tools that will facilitate fast and accurate translation of LSFM recorded brains to in vivo, non-distorted templates. In this study, we have developed a bidirectional multimodal atlas framework that includes brain templates based on both imaging modalities, region delineations from the Allen's Common Coordinate Framework, and a skull-derived stereotaxic coordinate system. The framework also provides algorithms for bidirectional transformation of results obtained using either MR or LSFM (iDISCO cleared) mouse brain imaging while the coordinate system enables users to easily assign in vivo coordinates across the different brain templates., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Synchrotron X-ray computed tomography (SXCT) allows 3D imaging of tissue with a very large field of view and an excellent micron resolution and enables the investigation of muscle fiber atrophy in 3D. The study aimed to explore the 3D micro-architecture of healthy skeletal muscle fibers and muscle fibers at different stages of atrophy (stroke sample = muscle atrophy; spinal cord injury (SCI) sample = severe muscle atrophy). Three muscle samples: a healthy control sample; a stroke sample (atrophic sample), and an SCI sample (severe atrophic sample) were imaged using SXCT, and muscle fiber populations were segmented and quantified for microarchitecture and morphology differences. The volume fraction of muscle fibers was 74.7%, 70.2%, and 35.3% in the healthy, stroke (atrophic), and SCI (severe atrophic) muscle fiber population samples respectively. In the SCI (severe atrophic sample), 3D image analysis revealed fiber splitting and fiber swelling. In the stroke sample (atrophic sample) muscle fiber buckling was observed but was only visible in the 3D analysis. 3D muscle fiber population analysis revealed new insights into the different stages of muscle fiber atrophy not to be observed nor quantified with a 2D histological analysis including fiber buckling, loss of fibers and fiber splitting., (© 2022. The Author(s).)

Efficient interhemispheric integration of neural activity between left and right primary motor cortex (M1) is critical for inter-limb motor control. We employed optogenetic stimulation to establish a framework for probing transcallosal M1-M1 interactions in rats. We performed optogenetic stimulation of excitatory neurons in right M1 of male Sprague-Dawley rats. We recorded the transcallosal evoked potential in contralateral left M1 via chronically implanted electrodes. Recordings were performed under anesthesia combination of dexmedetomidine and a low concentration of isoflurane. We systematically varied the stimulation intensity and duration to characterize the relationship between stimulation parameters in right M1 and the characteristics of the evoked intracortical potentials in left M1. Optogenetic stimulation of right M1 consistently evoked a transcallosal response in left M1 with a consistent negative peak (N1) that sometimes was preceded by a smaller positive peak (P1). Higher stimulation intensity or longer stimulation duration gradually increased N1 amplitude and reduced N1 variability across trials. A combination of stimulation intensities of 5-10 mW with stimulus durations of 1-10 ms were generally sufficient to elicit a robust transcallosal response in most animal, with our optic fiber setup. Optogenetically stimulated excitatory neurons in M1 can reliably evoke a transcallosal response in anesthetized rats. Characterizing the relationship between "stimulation dose" and "response magnitude" (i.e., the gain function) of transcallosal M1-to-M1 excitatory connections can be used to optimize the variables of optogenetic stimulation and ensure stimulation efficacy., Competing Interests: CSS was kindly provided with dental acrylic cement, mixing apparatus and application tools by GC Europe. HRS had received honoraria as speaker from Sanofi Genzyme, Denmark and Novartis, Denmark, as consultant from Sanofi Genzyme, Denmark, Lophora A/S, Denmark, Lundbeck Pharma A/S, Denmark. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Skoven, Tomasevic, Kvitsiani, Pakkenberg, Dyrby and Siebner.)

Noninvasive diffusion-weighted magnetic resonance imaging (dMRI) can be used to map the neural connectivity between distinct areas in the intact brain, but the standard resolution achieved fundamentally limits the sensitivity of such maps. We investigated the sensitivity and specificity of high-resolution postmortem dMRI and probabilistic tractography in rhesus macaque brains to produce retinotopic maps of the lateral geniculate nucleus (LGN) and extrastriate cortical visual area V5/MT based on their topographic connections with the previously established functional retinotopic map of primary visual cortex (V1). We also replicated the differential connectivity of magnocellular and parvocellular LGN compartments with V1 across visual field positions. Predicted topographic maps based on dMRI data largely matched the established retinotopy of both LGN and V5/MT. Furthermore, tractography based on in vivo dMRI data from the same macaque brains acquired at standard field strength (3T) yielded comparable topographic maps in many cases. We conclude that tractography based on dMRI is sensitive enough to reveal the intrinsic organization of ordered connections between topographically organized neural structures and their resultant functional organization., (© The Author(s) 2021. Published by Oxford University Press.)

Modern diffusion and functional magnetic resonance imaging (dMRI/fMRI) provide non-invasive high-resolution images from which multi-layered networks of whole-brain structural and functional connectivity can be derived. Unfortunately, the lack of observed correspondence between the connectivity profiles of the two modalities challenges the understanding of the relationship between the functional and structural connectome. Rather than focusing on correspondence at the level of connections we presently investigate correspondence in terms of modular organization according to shared canonical processing units. We use a stochastic block-model (SBM) as a data-driven approach for clustering high-resolution multi-layer whole-brain connectivity networks and use prediction to quantify the extent to which a given clustering accounts for the connectome within a modality. The employed SBM assumes a single underlying parcellation exists across modalities whilst permitting each modality to possess an independent connectivity structure between parcels thereby imposing concurrent functional and structural units but different structural and functional connectivity profiles. We contrast the joint processing units to their modality specific counterparts and find that even though data-driven structural and functional parcellations exhibit substantial differences, attributed to modality specific biases, the joint model is able to achieve a consensus representation that well accounts for both the functional and structural connectome providing improved representations of functional connectivity compared to using functional data alone. This implies that a representation persists in the consensus model that is shared by the individual modalities. We find additional support for this viewpoint when the anatomical correspondence between modalities is removed from the joint modeling. The resultant drop in predictive performance is in general substantial, confirming that the anatomical correspondence of processing units is indeed present between the two modalities. Our findings illustrate how multi-modal integration admits consensus representations well-characterizing each individual modality despite their biases and points to the importance of multi-layered connectomes as providing supplementary information regarding the brain's canonical processing units., Competing Interests: HS has received honoraria as speaker from Sanofi Genzyme, Denmark, and Novartis, Denmark, as consultant from Sanofi Genzyme, Denmark, Lophora, Denmark, and Lundbeck AS, Denmark, and as editor-in-chief (Neuroimage Clinical) and senior editor (NeuroImage) from Elsevier Publishers, Amsterdam, The Netherlands. He has received royalties as book editor from Springer Publishers, Stuttgart, Germany and from Gyldendal Publishers, Copenhagen, Denmark. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Albers, Liptrot, Ambrosen, Røge, Herlau, Andersen, Siebner, Hansen, Dyrby, Madsen, Schmidt and Mørup.)

Noninvasive estimation of axon diameter with diffusion MRI holds the potential to investigate the dynamic properties of the brain network and pathology of neurodegenerative diseases. Recent studies use powder averaging to account for complex white matter architectures, but these have not been validated for real axonal geometries from regions that contain fibre crossings. Here, we present 120-304μm long segmented axons from X-ray nano-holotomography volumes of a splenium and crossing fibre region of a vervet monkey brain. We show that the axons in the complex crossing fibre region, which contains callosal, association, and corticospinal connections, exhibit a wider diameter distribution than those of the splenium region. To accurately estimate the axon diameter in these regions, therefore, sensitivity to a wide range of diameters is required. We demonstrate how the q-value, b-value, signal-to-noise ratio and the assumed intra-axonal parallel diffusivity influence the range of measurable diameters with powder average approaches. Furthermore, we show how Gaussian distributed noise results in a wider range of measurable diameter at high b-values than Rician distributed noise, even at high signal-to-noise ratios of 100. The number of gradient directions is also shown to impose a lower bound on measurable diameter. Our results indicate that axon diameter estimation can be performed with only few b-shells, and that additional shells do not improve the accuracy of the estimate. For strong gradients available on human Connectom and preclinical scanners, Monte Carlo simulations of diffusion confirm that powder averaging techniques succeed in providing accurate estimates of axon diameter across a range of diameters, sequence parameters and diffusion times, even in complex white matter architectures. At relatively low b-values, the diameter estimate becomes sensitive to axonal microdispersion and the intra-axonal parallel diffusivity shows time dependency at both in vivo and ex vivo intrinsic diffusivities., Competing Interests: Declaration of Competing Interest None., (Copyright © 2021. Published by Elsevier Inc.)

In magnetic resonance imaging, the application of a strong diffusion weighting suppresses the signal contributions from the less diffusion-restricted constituents of the brain's white matter, thus enabling the estimation of the transverse relaxation time T 2 that arises from the more diffusion-restricted constituents such as the axons. However, the presence of cell nuclei and vacuoles can confound the estimation of the axonal T 2 , as diffusion within those structures is also restricted, causing the corresponding signal to survive the strong diffusion weighting. We devise an estimator of the axonal T 2 based on the directional spherical variance of the strongly diffusion-weighted signal. The spherical variance T 2 estimates are insensitive to the presence of isotropic contributions to the signal like those provided by cell nuclei and vacuoles. We show that with a strong diffusion weighting these estimates differ from those obtained using the directional spherical mean of the signal which contains both axonal and isotropically-restricted contributions. Our findings hint at the presence of an MRI-visible isotropically-restricted contribution to the signal in the white matter ex vivo fixed tissue (monkey) at 7T, and do not allow us to discard such a possibility also for in vivo human data collected with a clinical 3T system., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

The organization of the human brain remains elusive, yet is of great importance to the mechanisms of integrative brain function. At the macroscale, its structural and functional interpretation is conventionally assessed at the level of cortical units. However, the definition and validation of such cortical parcellations are problematic due to the absence of a true gold standard. We propose a framework for quantitative evaluation of brain parcellations via statistical prediction of connectomics data. Specifically, we evaluate the extent in which the network representation at the level of cortical units (defined as parcels) accounts for high-resolution brain connectivity. Herein, we assess the pertinence and comparative ranking of ten existing parcellation atlases to account for functional (FC) and structural connectivity (SC) data based on data from the Human Connectome Project (HCP), and compare them to data-driven as well as spatially-homogeneous geometric parcellations including geodesic parcellations with similar size distributions as the atlases. We find substantial discrepancy in parcellation structures that well characterize FC and SC and differences in what well represents an individual's functional connectome when compared against the FC structure that is preserved across individuals. Surprisingly, simple spatial homogenous parcellations generally provide good representations of both FC and SC, but are inferior when their within-parcellation distribution of individual parcel sizes is matched to that of a valid atlas. This suggests that the choice of fine grained and coarse representations used by existing atlases are important. However, we find that resolution is more critical than the exact border location of parcels., (Copyright © 2021. Published by Elsevier Inc.)

In recent years, the combination of whole-brain immunolabelling, light sheet fluorescence microscopy (LSFM) and subsequent registration of data with a common reference atlas, has enabled 3D visualization and quantification of fluorescent markers or tracers in the adult mouse brain. Today, the common coordinate framework version 3 developed by the Allen's Institute of Brain Science (AIBS CCFv3), is widely used as the standard brain atlas for registration of LSFM data. However, the AIBS CCFv3 is based on histological processing and imaging modalities different from those used for LSFM imaging and consequently, the data differ in both tissue contrast and morphology. To improve the accuracy and speed by which LSFM-imaged whole-brain data can be registered and quantified, we have created an optimized digital mouse brain atlas based on immunolabelled and solvent-cleared brains. Compared to the AIBS CCFv3 atlas, our atlas resulted in faster and more accurate mapping of neuronal activity as measured by c-Fos expression, especially in the hindbrain. We further demonstrated utility of the LSFM atlas by comparing whole-brain quantitative changes in c-Fos expression following acute administration of semaglutide in lean and diet-induced obese mice. In combination with an improved algorithm for c-Fos detection, the LSFM atlas enables unbiased and computationally efficient characterization of drug effects on whole-brain neuronal activity patterns. In conclusion, we established an optimized reference atlas for more precise mapping of fluorescent markers, including c-Fos, in mouse brains processed for LSFM.

Parkinson's disease (PD) is a progressive neurodegenerative disease that is typically diagnosed late in its progression. There is a need for biomarkers suitable for monitoring the disease progression at earlier stages to guide the development of novel neuroprotective therapies. One potential biomarker, α-synuclein, has been found in both the familial cases of PD, as well as the sporadic cases and is considered a key feature of PD. α-synuclein is naturally present in the retina, and it has been suggested that early symptoms of the visual system may be used as a biomarker for PD. Here, we use a viral vector to induce a unilateral expression of human wild-type α-synuclein in rats as a mechanistic model of protein aggregation in PD. We employed functional magnetic resonance imaging (fMRI) to investigate whether adeno-associated virus (AAV) mediated expression of human wild-type α-synuclein alter functional activity in the visual system. A total of 16 rats were injected with either AAV-α-synuclein ( n  = 7) or AAV-null ( n  = 9) in the substantia nigra pars compacta (SNc) of the left hemisphere. The expression of α-synuclein was validated by a motor assay and postmortem immunohistochemistry. Five months after the introduction of the AAV-vector, fMRI showed robust blood oxygen level-dependent (BOLD) responses to light stimulation in the visual systems of both control and AAV-α-synuclein animals. However, our results demonstrate that the expression of AAV-α-synuclein does not affect functional activation of the visual system. This negative finding suggests that fMRI-based read-outs of visual responses may not be a sensitive biomarker for PD., (Copyright © 2021 Østergaard et al.)

Metabolite diffusion measurable in humans in vivo with diffusion-weighted spectroscopy (DW-MRS) provides a window into the intracellular morphology and state of specific cell types. Anisotropic diffusion in white matter is governed by the microscopic properties of the individual cell types and their structural units (axons, soma, dendrites). However, anisotropy is also markedly affected by the macroscopic orientational distribution over the imaging voxel, particularly in DW-MRS, where the dimensions of the volume of interest (VOI) are much larger than those typically used in diffusion-weighted imaging. One way to address the confound of macroscopic structural features is to average the measurements acquired with uniformly distributed gradient directions to mimic a situation where fibers present in the VOI are orientationally uniformly distributed. This situation allows the extraction of relevant microstructural features such as transverse and longitudinal diffusivities within axons and the related microscopic fractional anisotropy. We present human DW-MRS data acquired at 7 T in two different white matter regions, processed and analyzed as described above, and find that intra-axonal diffusion of the neuronal metabolite N-acetyl aspartate is in good correspondence to simple model interpretations, such as multi-Gaussian diffusion from disperse fibers where the transverse diffusivity can be neglected. We also discuss the implications of our approach for current and future applications of DW-MRS for cell-specific measurements., (© 2020 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.)

Background: Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease leading to damage of white matter (WM) and grey matter (GM). Magnetic resonance imaging (MRI) is the modality of choice to assess brain damage in MS, but there is an unmet need in MRI for achieving higher sensitivity and specificity to MS-related microstructural alterations in WM and GM., Objective: To explore whether tensor-valued diffusion MRI (dMRI) can yield sensitive microstructural read-outs for focal demyelination in cerebral WM and deep GM (DGM)., Methods: Eight rats underwent L-α-Lysophosphatidylcholine (LPC) injections in the WM and striatum to introduce focal demyelination. Multimodal MRI was performed at 7 Tesla after 7 days. Tensor-valued dMRI was complemented by diffusion tensor imaging, quantitative MRI and proton magnetic resonance spectroscopy (MRS)., Results: Quantitative MRI and MRS confirmed that LPC injections caused inflammatory demyelinating lesions in WM and DGM. Tensor-valued dMRI illustrated a significant decline of microscopic fractional anisotropy (µFA) in both LPC-treated WM and DGM (P < 0.005) along with a marked increase of isotropic kurtosis (MK I ) in DGM (P < 0.0001)., Conclusion: Tensor-valued dMRI bears considerable potential for microstructural imaging in MS, suggesting a regional µFA decrease may be a sensitive indicator of MS lesions, while a regional MK I increase may be particularly sensitive in detecting DGM lesions of MS., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)

Axonal conduction velocity, which ensures efficient function of the brain network, is related to axon diameter. Noninvasive, in vivo axon diameter estimates can be made with diffusion magnetic resonance imaging, but the technique requires three-dimensional (3D) validation. Here, high-resolution, 3D synchrotron X-ray nano-holotomography images of white matter samples from the corpus callosum of a monkey brain reveal that blood vessels, cells, and vacuoles affect axonal diameter and trajectory. Within single axons, we find that the variation in diameter and conduction velocity correlates with the mean diameter, contesting the value of precise diameter determination in larger axons. These complex 3D axon morphologies drive previously reported 2D trends in axon diameter and g -ratio. Furthermore, we find that these morphologies bias the estimates of axon diameter with diffusion magnetic resonance imaging and, ultimately, impact the investigation and formulation of the axon structure-function relationship., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)

Diffusion-weighted magnetic resonance imaging (DW-MRI) tractography is a non-invasive tool to probe neural connections and the structure of the white matter. It has been applied successfully in studies of neurological disorders and normal connectivity. Recent work has revealed that tractography produces a high incidence of false-positive connections, often from "bottleneck" white matter configurations. The rich literature in histological connectivity analysis studies in the macaque monkey enables quantitative evaluation of the performance of tractography algorithms. In this study, we use the intricate connections of frontal, cingulate, and parietal areas, well established by the anatomical literature, to derive a symmetrical histological connectivity matrix composed of 59 cortical areas. We evaluate the performance of fifteen diffusion tractography algorithms, including global, deterministic, and probabilistic state-of-the-art methods for the connectivity predictions of 1711 distinct pairs of areas, among which 680 are reported connected by the literature. The diffusion connectivity analysis was performed on a different ex-vivo macaque brain, acquired using multi-shell DW-MRI protocol, at high spatial and angular resolutions. Across all tested algorithms, the true-positive and true-negative connections were dominant over false-positive and false-negative connections, respectively. Moreover, three-quarters of streamlines had endpoints location in agreement with histological data, on average. Furthermore, probabilistic streamline tractography algorithms show the best performances in predicting which areas are connected. Altogether, we propose a method for quantitative evaluation of tractography algorithms, which aims at improving the sensitivity and the specificity of diffusion-based connectivity analysis. Overall, those results confirm the usefulness of tractography in predicting connectivity, although errors are produced. Many of the errors result from bottleneck white matter configurations near the cortical grey matter and should be the target of future implementation of methods., (Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.)

Introduction: Diffuse traumatic axonal injury (TAI) is one of the key mechanisms leading to impaired consciousness after severe traumatic brain injury (TBI). In addition, preferential regional expression of TAI in the brain may also influence clinical outcome. Aim: We addressed the question whether the regional expression of microstructural changes as revealed by whole-brain diffusion tensor imaging (DTI) in the subacute stage after severe TBI may predict the duration of post-traumatic amnesia (PTA). Method: Fourteen patients underwent whole-brain DTI in the subacute stage after severe TBI. Mean fractional anisotropy (FA) and mean diffusivity (MD) were calculated for five bilateral brain regions: fronto-temporal, parieto-occipital, and midsagittal hemispheric white matter, as well as brainstem and basal ganglia. Region-specific calculation of mean FA and MD only considered voxels that showed no tissue damage, using an exclusive mask with all voxels that belonged to local brain lesions or microbleeds. Mean FA or MD of the five brain regions were entered in separate partial least squares (PLS) regression analyses to identify patterns of regional microstructural changes that account for inter-individual variations in PTA. Results: For FA, PLS analysis revealed two spatial patterns that significantly correlated with individual PTA. The lower the mean FA values in all five brain regions, the longer that PTA lasted. A pattern characterized by lower FA values in the deeper brain regions relative to the FA values in the hemispheric regions also correlated with longer PTA. Similar trends were found for MD, but opposite in sign. The spatial FA changes as revealed by PLS components predicted the duration of PTA. Individual PTA duration, as predicted by a leave-one-out cross-validation analysis, correlated with true PTA values (Spearman r = 0.68, p permutation = 0.008). Conclusion: Two coarse spatial patterns of microstructural damage, indexed as reduction in FA, were relevant to recovery of consciousness after TBI. One pattern expressed was consistent with diffuse microstructural damage across the entire brain. A second pattern was indicative of a preferential damage of deep midline brain structures., (Copyright © 2020 Andreasen, Andersen, Conde, Dyrby, Puonti, Kammersgaard, Madsen, Madsen, Poulsen and Siebner.)

Introduction : Motor skill learning already triggers the functional reorganization of regional brain activity after short periods of training. Recent studies suggest that microstructural change may emerge at similar timescales, but the spatiotemporal profiles of functional and structural plasticity have rarely been traced in parallel. Recently, we demonstrated that 5 days of endoscopic skill training induces changes in task-related brain activity in the ventral premotor cortex (PMv) and other areas of the frontoparietal grasping network. Here, we analyzed microstructural data, collected during the same experiment to investigate if microstructural plasticity overlaps temporally and spatially with the training-induced changes in task-related brain activity. Materials and Methods : Thirty-nine students were divided into a full-routine group ( n = 20), that underwent three endoscopy training sessions in the MR-scanner as well as a 5-day virtual reality (VR)-endoscopy training and a brief-routine group ( n = 19), that only performed the in-scanner endoscopy training sessions. Diffusion Tensor Imaging (DTI)-derived fractional anisotropy (FA) and resting-state functional magnetic resonance imaging (rs-fMRI) were collected at baseline, after the first and after the last VR-training session. Results : The full-routine group showed significant FA changes in a left-hemispheric subcortical cluster underlying the PMv region, for which we previously demonstrated functional plasticity during endoscopy training in the same sample. Functional (task-related fMRI) and structural (FA) changes showed the largest change from the first to the second scan, suggesting similar temporal dynamics. In the full-routine group, the FA change in the subcortical cluster underlying the left PMv scaled positively with the individual improvement in endoscopic surgery. Conclusion : Microstructural white-matter plasticity mirrors the spatiotemporal profile of task-dependent plasticity during a 5-day course of endoscopy skill training. The observed similarities motivate future research on the interplay between functional and structural plasticity during early skill acquisition., (Copyright © 2020 Irmen, Karabanov, Bögemann, Andersen, Madsen, Bisgaard, Dyrby and Siebner.)

Multiple sclerosis leads to diffuse damage of the central nervous system, affecting also the normal-appearing white matter. Demyelination and axonal degeneration reduce regional fractional anisotropy in normal-appearing white matter, which can be routinely mapped with diffusion tensor imaging. However, the standard fractional anisotropy metric is also sensitive to physiological variations in orientation dispersion of white matter fibres. This complicates the detection of disease-related damage in large parts of cerebral white matter where microstructure physiologically displays a high degree of fibre dispersion. To resolve this ambiguity, we employed a novel tensor-valued encoding method for diffusion MRI, which yields a microscopic fractional anisotropy metric that is unaffected by regional variations in orientation dispersion. In 26 patients with relapsing-remitting multiple sclerosis, 14 patients with primary-progressive multiple sclerosis and 27 age-matched healthy controls, we compared standard fractional anisotropy mapping with the novel microscopic fractional anisotropy mapping method, focusing on normal-appearing white matter. Mean microscopic fractional anisotropy and standard fractional anisotropy of normal-appearing white matter were significantly reduced in both patient groups relative to healthy controls, but microscopic fractional anisotropy yielded a better reflection of disease-related white-matter alterations. The reduction in mean microscopic fractional anisotropy showed a significant positive linear relationship with physical disability, as reflected by the expanded disability status scale. Mean reduction of microscopic fractional anisotropy in normal-appearing white matter also scaled positively with individual cognitive dysfunction, as measured with the symbol digit modality test. Mean microscopic fractional anisotropy reduction in normal-appearing white matter also showed a positive relationship with total white-matter lesion load as well as lesion load in specific tract systems. None of these relationships between normal-appearing white-matter microstructure and clinical, cognitive or structural measures emerged when using mean fractional anisotropy. Together, the results provide converging evidence that microscopic fractional anisotropy mapping substantially advances the assessment of cerebral white matter in multiple sclerosis by disentangling microstructure damage from variations in physiological fibre orientation dispersion at the stage of data acquisition. Since tensor-valued encoding can be implemented in routine diffusion MRI, microscopic fractional anisotropy mapping bears considerable potential for the future assessment of disease progression in normal-appearing white matter in both relapsing-remitting and progressive forms of multiple sclerosis as well as other white-matter-related brain diseases., (© The Author(s) (2020). Published by Oxford University Press on behalf of the Guarantors of Brain.)

Purpose: Non-invasive axon diameter distribution (ADD) mapping using diffusion MRI is an ill-posed problem. Current ADD mapping methods require knowledge of axon orientation before performing the acquisition. Instead, ActiveAx uses a 3D sampling scheme to estimate the orientation from the signal, providing orientationally invariant estimates. The mean diameter is estimated instead of the distribution for the solution to be tractable. Here, we propose an extension (ActiveAx ADD ) that provides non-parametric and orientationally invariant estimates of the whole distribution., Theory: The accelerated microstructure imaging with convex optimization (AMICO) framework accelerates mean diameter estimation using a linear formulation combined with Tikhonov regularization to stabilize the solution. Here, we implement a new formulation (ActiveAx ADD ) that uses Laplacian regularization to provide robust estimates of the whole ADD., Methods: The performance of ActiveAx ADD was evaluated using Monte Carlo simulations on synthetic white matter samples mimicking axon distributions reported in histological studies., Results: ActiveAx ADD provided robust ADD reconstructions when considering the isolated intra-axonal signal. However, our formulation inherited some common microstructure imaging limitations. When accounting for the extra axonal compartment, estimated ADDs showed spurious peaks and increased variability because of the difficulty of disentangling intra and extra axonal contributions., Conclusion: Laplacian regularization solves the ill-posedness regarding the intra axonal compartment. ActiveAx ADD can potentially provide non-parametric and orientationally invariant ADDs from isolated intra-axonal signals. However, further work is required before ActiveAx ADD can be applied to real data containing extra-axonal contributions, as disentangling the 2 compartment appears to be an overlooked challenge that affects microstructure imaging methods in general., (© 2019 International Society for Magnetic Resonance in Medicine.)

The limbic system encompasses a collection of brain areas primarily involved in higher cognitive and emotional processing. Altered function in the limbic circuitry may play a major role in various psychiatric disorders. This study aims to provide a high-quality ex vivo diffusion-weighted MRI (DWI) tractographic overview of the Göttingen minipig limbic system pathways, which are currently not well described. This may facilitate future translational large animal studies. The study used previously obtained post-mortem DWI scans in 3 female Göttingen minipigs aging 11-15 months. The tractography performed on the DWI data set was made using a probabilistic algorithm, and regions of interest (ROIs) were defined in accordance with a histological atlas. The investigated pathways included the fornix, mammillothalamic tract, stria terminalis, stria medullaris, habenulo-interpeduncular tract, and cingulum. All the investigated limbic connections could be visualized with a high detail yielding a comprehensive three-dimensional overview, which was emphasized by the inclusion of video material. The minipig limbic system pathways displayed using tractography closely resembled what was previously described in both human studies and neuronal tracing studies from other mammalian species. We encountered well-known inherent methodological challenges of tractography, e.g., partial volume effects and complex white matter regions, which may have contributed to derouted false-positive streamlines and the failure to visualize some of the minor limbic pathway ramifications. This underlines the importance of preexisting anatomical knowledge. Conclusively, we have, for the first time, provided an overview and substantial insight of the Göttingen minipig limbic system.

The dorsal hippocampal commissure (DHC) is a white matter tract that provides interhemispheric connections between temporal lobe brain regions. Despite the importance of these regions for learning and memory, there is scant evidence of a role for the DHC in successful memory performance. We used diffusion-weighted magnetic resonance imaging (DW-MRI) and white matter tractography to reconstruct the DHC in both humans (in vivo) and nonhuman primates (ex vivo). Across species, our findings demonstrate a close consistency between the known anatomy and tract reconstructions of the DHC. Anterograde tract-tracer techniques also highlighted the parahippocampal origins of DHC fibers in nonhuman primates. Finally, we derived diffusion tensor MRI metrics from the DHC in a large sample of human subjects to investigate whether interindividual variation in DHC microstructure is predictive of memory performance. The mean diffusivity of the DHC correlated with performance in a standardized recognition memory task, an effect that was not reproduced in a comparison commissure tract-the anterior commissure. These findings highlight a potential role for the DHC in recognition memory, and our tract reconstruction approach has the potential to generate further novel insights into the role of this previously understudied white matter tract in both health and disease., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The frontal lobe is central to distinctive aspects of human cognition and behavior. Some comparative studies link this to a larger frontal cortex and even larger frontal white matter in humans compared with other primates, yet others dispute these findings. The discrepancies between studies could be explained by limitations of the methods used to quantify volume differences across species, especially when applied to white matter connections. In this study, we used a novel tractography approach to demonstrate that frontal lobe networks, extending within and beyond the frontal lobes, occupy 66% of total brain white matter in humans and 48% in three monkey species: vervets (Chlorocebus aethiops), rhesus macaque (Macaca mulatta) and cynomolgus macaque (Macaca fascicularis), all male. The simian-human differences in proportional frontal tract volume were significant for projection, commissural, and both intralobar and interlobar association tracts. Among the long association tracts, the greatest difference was found for tracts involved in motor planning, auditory memory, top-down control of sensory information, and visuospatial attention, with no significant differences in frontal limbic tracts important for emotional processing and social behaviour. In addition, we found that a nonfrontal tract, the anterior commissure, had a smaller volume fraction in humans, suggesting that the disproportionally large volume of human frontal lobe connections is accompanied by a reduction in the proportion of some nonfrontal connections. These findings support a hypothesis of an overall rearrangement of brain connections during human evolution. SIGNIFICANCE STATEMENT Tractography is a unique tool to map white matter connections in the brains of different species, including humans. This study shows that humans have a greater proportion of frontal lobe connections compared with monkeys, when normalized by total brain white matter volume. In particular, tracts associated with language and higher cognitive functions are disproportionally larger in humans compared with monkeys, whereas other tracts associated with emotional processing are either the same or disproportionally smaller. This supports the hypothesis that the emergence of higher cognitive functions in humans is associated with increased extended frontal connectivity, allowing human brains more efficient cross talk between frontal and other high-order associative areas of the temporal, parietal, and occipital lobes., (Copyright © 2020 Barrett et al.)

Severe traumatic brain injury (TBI) produces shearing forces on long-range axons and brain vessels, causing axonal and vascular injury. To examine whether microbleeds and axonal injury colocalize after TBI, we performed whole-brain susceptibility-weighted imaging (SWI) and diffusion tensor imaging (DTI) in 14 patients during the subacute phase after severe TBI. SWI was used to determine the number and volumes of microbleeds in five brain regions: the frontotemporal lobe; parieto-occipital lobe; midsagittal region (cingular cortex, parasagittal white matter, and corpus callosum); deep nuclei (basal ganglia and thalamus); and brainstem. Averaged fractional anisotropy (FA) and mean diffusivity (MD) were measured to assess microstructural changes in the normal appearing white matter attributed to axonal injury in the same five regions. Regional expressions of microbleeds and microstructure were used in a partial least-squares model to predict the impairment of consciousness in the subacute stage after TBI as measured with the Coma Recovery Scale-Revised (CRS-R). Only in the midsagittal region, the expression of microbleeds was correlated with regional changes in microstructure as revealed by DTI. Microbleeds and microstructural DTI-based metrics of deep, but not superficial, brain regions were able to predict individual CRS-R. Our results suggest that microbleeds are not strictly related to axonal pathology in other than the midsagittal region. While each measure alone was predictive, the combination of both metrics scaled best with individual CRS-R. Structural alterations in deep brain structures are relevant in terms of determining the severity of impaired consciousness in the acute stage after TBI.

Multiple Sclerosis (MS) is characterized by demyelination and neurodegeneration of the central nervous system and causes excessive fatigue in more than 80% of the patients. The pathophysiologic mechanisms causing fatigue are still largely unknown. In 46 right-handed patients with relapsing-remitting MS and 25 right-handed controls, we performed diffusion MRI and applied streamline based probabilistic tractography to derive unilateral anatomical connectivity maps for the white matter of the right and left hemispheres. The maps provide an indication how often a streamline has passed through a given voxel. Since tractography based anatomical connectivity mapping (ACM) is sensitive to disease-induced changes in anatomical connectivity, we used ACM to test whether motor fatigue is associated with altered ipsi-hemispherical anatomical connectivity in the major motor output pathway, the corticospinal tract (CST). Patients had higher mean ACM values in the CST than healthy controls. This indicated that a higher number of streamlines, starting from voxels in the same hemisphere, travelled through the CST and may reflect an accumulated disease-induced disintegration of CST. The motor subscale of the Fatigue Scale for Motor and Cognitive functions (FSMC MOTOR ) was used to define sub-groups with (n = 29, FSMC MOTOR score ≥ 27) and without motor fatigue (n = 17, FSMS MOTOR score ≤ 26). Patients without fatigue only showed higher ACM values in right CST, while mean ACM values were unaltered in left CST. The higher the mean ACM values in the left relative to the right CST, the more patients reported motor fatigue. Left-right asymmetry in anatomical connectivity outside the CST did not scale with individual motor fatigue. Our results link lateralized changes of tractography-based microstructural properties in the CST with motor fatigue in relapsing-remitting MS., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Fiber tracking with diffusion-weighted MRI has become an essential tool for estimating in vivo brain white matter architecture. Fiber tracking results are sensitive to the choice of processing method and tracking criteria., Purpose: To assess the variability for an algorithm in group studies reproducibility is of critical context. However, reproducibility does not assess the validity of the brain connections. Phantom studies provide concrete quantitative comparisons of methods relative to absolute ground truths, yet do no capture variabilities because of in vivo physiological factors. The ISMRM 2017 TraCED challenge was created to fulfill the gap., Study Type: A systematic review of algorithms and tract reproducibility studies., Subjects: Single healthy volunteers., Field Strength/sequence: 3.0T, two different scanners by the same manufacturer. The multishell acquisition included b-values of 1000, 2000, and 3000 s/mm 2 with 20, 45, and 64 diffusion gradient directions per shell, respectively., Assessment: Nine international groups submitted 46 tractography algorithm entries each consisting 16 tracts per scan. The algorithms were assessed using intraclass correlation (ICC) and the Dice similarity measure., Statistical Tests: Containment analysis was performed to assess if the submitted algorithms had containment within tracts of larger volume submissions. This also serves the purpose to detect if spurious submissions had been made., Results: The top five submissions had high ICC and Dice >0.88. Reproducibility was high within the top five submissions when assessed across sessions or across scanners: 0.87-0.97. Containment analysis shows that the top five submissions are contained within larger volume submissions. From the total of 16 tracts as an outcome relatively the number of tracts with high, moderate, and low reproducibility were 8, 4, and 4., Data Conclusion: The different methods clearly result in fundamentally different tract structures at the more conservative specificity choices. Data and challenge infrastructure remain available for continued analysis and provide a platform for comparison., Level of Evidence: 5 Technical Efficacy Stage: 1 J. Magn. Reson. Imaging 2020;51:234-249., (© 2019 International Society for Magnetic Resonance in Medicine.)

Evaluation of the structural connectivity (SC) of the brain based on tractography has mainly focused on the choice of diffusion model, tractography algorithm, and their respective parameter settings. Here, we systematically validate SC derived from a post mortem monkey brain, while varying key acquisition parameters such as the b-value, gradient angular resolution and image resolution. As gold standard we use the connectivity matrix obtained invasively with histological tracers by Markov et al. (2014). As performance metric, we use cross entropy as a measure that enables comparison of the relative tracer labeled neuron counts to the streamline counts from tractography. We find that high angular resolution and high signal-to-noise ratio are important to estimate SC, and that SC derived from low image resolution (1.0 3 mm 3 ) are in better agreement with the tracer network, than those derived from high image resolution (0.5 3 mm 3 ) or at an even lower image resolution (2.0 3 mm 3 ). In contradiction, sensitivity and specificity analyses suggest that if the angular resolution is sufficient, the balanced compromise in which sensitivity and specificity are identical remains 60-64% regardless of the other scanning parameters. Interestingly, the tracer graph is assumed to be the gold standard but by thresholding, the balanced compromise increases to 70-75%. Hence, by using performance metrics based on binarized tracer graphs, one risks losing important information, changing the performance of SC graphs derived by tractography and their dependence of different scanning parameters., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Characterization of porous media is essential in a wide range of biomedical and industrial applications. Microstructural features can be probed non-invasively by diffusion magnetic resonance imaging (dMRI). However, diffusion encoding in conventional dMRI may yield similar signatures for very different microstructures, which represents a significant limitation for disentangling individual microstructural features in heterogeneous materials. To solve this problem, we propose an augmented multidimensional diffusion encoding (MDE) framework, which unlocks a novel encoding dimension to assess time-dependent diffusion specific to structures with different microscopic anisotropies. Our approach relies on spectral analysis of complex but experimentally efficient MDE waveforms. Two independent contrasts to differentiate features such as cell shape and size can be generated directly by signal subtraction from only three types of measurements. Analytical calculations and simulations support our experimental observations. Proof-of-concept experiments were applied on samples with known and distinctly different microstructures. We further demonstrate substantially different contrasts in different tissue types of a post mortem brain. Our simultaneous assessment of restriction size and shape may be instrumental in studies of a wide range of porous materials, enable new insights into the microstructure of biological tissues or be of great value in diagnostics.

Whether brain networks underlying the multimodal processing of language in humans are present in non-human primates is an unresolved question in primate evolution. Conceptual awareness in humans, which is the backbone of verbal and non-verbal semantic elaboration, involves intracerebral connectivity via the inferior fronto-occipital fascicle (IFOF). While non-human primates can communicate through visual information channels, there has been no formal demonstration that they possess a functional homologue of the human IFOF. Therefore, we undertook a post-mortem diffusion MRI tractography study in conjunction with Klingler micro-dissection to search for IFOF fiber tracts in brain of Old-World (vervet) monkeys. We found clear and concordant evidence from both techniques for the existence of bilateral fiber tracts connecting the frontal and occipital lobes. These tracts closely resembled the human IFOF with respect to trajectory, topological organization, and cortical terminal fields. Moreover, these fibers are clearly distinct from other bundles previously described in this region of monkey brain, i.e., the inferior longitudinal and uncinate fascicles, and the external and extreme capsules. This demonstration of an IFOF in brain of a species that diverged from the human lineage some 22 millions years ago enhances our comprehension about the evolution of language and social behavior.

Background: Synchrotron X-ray computed tomography (SXCT) allows for three-dimensional imaging of objects at a very high resolution and in large field-of-view., Purpose: The aim of this study was to use SXCT imaging for morphological analysis of muscle tissue, in order to investigate whether the analysis reveals complementary information to two-dimensional microscopy., Methods: Three-dimensional SXCT images of muscle biopsies were taken from participants with cerebral palsy and from healthy controls. We designed morphological measures from the two-dimensional slices and three-dimensional volumes of the images and measured the muscle fibre organization, which we term orientation consistency., Results: The muscle fibre cross-sectional areas were significantly larger in healthy participants than in participants with cerebral palsy when carrying out the analysis in three dimensions. However, a similar analysis carried out in two dimensions revealed no patient group difference. The present study also showed that three-dimensional orientation consistency was significantly larger for healthy participants than for participants with cerebral palsy., Conclusion: Individuals with CP have smaller muscle fibres than healthy control individuals. We argue that morphometric measures of muscle fibres in two dimensions are generally trustworthy only if the fibres extend perpendicularly to the slice plane, and otherwise three-dimensional aspects should be considered. In addition, the muscle tissue of individuals with CP showed a decreased level of orientation consistency when compared to healthy control tissue. We suggest that the observed disorganization of the tissue may be induced by atrophy caused by physical inactivity and insufficient neural activation., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

This article gives an overview of microstructure imaging of the brain with diffusion MRI and reviews the state of the art. The microstructure-imaging paradigm aims to estimate and map microscopic properties of tissue using a model that links these properties to the voxel scale MR signal. Imaging techniques of this type are just starting to make the transition from the technical research domain to wide application in biomedical studies. We focus here on the practicalities of both implementing such techniques and using them in applications. Specifically, the article summarizes the relevant aspects of brain microanatomy and the range of diffusion-weighted MR measurements that provide sensitivity to them. It then reviews the evolution of mathematical and computational models that relate the diffusion MR signal to brain tissue microstructure, as well as the expanding areas of application. Next we focus on practicalities of designing a working microstructure imaging technique: model selection, experiment design, parameter estimation, validation, and the pipeline of development of this class of technique. The article concludes with some future perspectives on opportunities in this topic and expectations on how the field will evolve in the short-to-medium term., (Copyright © 2017 John Wiley & Sons, Ltd.)

The axonal composition of cortical projections originating in premotor, supplementary motor (SMA), primary motor (a4), somatosensory and parietal areas and descending towards the brain stem and spinal cord was characterized in the monkey with histological tract tracing, electron microscopy (EM) and diffusion MRI (dMRI). These 3 approaches provided complementary information. Histology provided accurate assessment of axonal diameters and size of synaptic boutons. dMRI revealed the topography of the projections (tractography), notably in the internal capsule. From measurements of axon diameters axonal conduction velocities were computed. Each area communicates with different diameter axons and this generates a hierarchy of conduction delays in this order: a4 (the shortest), SMA, premotor (F7), parietal, somatosensory, premotor F4 (the longest). We provide new interpretations for i) the well-known different anatomical and electrophysiological estimates of conduction velocity; ii) why conduction delays are probably an essential component of the cortical motor command; and iii) how histological and dMRI tractography can be integrated.

Diffusion MRI fiber tractography is widely used to probe the structural connectivity of the brain, with a range of applications in both clinical and basic neuroscience. Despite widespread use, tractography has well-known pitfalls that limits the anatomical accuracy of this technique. Numerous modern methods have been developed to address these shortcomings through advances in acquisition, modeling, and computation. To test whether these advances improve tractography accuracy, we organized the 3-D Validation of Tractography with Experimental MRI (3D-VoTEM) challenge at the ISBI 2018 conference. We made available three unique independent tractography validation datasets - a physical phantom and two ex vivo brain specimens - resulting in 176 distinct submissions from 9 research groups. By comparing results over a wide range of fiber complexities and algorithmic strategies, this challenge provides a more comprehensive assessment of tractography's inherent limitations than has been reported previously. The central results were consistent across all sub-challenges in that, despite advances in tractography methods, the anatomical accuracy of tractography has not dramatically improved in recent years. Taken together, our results independently confirm findings from decades of tractography validation studies, demonstrate inherent limitations in reconstructing white matter pathways using diffusion MRI data alone, and highlight the need for alternative or combinatorial strategies to accurately map the fiber pathways of the brain., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The identification and reconstruction of axonal pathways in the living brain or "ex-vivo" is promising a revolution in connectivity studies bridging the gap from animal to human neuroanatomy with extensions to brain structural-functional correlates. Unfortunately, the methods suffer from juvenile drawbacks. In this perspective paper we mention several computational and developmental principles, which might stimulate a new generation of algorithms and a discussion bridging the neuroimaging and neuroanatomy communities.

Extracting microanatomical information beyond the image resolution of MRI would provide valuable tools for diagnostics and neuroscientific research. A number of mathematical models already suggest microstructural interpretations of diffusion MRI (dMRI) data. Examples of such microstructural features could be cell bodies and neurites, e.g. the axon's diameter or their orientational distribution for global connectivity analysis using tractography, and have previously only been possible to access through conventional histology of post mortem tissue or invasive biopsies. The prospect of gaining the same knowledge non-invasively from the whole living human brain could push the frontiers for the diagnosis of neurological and psychiatric diseases. It could also provide a general understanding of the development and natural variability in the healthy brain across a population. However, due to a limited image resolution, most of the dMRI measures are indirect estimations and may depend on the whole chain from experimental parameter settings to model assumptions and implementation. Here, we review current literature in this field and highlight the integrative work across anatomical length scales that is needed to validate and trust a new dMRI method. We encourage interdisciplinary collaborations and data sharing in regards to applying and developing new validation techniques to improve the specificity of future dMRI methods., (Copyright © 2018. Published by Elsevier Inc.)

Background: Pigs and minipigs are increasingly used as non-primate large animal models for preclinical research on nervous system disorders resulting in motor dysfunction. Knowledge of the minipig pyramidal tract is therefore essential to support such models., Aim and Methods: This study used 5 female Göttingen minipigs aging 11-15 months. The Göttingen minipig corticospinal tract was investigated, in the same animals, with in vivo neuronal tracing and with postmortem diffusion weighted MRI tractography to provide a thorough insight in the encephalic distribution of this primary motor pathway and its decussation at the craniocervical junction., Results: The two methods similarly outlined the course of the pyramidal tract from its origin in the motor cortex down through the internal capsule to the craniocervical junction, where both methods displayed an axonal crossover at the pyramid decussation. The degree of crossover was quantified with unbiased stereology, where 81-93% of the traced corticospinal fibers crossed to the contralateral spinal cord. Accordingly, in the upper cervical spinal cord the corticospinal tract is primarily distributed in the contralateral lateral funiculus and in close relation to the gray matter, wherein some direct terminations on large ventral column gray matter neurons could be identified., Discussion: The combination of neuronal tracing and tractography exploited the strengths of the respective methods to gain a better understanding of the encephalic distribution and craniocervical decussation of the Göttingen minipig corticospinal tract. Moreover, a quantification of the crossing fibers was obtained from the tracing data, which was not possible with tractography. Our data indicate that the porcine corticospinal system is quite lateralized down to the investigated upper cervical levels. However, further elucidation of this point will require a full examination of the corticospinal tracing pattern into the caudal spinal cord combined with an analysis of the direct versus indirect termination pattern on the lower motor neurons., (Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.)

Purpose: To illustrate the potential bias caused by imaging gradients in correlation MRI sequences using longitudinal magnetization storage (LS) and examine the case of filter exchange imaging (FEXI) yielding maps of the apparent exchange rate (AXR)., Methods: The effects of imaging gradients in FEXI were observed on yeast cells. To analyze the AXR bias, signal evolution was calculated by applying matrix exponential operators., Results: A sharp threshold for the slice thickness was identified, below which the AXR is increasingly underestimated. The bias can be understood in terms of an extended low-pass diffusion filtering during the LS interval, which is more pronounced at lower exchange rates. For a total exchange rate constant larger than 1 s -1 , the AXR bias is expected to be negligible when slices thicker than 2.5 mm are used., Conclusion: In correlation experiments like FEXI, relying on LS with variable duration, imaging gradients may cause disrupting effects that cannot be easily mitigated and should be carefully considered for unbiased results. In typical clinical applications of FEXI, the imaging gradients are expected to cause a negligible AXR bias. However, the AXR bias may be significant in preclinical settings or whenever thin imaging slices are used. Magn Reson Med 79:2228-2235, 2018. © 2017 International Society for Magnetic Resonance in Medicine., (© 2017 International Society for Magnetic Resonance in Medicine.)

Molecular diffusion measured with diffusion weighted MRI (DWI) offers a probe for tissue microstructure. However, inferring microstructural properties from conventional DWI data is a complex inverse problem and has to account for heterogeneity in sizes, shapes and orientations of the tissue compartments contained within an imaging voxel. Alternative experimental means for disentangling the signal signatures of such features could provide a stronger link between the data and its interpretation. Double diffusion encoding (DDE) offers the possibility to factor out variation in compartment shapes from orientational dispersion of anisotropic domains by measuring the correlation between diffusivity in multiple directions. Time dependence of the diffusion is another effect reflecting the dimensions and distributions of barriers. In this paper we extend on DDE with a modified version of the oscillating gradient spin echo (OGSE) experiment, giving a basic contrast mechanism closely linked to both the temporal diffusion spectrum and the compartment anisotropy. We demonstrate our new method on post mortem brain tissue and show that we retrieve the correct temporal diffusion tensor spectrum in synthetic data from Monte Carlo simulations of random walks in a range of disordered geometries of different sizes and shapes.

Background: Progressive multiple sclerosis (MS) is characterised by diffuse changes on brain magnetic resonance imaging (MRI), which complicates the use of MRI as a diagnostic and prognostic marker. The relationship between MRI measures (conventional and non-conventional) and clinical disability in progressive MS therefore warrants further investigation., Objective: To investigate the relationship between clinical disability and MRI measures in patients with progressive MS., Methods: Data from 93 primary and secondary progressive MS patients who had participated in 3 phase 2 clinical trials were included in this cross-sectional study. From 3T MRI baseline scans we calculated total T2 lesion volume and analysed magnetisation transfer ratio (MTR) and the diffusion tensor imaging indices fractional anisotropy (FA) and mean diffusivity (MD) in T2 lesions, normal-appearing white matter (NAWM) and cortical grey matter. Disability was assessed by the Expanded Disability Status Scale (EDSS) and the MS functional composite., Results: T2 lesion volume was associated with impairment by all clinical measures. MD and MTR in T2 lesions were significantly related to disability, and lower FA values correlated with worse hand function in NAWM. In multivariable analyses, increasing clinical disability was independently correlated with increasing T2 lesion volumes and MTR in T2 lesions., Conclusion: In progressive MS, clinical disability is related to lesion volume and microstructure., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Clinical depression is accompanied by changes in sleep patterning, which is controlled in a circadian fashion. It is thus desirable that animal models of depression mirror such diurnally-specific state alterations, along with other behavioral and physiological changes. We previously found several changes in behavior indicative of a depression-like phenotype in offspring of rats subjected to repeated, variable prenatal stress (PNS), including increased locomotor activity during specific periods of the circadian cycle. We, therefore, investigated whether PNS rats also exhibit alterations in sleep/wakefulness behavior around the change from light-to-dark phase. Control and PNS Sprague-Dawley rats were implanted with electrodes for continuous monitoring of electroencephalic activity used to determine behavioral state. The distribution of slow-wave sleep (SWS), rapid eye movement sleep (REMS) and wakefulness was compared for periods before and after lights were turned off, between baseline conditions and after exposure to an acute stressor. Both REMS and SWS amounts were increased in PNS rats relative to control animals in the beginning of the dark phase. REMS changes were due to an increase in REMS bout number, rather than in bout duration. During this circadian time period, we did not find any sex differences in the state changes. These results indicate that PNS affects baseline sleep patterning in both male and female rats around active-phase onset.

The parietal lobe has a unique place in the human brain. Anatomically, it is at the crossroad between the frontal, occipital, and temporal lobes, thus providing a middle ground for multimodal sensory integration. Functionally, it supports higher cognitive functions that are characteristic of the human species, such as mathematical cognition, semantic and pragmatic aspects of language, and abstract thinking. Despite its importance, a comprehensive comparison of human and simian intraparietal networks is missing. In this study, we used diffusion imaging tractography to reconstruct the major intralobar parietal tracts in twenty-one datasets acquired in vivo from healthy human subjects and eleven ex vivo datasets from five vervet and six macaque monkeys. Three regions of interest (postcentral gyrus, superior parietal lobule and inferior parietal lobule) were used to identify the tracts. Surface projections were reconstructed for both species and results compared to identify similarities or differences in tract anatomy (i.e., trajectories and cortical projections). In addition, post-mortem dissections were performed in a human brain. The largest tract identified in both human and monkey brains is a vertical pathway between the superior and inferior parietal lobules. This tract can be divided into an anterior (supramarginal gyrus) and a posterior (angular gyrus) component in both humans and monkey brains. The second prominent intraparietal tract connects the postcentral gyrus to both supramarginal and angular gyri of the inferior parietal lobule in humans but only to the supramarginal gyrus in the monkey brain. The third tract connects the postcentral gyrus to the anterior region of the superior parietal lobule and is more prominent in monkeys compared to humans. Finally, short U-shaped fibres in the medial and lateral aspects of the parietal lobe were identified in both species. A tract connecting the medial parietal cortex to the lateral inferior parietal cortex was observed in the monkey brain only. Our findings suggest a consistent pattern of intralobar parietal connections between humans and monkeys with some differences for those areas that have cytoarchitectonically distinct features in humans. The overall pattern of intraparietal connectivity supports the special role of the inferior parietal lobule in cognitive functions characteristic of humans., (Copyright © 2017. Published by Elsevier Ltd.)

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.

The corpus callosum establishes the anatomical continuity between the 2 hemispheres and coordinates their activity. Using histological tracing, single axon reconstructions, and diffusion tractography, we describe a callosal projection to n caudatus and putamen in monkeys and humans. In both species, the origin of this projection is more restricted than that of the ipsilateral projection. In monkeys, it consists of thin axons (0.4-0.6 µm), appropriate for spatial and temporal dispersion of subliminal inputs. For prefrontal cortex, contralateral minus ipsilateral delays to striatum calculated from axon diameters and conduction distance are <2 ms in the monkey and, by extrapolation, <4 ms in humans. This delay corresponds to the performance in Poffenberger's paradigm, a classical attempt to estimate central conduction delays, with a neuropsychological task. In both species, callosal cortico-striatal projections originate from prefrontal, premotor, and motor areas. In humans, we discovered a new projection originating from superior parietal lobule, supramarginal, and superior temporal gyrus, regions engaged in language processing. This projection crosses in the isthmus the lesion of which was reported to dissociate syntax and prosody. The projection might originate from an overproduction of callosal projections in development, differentially pruned depending on species., (© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)