7T MP2RAGE for cortical myelin segmentation: Impact of aging

BACKGROUND

Myelin and iron are major contributors to the cortical MR signal. The aim of this study was to investigate 1. Can MP2RAGE-derived contrasts at 7T in combination with k-means clustering be used to distinguish between heavily and sparsely myelinated layers in cortical gray matter (GM)? 2. Does this approach provide meaningful biological information?

METHODS

The following contrasts were generated from the 7T MP2RAGE images from 45 healthy controls (age: 19-75, f/m = 23/22) from the ATAG data repository: 1. T1 weighted image (UNI). 2. T1 relaxation image (T1map). 3. INVC/T1map ratio (RATIO). K-means clustering identified 6 clusters/tissue maps (csf, csf/gm-transition, wm, wm/gm transition, heavily myelinated cortical GM (dGM), sparsely myelinated cortical GM (sGM)). These tissue maps were then processed with SPM/DARTEL (volume-based analyses) and Freesurfer (surface-based analyses) and dGM and sGM volume/thickness of young adults (n = 27, 19-27 years) compared to those of older adults (n = 18, 42-75 years) at p<0.001 uncorrected.

RESULTS

The resulting maps showed good agreement with histological maps in the literature. Volume- and surface analyses found age-related dGM loss/thinning in the mid-posterior cingulate and parahippocampal/entorhinal gyrus and age-related sGM losses in lateral, mesial and orbitofrontal frontal, insular cortex and superior temporal gyrus.

CONCLUSION

The MP2RAGE derived UNI, T1map and RATIO contrasts can be used to identify dGM and sGM. Considering the close relationship between cortical myelo- and cytoarchitecture, the findings reported here indicate that this new technique might provide new insights into the nature of cortical GM loss in physiological and pathological conditions.

The Potential of Myelin-Sensitive Imaging: Redefining Spatiotemporal Patterns of Myeloarchitecture

Recent advances in magnetic resonance imaging (MRI) have paved the way for approximation of myelin content in vivo. In this review, our main goal was to determine how to best capitalize on myelin-sensitive imaging. First, we briefly overview the theoretical and empirical basis for the myelin sensitivity of different MRI markers and, in doing so, highlight how multimodal imaging approaches are important for enhancing specificity to myelin. Then, we discuss recent studies that have probed the nonuniform distribution of myelin across cortical layers and along white matter tracts. These approaches, collectively known as myelin profiling, have provided detailed depictions of myeloarchitecture in both the postmortem and living human brain. Notably, MRI-based profiling studies have recently focused on investigating whether it can capture interindividual variability in myelin characteristics as well as trajectories across the lifespan. Finally, another line of recent evidence emphasizes the contribution of region-specific myelination to large-scale organization, demonstrating the impact of myelination on global brain networks. In conclusion, we suggest that combining well-validated MRI markers with profiling techniques holds strong potential to elucidate individual differences in myeloarchitecture, which has important implications for understanding brain function and disease.

Mesoscopic in vivo human T2* dataset acquired using quantitative MRI at 7 Tesla

Mesoscopic (0.1-0.5 mm) interrogation of the living human brain is critical for advancing neuroscience and bridging the resolution gap with animal models. Despite the variety of MRI contrasts measured in recent years at the mesoscopic scale, in vivo quantitative imaging of T₂^* has not been performed. Here we provide a dataset containing empirical T₂^* measurements acquired at 0.35 × 0.35 × 0.35 mm³ voxel resolution using 7 Tesla MRI. To demonstrate unique features and high quality of this dataset, we generate flat map visualizations that reveal fine-scale cortical substructures such as layers and vessels, and we report quantitative depth-dependent T₂^* (as well as R₂^*) values in primary visual cortex and auditory cortex that are highly consistent across subjects. This dataset is freely available at https://doi.org/10.17605/OSF.IO/N5BJ7, and may prove useful for anatomical investigations of the human brain, as well as for improving our understanding of the basis of the T₂^*-weighted (f)MRI signal.

Identification of Laminar Composition in Cerebral Cortex Using Low-Resolution Magnetic Resonance Images and Trust Region Optimization Algorithm

Pathological changes in the cortical lamina can cause several mental disorders. Visualization of these changes in vivo would enhance their diagnostics. Recently a framework for visualizing cortical structures by magnetic resonance imaging (MRI) has emerged. This is based on mathematical modeling of multi-component T1 relaxation at the sub-voxel level. This work proposes a new approach for their estimation. The approach is validated using simulated data. Sixteen MRI experiments were carried out on healthy volunteers. A modified echo-planar imaging (EPI) sequence was used to acquire 105 individual volumes. Data simulating the images were created, serving as the ground truth. The model was fitted to the data using a modified Trust Region algorithm. In single voxel experiments, the estimation accuracy of the T1 relaxation times depended on the number of optimization starting points and the level of noise. A single starting point resulted in a mean percentage error (MPE) of 6.1%, while 100 starting points resulted in a perfect fit. The MPE was <5% for the signal-to-noise ratio (SNR) ≥ 38 dB. Concerning multiple voxel experiments, the MPE was <5% for all components. Estimation of T1 relaxation times can be achieved using the modified algorithm with MPE < 5%.

Heritable functional architecture in human visual cortex

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We analyzed retinotopic maps from monozygotic and dizygotic twin pairs.

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Visual field maps in V1-V3 are more similar in monozygotic twins.

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Heritability is greater in V1 and V3 for polar angle and population receptive field sizes.

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Eccentricity maps show lesser degree of heritability.

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Further evidence for link between cortical morphology and topology of retinotopic maps.

How much of the functional organization of our visual system is inherited? Here we tested the heritability of retinotopic maps in human visual cortex using functional magnetic resonance imaging. We demonstrate that retinotopic organization shows a closer correspondence in monozygotic (MZ) compared to dizygotic (DZ) twin pairs, suggesting a partial genetic determination. Using population receptive field (pRF) analysis to examine the preferred spatial location and selectivity of these neuronal populations, we estimate a heritability around 10–20% for polar angle preferences and spatial selectivity, as quantified by pRF size, in extrastriate areas V2 and V3. Our findings are consistent with heritability in both the macroscopic arrangement of visual regions and stimulus tuning properties of visual cortex. This could constitute a neural substrate for variations in a range of perceptual effects, which themselves have been found to be at least partially genetically determined. These findings also add convergent evidence for the hypothesis that functional map topology is linked with cortical morphology.

Improved cortical surface reconstruction using sub-millimeter resolution MPRAGE by image denoising

Automatic cerebral cortical surface reconstruction is a useful tool for cortical anatomy quantification, analysis and visualization. Recently, the Human Connectome Project and several studies have shown the advantages of using T₁-weighted magnetic resonance (MR) images with sub-millimeter isotropic spatial resolution instead of the standard 1-mm isotropic resolution for improved accuracy of cortical surface positioning and thickness estimation. Nonetheless, sub-millimeter resolution images are noisy by nature and require averaging multiple repetitions to increase the signal-to-noise ratio for precisely delineating the cortical boundary. The prolonged acquisition time and potential motion artifacts pose significant barriers to the wide adoption of cortical surface reconstruction at sub-millimeter resolution for a broad range of neuroscientific and clinical applications. We address this challenge by evaluating the cortical surface reconstruction resulting from denoised single-repetition sub-millimeter T₁-weighted images. We systematically characterized the effects of image denoising on empirical data acquired at 0.6 mm isotropic resolution using three classical denoising methods, including denoising convolutional neural network (DnCNN), block-matching and 4-dimensional filtering (BM4D) and adaptive optimized non-local means (AONLM). The denoised single-repetition images were found to be highly similar to 6-repetition averaged images, with a low whole-brain averaged mean absolute difference of ~0.016, high whole-brain averaged peak signal-to-noise ratio of ~33.5 dB and structural similarity index of ~0.92, and minimal gray matter–white matter contrast loss (2% to 9%). The whole-brain mean absolute discrepancies in gray matter–white matter surface placement, gray matter–cerebrospinal fluid surface placement and cortical thickness estimation were lower than 165 μm, 155 μm and 145 μm—sufficiently accurate for most applications. These discrepancies were approximately one third to half of those from 1-mm isotropic resolution data. The denoising performance was equivalent to averaging ~2.5 repetitions of the data in terms of image similarity, and 1.6–2.2 repetitions in terms of the cortical surface placement accuracy. The scan-rescan variability of the cortical surface positioning and thickness estimation was lower than 170 μm. Our unique dataset and systematic characterization support the use of denoising methods for improved cortical surface reconstruction at sub-millimeter resolution.

Improving in vivo human cerebral cortical surface reconstruction using data-driven super-resolution

Accurate and automated reconstruction of the in vivo human cerebral cortical surface from anatomical magnetic resonance (MR) images facilitates the quantitative analysis of cortical structure. Anatomical MR images with sub-millimeter isotropic spatial resolution improve the accuracy of cortical surface and thickness estimation compared to the standard 1-millimeter isotropic resolution. Nonetheless, sub-millimeter resolution acquisitions require averaging multiple repetitions to achieve sufficient signal-to-noise ratio and are therefore long and potentially vulnerable to subject motion. We address this challenge by synthesizing sub-millimeter resolution images from standard 1-millimeter isotropic resolution images using a data-driven supervised machine learning-based super-resolution approach achieved via a deep convolutional neural network. We systematically characterize our approach using a large-scale simulated dataset and demonstrate its efficacy in empirical data. The super-resolution data provide improved cortical surfaces similar to those obtained from native sub-millimeter resolution data. The whole-brain mean absolute discrepancy in cortical surface positioning and thickness estimation is below 100 μm at the single-subject level and below 50 μm at the group level for the simulated data, and below 200 μm at the single-subject level and below 100 μm at the group level for the empirical data, making the accuracy of cortical surfaces derived from super-resolution sufficient for most applications.

Forging a path to mesoscopic imaging success with ultra-high field functional magnetic resonance imaging

Functional magnetic resonance imaging (fMRI) studies with ultra-high field (UHF, 7+ Tesla) technology enable the acquisition of high-resolution images. In this work, we discuss recent achievements in UHF fMRI at the mesoscopic scale, on the order of cortical columns and layers, and examine approaches to addressing common challenges. As researchers push to smaller and smaller voxel sizes, acquisition and analysis decisions have greater potential to degrade spatial accuracy, and UHF fMRI data must be carefully interpreted. We consider the impact of acquisition decisions on the spatial specificity of the MR signal with a representative dataset with 0.8 mm isotropic resolution. We illustrate the trade-offs in contrast with noise ratio and spatial specificity of different acquisition techniques and show that acquisition blurring can increase the effective voxel size by as much as 50% in some dimensions. We further describe how different sources of degradations to spatial resolution in functional data may be characterized. Finally, we emphasize that progress in UHF fMRI depends not only on scientific discovery and technical advancement, but also on informal discussions and documentation of challenges researchers face and overcome in pursuit of their goals. This article is part of the theme issue 'Key relationships between non-invasive functional neuroimaging and the underlying neuronal activity'.

Cortical projection neurons as a therapeutic target in multiple sclerosis

INTRODUCTION

Multiple sclerosis (MS) is a chronic inflammatory-demyelinating disease of the central nervous system associated with lesions of the cortical gray matter and subcortical white matter. Recently, cortical lesions have become a major focus of research because cortical pathology and neuronal damage are critical determinants of irreversible clinical progression. Recent transcriptomic studies point toward cell type-specific changes in cortical neurons in MS with a selective vulnerability of excitatory projection neuron subtypes.

AREAS COVERED

We discuss the cortical mapping and the molecular properties of excitatory projection neurons and their role in MS lesion pathology while placing an emphasis on their subtype-specific transcriptomic changes and levels of vulnerability. We also examine the latest magnetic resonance imaging techniques to study cortical MS pathology as a key tool for monitoring disease progression and treatment efficacy. Finally, we consider possible therapeutic avenues and novel strategies to protect excitatory cortical projection neurons. Literature search methodology: PubMed articles from 2000-2020.

EXPERT OPINION

Excitatory cortical projection neurons are an emerging therapeutic target in the treatment of progressive MS. Understanding neuron subtype-specific molecular pathologies and their exact spatial mapping will help establish starting points for the development of novel cell type-specific therapies and biomarkers in MS.

The Effect of Onset Age of Visual Deprivation on Visual Cortex Surface Area Across-Species

Blindness early in life induces permanent alterations in brain anatomy, including reduced surface area of primary visual cortex (V1). Bilateral enucleation early in development causes greater reductions in primary visual cortex surface area than at later times. However, the time at which cortical surface area expansion is no longer sensitive to enucleation is not clearly established, despite being an important milestone for cortical development. Using histological and MRI techniques, we investigated how reductions in the surface area of V1 depends on the timing of blindness onset in rats, ferrets and humans. To compare data across species, we translated ages of all species to a common neuro-developmental event-time (ET) scale. Consistently, blindness during early cortical expansion induced large (~40%) reductions in V1 surface area, in rats and ferrets, while blindness occurring later had diminishing effects. Longitudinal measurements on ferrets confirmed that early enucleation disrupted cortical expansion, rather than inducing enhanced pruning. We modeled the ET associated with the conclusion of the effect of blindness on surface area at maturity (ETc), relative to the normal conclusion of visual cortex surface area expansion, (ETdev). A final analysis combining our data with extant published data confirmed that ETc occurred well before ETdev.

Thickness of Deep Layers in the Fusiform Face Area Predicts Face Recognition

People with superior face recognition have relatively thin cortex in face-selective brain areas, whereas those with superior vehicle recognition have relatively thick cortex in the same areas. We suggest that these opposite correlations reflect distinct mechanisms influencing cortical thickness (CT) as abilities are acquired at different points in development. We explore a new prediction regarding the specificity of these effects through the depth of the cortex: that face recognition selectively and negatively correlates with thickness of the deepest laminar subdivision in face-selective areas. With ultrahigh resolution MRI at 7T, we estimated the thickness of three laminar subdivisions, which we term "MR layers," in the right fusiform face area (FFA) in 14 adult male humans. Face recognition was negatively associated with the thickness of deep MR layers, whereas vehicle recognition was positively related to the thickness of all layers. Regression model comparisons provided overwhelming support for a model specifying that the magnitude of the association between face recognition and CT differs across MR layers (deep vs. superficial/middle) whereas the magnitude of the association between vehicle recognition and CT is invariant across layers. The total CT of right FFA accounted for 69% of the variance in face recognition, and thickness of the deep layer alone accounted for 84% of this variance. Our findings demonstrate the functional validity of MR laminar estimates in FFA. Studying the structural basis of individual differences for multiple abilities in the same cortical area can reveal effects of distinct mechanisms that are not apparent when studying average variation or development.

Comparison of 3T and 7T MRI for the visualization of globus pallidus sub-segments

The success of deep brain stimulation (DBS) targeting the internal globus pallidus (GPi) depends on the accuracy of electrode localization inside the GPi. In this study, we sought to compare visualization of the medial medullary lamina (MML) and accessory medullary lamina (AML) between proton density-weighted (PDW) and T2-weighted (T2W) sequences on 3T and 7T MRI scanners. Eleven healthy participants (five men and six women; age, 19–28 years; mean, 21.5) and one 61-year-old man were scanned using two-dimensional turbo spin-echo PDW and T2W sequences on 3T and 7T MRI scanners with a 32-channel receiver head coil and a single-channel transmission coil. Profiles of signal intensity were obtained from the pixel values of straight lines over the GP regions crossing the MML and AML. Contrast ratios (CRs) for GPe/MML, GPie/MML, GPie/AML, and GPii/AML were calculated. Qualitatively, 7T visualized both the MML and AML, whereas 3T visualized the MML less clearly and hardly depicted the AML. The T2W sequence at 7T yielded significantly higher CRs for GPie/MML, GPie/AML, and GPii/AML than the PDW sequence at 7T or 3T. The T2W sequence at 7T allows visualization of the internal structures of GPi segments with high signal intensity and contrast.

Myelin and Modeling: Bootstrapping Cortical Microcircuits

Histological studies of myelin-stained sectioned cadaver brain and in vivo myelin-weighted magnetic resonance imaging (MRI) show that the cerebral cortex is organized into cortical areas with generally well-defined boundaries, which have consistent internal patterns of myelination. The process of myelination is largely driven by neural experience, in which the axonal passage of action potentials stimulates neighboring oligodendrocytes to perform their task. This bootstrapping process, such that the traffic of action potentials facilitates increased traffic, suggests the hypothesis that the specific pattern of myelination (myeloarchitecture) in each cortical area reveals the principal cortical microcircuits required for the function of that area. If this idea is correct, the observable sequential maturation of specific brain areas can provide evidence for models of the stages of cognitive development.

Detailed T1-Weighted Profiles from the Human Cortex Measured in Vivo at 3 Tesla MRI

Studies into cortical thickness in psychiatric diseases based on T1-weighted MRI frequently report on aberrations in the cerebral cortex. Due to limitations in image resolution for studies conducted at conventional MRI field strengths (e.g. 3 Tesla (T)) this information cannot be used to establish which of the cortical layers may be implicated. Here we propose a new analysis method that computes one high-resolution average cortical profile per brain region extracting myeloarchitectural information from T1-weighted MRI scans that are routinely acquired at a conventional field strength. To assess this new method, we acquired standard T1-weighted scans at 3 T and compared them with state-of-the-art ultra-high resolution T1-weighted scans optimised for intracortical myelin contrast acquired at 7 T. Average cortical profiles were computed for seven different brain regions. Besides a qualitative comparison between the 3 T scans, 7 T scans, and results from literature, we tested if the results from dynamic time warping-based clustering are similar for the cortical profiles computed from 7 T and 3 T data. In addition, we quantitatively compared cortical profiles computed for V1, V2 and V7 for both 7 T and 3 T data using a priori information on their relative myelin concentration. Although qualitative comparisons show that at an individual level average profiles computed for 7 T have more pronounced features than 3 T profiles the results from the quantitative analyses suggest that average cortical profiles computed from T1-weighted scans acquired at 3 T indeed contain myeloarchitectural information similar to profiles computed from the scans acquired at 7 T. The proposed method therefore provides a step forward to study cortical myeloarchitecture in vivo at conventional magnetic field strength both in health and disease.

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.

Advantages of cortical surface reconstruction using submillimeter 7 T MEMPRAGE

Recent advances in MR technology have enabled increased spatial resolution for routine functional and anatomical imaging, which has created demand for software tools that are able to process these data. The availability of high-resolution data also raises the question of whether higher resolution leads to substantial gains in accuracy of quantitative morphometric neuroimaging procedures, in particular the cortical surface reconstruction and cortical thickness estimation. In this study we adapted the FreeSurfer cortical surface reconstruction pipeline to process structural data at native submillimeter resolution. We then quantified the differences in surface placement between meshes generated from (0.75 mm)³ isotropic resolution data acquired in 39 volunteers and the same data downsampled to the conventional 1 mm³ voxel size. We find that when processed at native resolution, cortex is estimated to be thinner in most areas, but thicker around the Cingulate and the Calcarine sulci as well as in the posterior bank of the Central sulcus. Thickness differences are driven by two kinds of effects. First, the gray-white surface is found closer to the white matter, especially in cortical areas with high myelin content, and thus low contrast, such as the Calcarine and the Central sulci, causing local increases in thickness estimates. Second, the gray-CSF surface is placed more interiorly, especially in the deep sulci, contributing to local decreases in thickness estimates. We suggest that both effects are due to reduced partial volume effects at higher spatial resolution. Submillimeter voxel sizes can therefore provide improved accuracy for measuring cortical thickness.

Uses, misuses, new uses and fundamental limitations of magnetic resonance imaging in cognitive science

When blood oxygenation level-dependent (BOLD) contrast functional magnetic resonance imaging (fMRI) was discovered in the early 1990s, it provoked an explosion of interest in exploring human cognition, using brain mapping techniques based on MRI. Standards for data acquisition and analysis were rapidly put in place, in order to assist comparison of results across laboratories. Recently, MRI data acquisition capabilities have improved dramatically, inviting a rethink of strategies for relating functional brain activity at the systems level with its neuronal substrates and functional connections. This paper reviews the established capabilities of BOLD contrast fMRI, the perceived weaknesses of major methods of analysis, and current results that may provide insights into improved brain modelling. These results have inspired the use of in vivo myeloarchitecture for localizing brain activity, individual subject analysis without spatial smoothing and mapping of changes in cerebral blood volume instead of BOLD activation changes. The apparent fundamental limitations of all methods based on nuclear magnetic resonance are also discussed.This article is part of the themed issue 'Interpreting BOLD: a dialogue between cognitive and cellular neuroscience'.

Recent applications of UHF-MRI in the study of human brain function and structure: a review

The increased availability of ultra-high-field (UHF) MRI has led to its application in a wide range of neuroimaging studies, which are showing promise in transforming fundamental approaches to human neuroscience. This review presents recent work on structural and functional brain imaging, at 7 T and higher field strengths. After a short outline of the effects of high field strength on MR images, the rapidly expanding literature on UHF applications of blood-oxygenation-level-dependent-based functional MRI is reviewed. Structural imaging is then discussed, divided into sections on imaging weighted by relaxation time, including quantitative relaxation time mapping, phase imaging and quantitative susceptibility mapping, angiography, diffusion-weighted imaging, and finally magnetization-transfer imaging. The final section discusses studies using the high spatial resolution available at UHF to identify explicit links between structure and function. Copyright © 2015 John Wiley & Sons, Ltd.

Motion-Correction Enabled Ultra-High Resolution In-Vivo 7T-MRI of the Brain

Objectives

To demonstrate the image quality that can be obtained for multiple contrasts using ultra-high resolution MRI (highest nominal resolution: 350 μm isotropic) at 7T using appropriate motion-correction.

Materials and Methods

An MRI-based fat-excitation motion navigator (which requires no additional hardware) was incorporated into T1-weighted (MP2RAGE, 350 μm nominal isotropic resolution, total scan time 124 mins over 2 sessions. The MP2RAGE also provides quantitative T1-maps), 3D-TSE (380 μm nominal isotropic resolution, total scan time 58 mins) and T2*-weighted protocols (3D-GRE, 380 μm nominal isotropic resolution, total scan time 42 mins) on a 7T MR system. Images from each contrast are presented from a single healthy adult male volunteer (34 years) for direct comparison. The subject provided written consent in accordance with the local review board.

Results

Images of various brain structures are revealed at unprecedented quality for in-vivo MRI. The presented images permit, for example, to delimit the internal structure of the basal ganglia and thalamus. The single digitationes of the hippocampus are visible, and the gyrus dentatus can be visualized. Intracortical contrast was also observed in the neocortex, including the stria of Gennari of the primary visual cortex.

Conclusions

Appropriate motion-correction allows MRI scans to be performed with extended scan times enabling exceptionally high resolution scans with high image quality, with the use of a 7T scanner allowing large brain coverage for 350–380 μm isotropic voxels with total scan times for each contrast ranging from 42 to 124 minutes.

Lines of Baillarger in vivo and ex vivo: Myelin contrast across lamina at 7T MRI and histology

The human cerebral cortex is characterized by a number of features that are not uniformly distributed, such as the presence of multiple cytoarchitectonic elements and of myelinated layers running tangentially to the cortex surface. The presence and absence of these features are the basis of the parcellation of the cerebral cortex in several areas. A number of areas show myelin increases localized within the cortex, e.g., the stria of Gennari located in layer IV of the primary visual cortex. Sub-millimeter MRI can resolve myelin variations across the human cortex and may allow in vivo parcellation of these brain areas. Here, we image within-area myelination. We modified a T1-weighted (T1-w) MPRAGE sequence to enhance myelin visualization within the cortex. First, we acquired images from an ex vivo sample, and compared MRI laminar profiles from calcarine (corresponding to primary visual cortex) and extra-calcarine areas with histology sections from the same locations. Laminar profiles between myelin stained sections and the T1-w images were similar both in calcarine as well as extra-calcarine cortex. In calcarine cortex, the profile reveals the stria of Gennari. In extra-calcarine cortex, a similar profile exists which we suggest corresponds to the lines of Baillarger. Next, we adapted the same sequence to image within-area myelination in vivo. Also in in vivo data, we discriminated similar laminar profiles in calcarine and extra-calcarine cortex, extending into parietal and frontal lobes. We argue that this myelin pattern outside the calcarine cortex represents the lines of Baillarger.

Automatic segmentation of the hippocampus for preterm neonates from early-in-life to term-equivalent age

Introduction

The hippocampus, a medial temporal lobe structure central to learning and memory, is particularly vulnerable in preterm-born neonates. To date, segmentation of the hippocampus for preterm-born neonates has not yet been performed early-in-life (shortly after birth when clinically stable). The present study focuses on the development and validation of an automatic segmentation protocol that is based on the MAGeT-Brain (Multiple Automatically Generated Templates) algorithm to delineate the hippocampi of preterm neonates on their brain MRIs acquired at not only term-equivalent age but also early-in-life.

Methods

First, we present a three-step manual segmentation protocol to delineate the hippocampus for preterm neonates and apply this protocol on 22 early-in-life and 22 term images. These manual segmentations are considered the gold standard in assessing the automatic segmentations. MAGeT-Brain, automatic hippocampal segmentation pipeline, requires only a small number of input atlases and reduces the registration and resampling errors by employing an intermediate template library. We assess the segmentation accuracy of MAGeT-Brain in three validation studies, evaluate the hippocampal growth from early-in-life to term-equivalent age, and study the effect of preterm birth on the hippocampal volume. The first experiment thoroughly validates MAGeT-Brain segmentation in three sets of 10-fold Monte Carlo cross-validation (MCCV) analyses with 187 different groups of input atlases and templates. The second experiment segments the neonatal hippocampi on 168 early-in-life and 154 term images and evaluates the hippocampal growth rate of 125 infants from early-in-life to term-equivalent age. The third experiment analyzes the effect of gestational age (GA) at birth on the average hippocampal volume at early-in-life and term-equivalent age using linear regression.

Results

The final segmentations demonstrate that MAGeT-Brain consistently provides accurate segmentations in comparison to manually derived gold standards (mean Dice's Kappa > 0.79 and Euclidean distance <1.3 mm between centroids). Using this method, we demonstrate that the average volume of the hippocampus is significantly different (p < 0.0001) in early-in-life (621.8 mm³) and term-equivalent age (958.8 mm³). Using these differences, we generalize the hippocampal growth rate to 38.3 ± 11.7 mm³/week and 40.5 ± 12.9 mm³/week for the left and right hippocampi respectively. Not surprisingly, younger gestational age at birth is associated with smaller volumes of the hippocampi (p = 0.001).

Conclusions

MAGeT-Brain is capable of segmenting hippocampi accurately in preterm neonates, even at early-in-life. Hippocampal asymmetry with a larger right side is demonstrated on early-in-life images, suggesting that this phenomenon has its onset in the 3rd trimester of gestation. Hippocampal volume assessed at the time of early-in-life and term-equivalent age is linearly associated with GA at birth, whereby smaller volumes are associated with earlier birth.

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We develop a MAGeT-Brain based automatic protocol to segment hippocampus in preterm neonates.

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MAGeT-Brain can accurately segment hippocampus in preterm neonates, even at early-in-life.

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Hippocampal asymmetry with a larger right side is demonstrated on early-in-life images.

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Smaller hippocampal volumes are associated with earlier birth in preterm neonates.

Visual imagery and functional connectivity in blindness: a single-case study

We present a case report on visual brain plasticity after total blindness acquired in adulthood. SH lost her sight when she was 27. Despite having been totally blind for 43 years, she reported to strongly rely on her vivid visual imagery. Three-Tesla magnetic resonance imaging (MRI) of SH and age-matched controls was performed. The MRI sequence included anatomical MRI, resting-state functional MRI, and task-related functional MRI where SH was instructed to imagine colours, faces, and motion. Compared to controls, voxel-based analysis revealed white matter loss along SH's visual pathway as well as grey matter atrophy in the calcarine sulci. Yet we demonstrated activation in visual areas, including V1, using functional MRI. Of the four identified visual resting-state networks, none showed alterations in spatial extent; hence, SH's preserved visual imagery seems to be mediated by intrinsic brain networks of normal extent. Time courses of two of these networks showed increased correlation with that of the inferior posterior default mode network, which may reflect adaptive changes supporting SH's strong internal visual representations. Overall, our findings demonstrate that conscious visual experience is possible even after years of absence of extrinsic input.

Patterns of myeloarchitecture in lower limb amputees: an MRI study

Functional studies of cortical plasticity in humans suggest that the motor cortex reorganizes when the descending motor output pathway is disrupted as a result of limb amputation. The question thus arises if the underlying anatomical organization of the motor cortex is also altered in limb amputation. Owing to challenges involved in imaging the thin cerebral cortex in vivo, there is limited data available on the anatomical or morphological plasticity of the motor cortex in amputation. In this paper, we study the morphology of the primary motor cortex in four lower limb amputees with 37 or more years of amputation and four age and gender-matched controls using 0.7 mm isotropic, T₁-weighted MRI optimized to produce enhanced intracortical contrast based on myelin content. We segment the cortex into myelinated and unmyelinated gray matter. We determine the myelinated thickness which is the thickness of the well-myelinated tissue in the deeper layers of the cortex. We compare the bilateral differences in the myelinated thickness between amputees and controls. We also compare bilateral differences in cortical thickness between the two groups. Our measurements show no statistically significant difference between the amputees and controls in the myelinated thickness and in cortical thickness, in the region of the primary motor cortex representing the lower leg.

Characterizing the contrast of white matter and grey matter in high-resolution phase difference enhanced imaging of human brain at 3.0 T

OBJECTIVES

The purpose of this study was to address the feasibility of characterizing the contrast both between and within grey matter and white matter using the phase difference enhanced (PADRE) technique.

METHODS

PADRE imaging was performed in 33 healthy volunteers. Vessel enhancement (VE), tissue enhancement (TE), and PADRE images were reconstructed from source images and were evaluated with regard to differentiation of grey-to-white matter interface, the stria of Gennari, and the two layers, internal sagittal stratum (ISS) and external sagittal stratum (ESS), of optic radiation.

RESULTS

White matter regions showed decreased signal intensity compared to grey matter regions. Discrimination was sharper between white matter and cortical grey matter in TE images than in PADRE images, but was poorly displayed in VE images. The stria of Gennari was observed on all three image sets. Low-signal-intensity bands displayed in VE images representing the optic radiation were delineated as two layers of different signal intensities in TE and PADRE images. Statistically significant differences in phase shifts were found between frontal grey and white matter, as well as between ISS and ESS (p < 0.01).

CONCLUSIONS

The PADRE technique is capable of identifying grey-to-white matter interface, the stria of Gennari, and ISS and ESS, with improved contrast in PADRE and TE images compared to VE images.

KEY POINTS

• Phase difference enhanced (PADRE) imaging can yield diverse contrasts between tissues • The PADRE technique utilizes the inherent variety of magnetic susceptibilities • PADRE MR imaging provides better visualization of certain cerebral anatomy in vivo • PADRE imaging is able to delineate the stria of Gennari in the primary visual cortex • PADRE imaging is able to identify the two optic radiation layers.

Comparing like with like: the power of knowing where you are

Magnetic resonance imaging can now provide human brain images of structure, function, and connectivity with isotropic voxels smaller than one millimeter, and thus much smaller than the cortical thickness. This resolution, achievable in a scan time of less than 1 h, enables visualization of myeloarchitectural layer structure, intracortical variations in functional activity--recorded in changes in blood oxygenation level dependent signal or cerebral blood volume CBV--and intracortical axonal orientational structure via diffusion-weighted magnetic resonance imaging. While recent improvements in radiofrequency receiver coils now enable excellent image data to be obtained at 3T, scanning at the ultra-high field of 7 T offers further gains in signal-to-noise ratio and speed of image acquisition, with a structural image resolution of about 300 μm. These improvements throw into sharp question the strategies that have become conventional for the analysis of functional imaging data, especially the practice of spatial smoothing of raw functional data before further analysis. Creation of a native cortical map for each human subject that provides a reliable individual parcellation into cortical areas related to Brodmann Areas enables a strikingly different approach to functional image analysis. This proposed approach involves surface registration of the cortices of groups of subjects using maps of the longitudinal relaxation time T1 as an index of myelination, and methods for inferring statistical significance that do not entail spatial smoothing. The outcome should be a far more precise comparison of like-with-like cortical areas across subjects, with the potential to greatly increase experimental power, to discriminate activity in neighboring cortical areas, and to enable correlation of function and connectivity with specific cytoarchitecture. Such analyses should enable a far more convincing modeling of brain mechanisms than current graph-based methods that require gross over-simplification of brain activity patterns in order to be computationally tractable.

High-Resolution Mapping of Myeloarchitecture In Vivo: Localization of Auditory Areas in the Human Brain

The precise delineation of auditory areas in vivo remains problematic. Histological analysis of postmortem tissue indicates that the relation of areal borders to macroanatomical landmarks is variable across subjects. Furthermore, functional parcellation schemes based on measures of, for example, frequency preference (tonotopy) remain controversial. Here, we propose a 7 Tesla magnetic resonance imaging method that enables the anatomical delineation of auditory cortical areas in vivo and in individual brains, through the high-resolution visualization (0.6 × 0.6 × 0.6 mm(3)) of intracortical anatomical contrast related to myelin. The approach combines the acquisition and analysis of images with multiple MR contrasts (T1, T2*, and proton density). Compared with previous methods, the proposed solution is feasible at high fields and time efficient, which allows collecting myelin-related and functional images within the same measurement session. Our results show that a data-driven analysis of cortical depth-dependent profiles of anatomical contrast allows identifying a most densely myelinated cortical region on the medial Heschl's gyrus. Analyses of functional responses show that this region includes neuronal populations with typical primary functional properties (single tonotopic gradient and narrow frequency tuning), thus indicating that it may correspond to the human homolog of monkey A1.

The fine-scale functional correlation of striate cortex in sighted and blind people

To what extent are spontaneous neural signals within striate cortex organized by vision? We examined the fine-scale pattern of striate cortex correlations within and between hemispheres in rest-state BOLD fMRI data from sighted and blind people. In the sighted, we find that corticocortico correlation is well modeled as a Gaussian point-spread function across millimeters of striate cortical surface, rather than degrees of visual angle. Blindness produces a subtle change in the pattern of fine-scale striate correlations between hemispheres. Across participants blind before the age of 18, the degree of pattern alteration covaries with the strength of long-range correlation between left striate cortex and Broca's area. This suggests that early blindness exchanges local, vision-driven pattern synchrony of the striate cortices for long-range functional correlations potentially related to cross-modal representation.

High-Resolution MR Imaging of the Human Brainstem In vivo at 7 Tesla

The human brainstem, which comprises a multitude of axonal nerve fibers and nuclei, plays an important functional role in the human brain. Depicting its anatomy non-invasively with high spatial resolution may thus in turn help to better relate normal and pathological anatomical variations to medical conditions as well as neurological and peripheral functions. We explored the potential of high-resolution magnetic resonance imaging (MRI) at 7 T for depicting the intricate anatomy of the human brainstem in vivo by acquiring and generating images with multiple contrasts: T 2-weighted images, quantitative maps of longitudinal relaxation rate (R 1 maps) and effective transverse relaxation rate ([Formula: see text] maps), magnetic susceptibility maps, and direction-encoded track-density images. Images and quantitative maps were compared with histological stains and anatomical atlases to identify nerve nuclei and nerve fibers. Among the investigated contrasts, susceptibility maps displayed the largest number of brainstem structures. Contrary to R 1 maps and T 2-weighted images, which showed rather homogeneous contrast, [Formula: see text] maps, magnetic susceptibility maps, and track-density images clearly displayed a multitude of smaller and larger fiber bundles. Several brainstem nuclei were identifiable in sections covering the pons and medulla oblongata, including the spinal trigeminal nucleus and the reticulotegmental nucleus on magnetic susceptibility maps as well as the inferior olive on R 1, [Formula: see text], and susceptibility maps. The substantia nigra and red nuclei were visible in all contrasts. In conclusion, high-resolution, multi-contrast MR imaging at 7 T is a versatile tool to non-invasively assess the individual anatomy and tissue composition of the human brainstem.

Trends and properties of human cerebral cortex: correlations with cortical myelin content

"In vivo Brodmann mapping" or non-invasive cortical parcellation using MRI, especially by measuring cortical myelination, has recently become a popular research topic, though myeloarchitectonic cortical parcellation in humans previously languished in favor of cytoarchitecture. We review recent in vivo myelin mapping studies and discuss some of the different methods for estimating myelin content. We discuss some ways in which myelin maps may improve surface registration and be useful for cross-modal and cross-species comparisons, including some preliminary cross-species results. Next, we consider neurobiological aspects of why some parts of cortex are more myelinated than others. Myelin content is inversely correlated with intracortical circuit complexity - in general, more myelin content means simpler and perhaps less dynamic intracortical circuits. Using existing PET data and functional network parcellations, we examine metabolic differences in the differently myelinated cortical functional networks. Lightly myelinated cognitive association networks tend to have higher aerobic glycolysis than heavily myelinated early sensory-motor ones, perhaps reflecting greater ongoing dynamic anabolic cortical processes. This finding is consistent with the hypothesis that intracortical myelination may stabilize intracortical circuits and inhibit synaptic plasticity. Finally, we discuss the future of the in vivo myeloarchitectural field and cortical parcellation--"in vivo Brodmann mapping"--in general.

What can we learn from T2* maps of the cortex?

Studies have shown that T2* contrast can reveal features of cortical anatomy. However, understanding the relationship between T2* contrast and the underlying cyto- and myelo-architecture is not an easy task, given the number of confounds, such as myelin, iron, blood vessels and structure orientation. Moreover, it is difficult to obtain reliable T2* measurements in the cortex due to its thin and folded geometry and the presence of artifacts. This review addresses issues associated with T2* mapping in the human cortex. After describing the theory behind T2* relaxation, a list of practical steps is proposed to reliably acquire and process T2* data and then map these values within the cortex using surface-based analysis. The last section addresses the question: "What can we gain from T2* cortical mapping?", with particular emphasis on Brodmann mapping.

In vivo functional and myeloarchitectonic mapping of human primary auditory areas

In contrast to vision, where retinotopic mapping alone can define areal borders, primary auditory areas such as A1 are best delineated by combining in vivo tonotopic mapping with postmortem cyto- or myeloarchitectonics from the same individual. We combined high-resolution (800 μm) quantitative T(1) mapping with phase-encoded tonotopic methods to map primary auditory areas (A1 and R) within the "auditory core" of human volunteers. We first quantitatively characterize the highly myelinated auditory core in terms of shape, area, cortical depth profile, and position, with our data showing considerable correspondence to postmortem myeloarchitectonic studies, both in cross-participant averages and in individuals. The core region contains two "mirror-image" tonotopic maps oriented along the same axis as observed in macaque and owl monkey. We suggest that these two maps within the core are the human analogs of primate auditory areas A1 and R. The core occupies a much smaller portion of tonotopically organized cortex on the superior temporal plane and gyrus than is generally supposed. The multimodal approach to defining the auditory core will facilitate investigations of structure-function relationships, comparative neuroanatomical studies, and promises new biomarkers for diagnosis and clinical studies.

Layer-specific diffusion weighted imaging in human primary visual cortex in vitro

One of the most prominent characteristics of the human neocortex is its laminated structure. The first person to observe this was Francesco Gennari in the second half the 18th century: in the middle of the depth of primary visual cortex, myelinated fibres are so abundant that he could observe them with bare eyes as a white line. Because of its saliency, the stria of Gennari has a rich history in cyto- and myeloarchitectural research as well as in magnetic resonance (MR) microscopy. In the present paper we show for the first time the layered structure of the human neocortex with ex vivo diffusion weighted imaging (DWI). To achieve the necessary spatial and angular resolution, primary visual cortex samples were scanned on an 11.7 T small-animal MR system to characterize the diffusion properties of the cortical laminae and the stria of Gennari in particular. The results demonstrated that fractional anisotropy varied over cortical depth, showing reduced anisotropy in the stria of Gennari, the inner band of Baillarger and the deepest layer of the cortex. Orientation density functions showed multiple components in the stria of Gennari and deeper layers of the cortex. Potential applications of layer-specific diffusion imaging include characterization of clinical abnormalities, cortical mapping and (intra)cortical tractography. We conclude that future high-resolution in vivo cortical DWI investigations should take into account the layer-specificity of the diffusion properties.

Layer-specific intracortical connectivity revealed with diffusion MRI

In this work, we show for the first time that the tangential diffusion component is orientationally coherent at the human cortical surface. Using diffusion magnetic resonance imaging (dMRI), we have succeeded in tracking intracortical fiber pathways running tangentially within the cortex. In contrast with histological methods, which reveal little regarding 3-dimensional organization in the human brain, dMRI delivers additional understanding of the layer dependence of the fiber orientation. A postmortem brain block was measured at very high angular and spatial resolution. The dMRI data had adequate resolution to allow analysis of the fiber orientation within 4 notional cortical laminae. We distinguished a lamina at the cortical surface where diffusion was tangential along the surface, a lamina below the surface where diffusion was mainly radial, an internal lamina covering the Stria of Gennari, where both strong radial and tangential diffusion could be observed, and a deep lamina near the white matter, which also showed mainly radial diffusion with a few tangential compartments. The measurement of the organization of the tangential diffusion component revealed a strong orientational coherence at the cortical surface.

The retinotopic organization of striate cortex is well predicted by surface topology

In 1918, Gordon Holmes combined observations of visual-field scotomas across brain-lesioned soldiers to produce a schematic map of the projection of the visual field upon the striate cortex. One limit to the precision of his result, and the mapping of anatomy to retinotopy generally, is the substantial individual variation in the size, volumetric position, and cortical magnification of area V1. When viewed within the context of the curvature of the cortical surface, however, the boundaries of striate cortex fall at a consistent location across individuals. We asked whether the surface topology of the human brain can be used to accurately predict the internal, retinotopic function of striate cortex as well. We used fMRI to measure polar angle and eccentricity in 25 participants and combined their maps within a left-right, transform-symmetric representation of the cortical surface. These data were then fit using a deterministic, algebraic model of visual-field representation. We found that an anatomical image alone can be used to predict the retinotopic organization of striate cortex for an individual with accuracy equivalent to 10-25 min of functional mapping. This indicates tight developmental linkage of structure and function within a primary, sensory cortical area.

T₂* mapping and B₀ orientation-dependence at 7 T reveal cyto- and myeloarchitecture organization of the human cortex

Ultra-high field MRI (≥ 7 T) has recently shown great sensitivity to depict patterns of tissue microarchitecture. Moreover, recent studies have demonstrated a dependency between T₂* and orientation of white matter fibers with respect to the main magnetic field B₀. In this study we probed the potential of T₂* mapping at 7 T to provide new markers of cortical architecture. We acquired multi-echo measurements at 7 T and mapped T₂* over the entire cortex of eight healthy individuals using surface-based analysis. B₀ dependence was tested by computing the angle θ(z) between the normal of the surface and the direction of B₀, then fitting T₂*(θ(z)) using model from the literature. Average T₂* in the cortex was 32.20 +/- 1.35 ms. Patterns of lower T₂* were detected in the sensorimotor, visual and auditory cortices, likely reflecting higher myelin content. Significantly lower T₂* was detected in the left hemisphere of the auditory region (p<0.005), suggesting higher myelin content, in accordance with previous investigations. B₀ orientation dependence was detected in some areas of the cortex, the strongest being in the primary motor cortex (∆R₂*=4.10 Hz). This study demonstrates that quantitative T₂* measures at 7 T MRI can reveal patterns of cytoarchitectural organization of the human cortex in vivo and that B₀ orientation dependence can probe the coherency and orientation of gray matter fibers in the cortex, shedding light into the potential use of this type of contrast to characterize cyto-/myeloarchitecture and to understand the pathophysiology of diseases associated with changes in iron and/or myelin concentration.

Identification of cortical lamination in awake monkeys by high resolution magnetic resonance imaging

Brodmann divided the neocortex into 47 different cortical areas based on histological differences in laminar myeloarchitectonic and cytoarchitectonic defined structure. The ability to do so in vivo with anatomical magnetic resonance (MR) methods in awake subjects would be extremely advantageous for many functional studies. However, due to the limitations of spatial resolution and contrast, this has been difficult to achieve in awake subjects. Here, we report that by using a combination of MR microscopy and novel contrast effects, cortical layers can be delineated in the visual cortex of awake subjects (nonhuman primates) at 4.7 T. We obtained data from 30-min acquisitions at voxel size of 62.5 × 62.5 × 1000 μm(3) (4 nl). Both the phase and magnitude components of the T(2)*-weighted image were used to generate laminar profiles which are believed to reflect variations in myelin and local cell density content across cortical depth. Based on this, we were able to identify six layers characteristic of the striate cortex (V1). These were the stripe of Kaes-Bechterew (in layer II/III), the stripe of Gennari (in layer IV), the inner band of Baillarger (in layer V), as well as three sub-layers within layer IV (IVa, IVb, and IVc). Furthermore, we found that the laminar structure of two extrastriate visual cortex (V2, V4) can also be detected. Following the tradition of Brodmann, this significant improvement in cortical laminar visualization should make it possible to discriminate cortical regions in awake subjects corresponding to differences in myeloarchitecture and cytoarchitecture.

Critical comments on dynamic causal modelling

Dynamic causal modelling (DCM) (Friston et al., 2003) is a technique designed to investigate the influence between brain areas using time series data obtained by EEG/MEG or functional magnetic resonance imaging (fMRI). The basic idea is to fit various models to time series data, and select one of those models using Bayesian model comparison. Here, we present a critical evaluation of DCM in which we show that DCM can be challenged on several grounds. We will discuss three main points relating to combinatorial explosion, the validity of the model selection procedure, and problems with respect to model validation.