Layer-specific variation of iron content in cerebral cortex as a source of MRI contrast

Improved susceptibility weighted imaging method using multi-echo acquisition

PURPOSE

To introduce novel acquisition and postprocessing approaches for susceptibility weighted imaging (SWI) to remove background field inhomogeneity artifacts in both magnitude and phase data.

METHODS

The proposed method acquires three echoes in a three-dimensional gradient echo (GRE) sequence, with a field compensation gradient (z-shim gradient) applied to the third echo. The artifacts in the magnitude data are compensated by signal estimation from all three echoes. The artifacts in phase signals are removed by modeling the background phase distortions using Gaussians. The method was applied in vivo and compared with conventional SWI.

RESULTS

The method successfully compensates for background field inhomogeneity artifacts in magnitude and phase images, and demonstrated improved SWI images. In particular, vessels in frontal lobe, which were not observed in conventional SWI, were identified in the proposed method.

CONCLUSION

The new method improves image quality in SWI by restoring signal in the frontal and temporal regions.

Comparison of histological techniques to visualize iron in paraffin-embedded brain tissue of patients with Alzheimer's disease

Better knowledge of the distribution of iron in the brains of Alzheimer's disease (AD) patients may facilitate the development of an in vivo magnetic resonance (MR) marker for AD and may cast light on the role of this potentially toxic molecule in the pathogenesis of AD. Several histological iron staining techniques have been used in the past but they have not been systematically tested for sensitivity and specificity. This article compares three histochemical techniques and ferritin immunohistochemistry to visualize iron in paraffin-embedded human AD brain tissue. The specificity of the histochemical techniques was tested by staining sections after iron extraction. Iron was demonstrated in the white matter, in layers IV/V of the frontal neocortex, in iron containing plaques, and in microglia. In our hands, these structures were best visualized using the Meguro iron stain, a method that has not been described for iron staining in human brain or AD in particular. Ferritin immunohistochemistry stained microglia and iron containing plaques similar to the Meguro method but was less intense in myelin-associated iron. The Meguro method is most suitable for identifying iron-positive structures in paraffin-embedded human AD brain tissue.

Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures

The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a "deep gray matter parcellation map" (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established "white matter parcellation map" (WMPM) from the same subject's T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the "Everything Parcellation Map in Eve Space," also known as the "EvePM." It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting "almost perfect" agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron concentrations in gray matter structures measured by Hallgren and Sourander (1958) allowed interpolation of the average iron concentration of several deep gray matter regions delineated in the EvePM.

MRI parcellation of ex vivo medial temporal lobe

Recent advancements in radio frequency coils, field strength and sophisticated pulse sequences have propelled modern brain mapping and have made validation to biological standards - histology and pathology - possible. The medial temporal lobe has long been established as a pivotal brain region for connectivity, function and unique structure in the human brain, and reveals disconnection in mild Alzheimer's disease. Specific brain mapping of mesocortical areas affected with neurofibrillary tangle pathology early in disease progression provides not only an accurate description for location of these areas but also supplies spherical coordinates that allow comparison between other ex vivo cases and larger in vivo datasets. We have identified several cytoarchitectonic features in the medial temporal lobe with high resolution ex vivo MRI, including gray matter structures such as the entorhinal layer II 'islands', perirhinal layer II-III columns, presubicular 'clouds', granule cell layer of the dentate gyrus as well as lamina of the hippocampus. Localization of Brodmann areas 28 and 35 (entorhinal and perirhinal, respectively) demonstrates MRI based area boundaries validated with multiple methods and histological stains. Based on our findings, both myelin and Nissl staining relate to contrast in ex vivo MRI. Precise brain mapping serves to create modern atlases for cortical areas, allowing accurate localization with important applications to detecting early disease processes.

Measuring iron in the brain using quantitative susceptibility mapping and X-ray fluorescence imaging

Measuring iron content in the brain has important implications for a number of neurodegenerative diseases. Quantitative susceptibility mapping (QSM), derived from magnetic resonance images, has been used to measure total iron content in vivo and in post mortem brain. In this paper, we show how magnetic susceptibility from QSM correlates with total iron content measured by X-ray fluorescence (XRF) imaging and by inductively coupled plasma mass spectrometry (ICPMS). The relationship between susceptibility and ferritin iron was estimated at 1.10±0.08 ppb susceptibility per μg iron/g wet tissue, similar to that of iron in fixed (frozen/thawed) cadaveric brain and previously published data from unfixed brains. We conclude that magnetic susceptibility can provide a direct and reliable quantitative measurement of iron content and that it can be used clinically at least in regions with high iron content.

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.

Brain iron MRI: a biomarker for amyotrophic lateral sclerosis

PURPOSE

To evaluate the usefulness of MRI detection of hypointensity areas (iron deposits) in the brain using a dedicated MRI technique in patients with ALS in establishing this sign as a potential surrogate biomarker that correlates with the severity of disease.

MATERIALS AND METHODS

Forty-six ALS patients and 26 age-matched controls were examined by MRI. The ALS Functional Rating Scale (ALSFRS) score was determined before the first MRI examination. The sub-set of 25 ALS patients was re-examined around 6 months after the first MRI examination. The MRI examination consisted of routine T1W, T2W, and FLAIR sequences with the addition of a thin slice heavily T2* weighted sequence to accentuate magnetic susceptibility artifacts.

RESULTS

T2*W sequence is superior to any other MRI sequence in detecting hypointensities in the brain of ALS patients. Hypointensities were found only in the precentral gyruses gray matter (PGGM) and were detected in 42 patients. The extent of hypointensities was measured and scored (0-3) and correlated with ALSFRS (r = -0.545). Twenty-five patients were re-examined 6 months later, and the majority of them showed the shift toward higher MRI scores. No control subjects had hypointensities in PGGM.

CONCLUSION

The detection of hypointensities in PGGM appears to be a very promising surrogate MRI biomarker for ALS due to its simplicity, high sensitivity and specificity, suitability for longitudinal studies, and relationship with the pathogenesis of the disease.

MR susceptibility imaging

This work reviews recent developments in the use of magnetic susceptibility contrast for human MRI, with a focus on the study of brain anatomy. The increase in susceptibility contrast with modern high field scanners has led to novel applications and insights into the sources and mechanism contributing to this contrast in brain tissues. Dedicated experiments have demonstrated that in most of healthy brain, iron and myelin dominate tissue susceptibility variations, although their relative contribution varies substantially. Local variations in these compounds can affect both amplitude and frequency of the MRI signal. In white matter, the myelin sheath introduces an anisotropic susceptibility that has distinct effects on the water compartments inside the axons, between the myelin sheath, and the axonal space, and renders their signals dependent on the angle between the axon and the magnetic field. This offers opportunities to derive tissue properties specific to these cellular compartments.

Cortical depth dependent functional responses in humans at 7T: improved specificity with 3D GRASE

Ultra high fields (7T and above) allow functional imaging with high contrast-to-noise ratios and improved spatial resolution. This, along with improved hardware and imaging techniques, allow investigating columnar and laminar functional responses. Using gradient-echo (GE) (T2* weighted) based sequences, layer specific responses have been recorded from human (and animal) primary visual areas. However, their increased sensitivity to large surface veins potentially clouds detecting and interpreting layer specific responses. Conversely, spin-echo (SE) (T2 weighted) sequences are less sensitive to large veins and have been used to map cortical columns in humans. T2 weighted 3D GRASE with inner volume selection provides high isotropic resolution over extended volumes, overcoming some of the many technical limitations of conventional 2D SE-EPI, whereby making layer specific investigations feasible. Further, the demonstration of columnar level specificity with 3D GRASE, despite contributions from both stimulated echoes and conventional T2 contrast, has made it an attractive alternative over 2D SE-EPI. Here, we assess the spatial specificity of cortical depth dependent 3D GRASE functional responses in human V1 and hMT by comparing it to GE responses. In doing so we demonstrate that 3D GRASE is less sensitive to contributions from large veins in superficial layers, while showing increased specificity (functional tuning) throughout the cortex compared to GE.

Origin of B0 orientation dependent R2(*) (=1/T2(*)) in white matter

Recent MRI studies have demonstrated that the relative orientation of white matter fibers to the B0 field significantly affects R2(*) measurement. In this work, the origin of this effect was investigated by measuring R2 and R2(*) in multiple orientations and fitting the results to magnetic susceptibility-based models and magic angle-based models. To further explore the source of magnetic susceptibility effect, the contribution of tissue iron to the orientation dependent R2(*) contrast was investigated. Additionally, the effects of temperature on R2(*) and orientation dependent R2(*) contrasts were studied to understand the differences reported between a fixed specimen at room temperature and in vivo at body temperature. The results suggest that the B0 dependent R2(*) variation is better explained by the magnetic susceptibility-based model with susceptibility anisotropy. However, extracting tissue iron did not reduce the orientation dependent R2(*) contrast, suggesting iron is not the origin of the contrast. This leaves susceptibility effects from myelin as the most probable origin of the contrast. Temperature showed large contribution on both R2(*) and orientation dependent R2(*) contrasts, explaining a portion of the contrast difference between the in-vivo and in-vitro conditions.

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.

Imaging of iron

Magnetic resonance imaging (MRI) enables a noninvasive in vivo quantification of iron in various organs. Several techniques have been developed that detect signal alterations derived mainly from the magnetic properties of ferritin and hemosiderin, the major iron storage compounds. High magnetic susceptibility of ferritin shortens the transversal relaxation time of nearby water protons and thus induces a focal signal extinction of iron-rich areas in T2-weighted (T2w) MRI. T2w tissue contrast is additionally influenced by other factors such as water content, myelin density, and the presence of other metals. Therefore, more specific methods are needed with higher specificity to iron. These in vivo techniques can be divided into three groups: relaxometry, magnetic field correlation imaging and phase-based contrast covering susceptibility-weighted imaging, and quantitative susceptibility mapping. The differential diagnosis of various neurological disorders is aided by characteristic patterns of iron depositions. Reliable estimates of cerebral tissue iron concentration are equally important in studying physiological age-related as well as pathological conditions in neurodegenerative, neuroinflammatory, and vascular diseases. In the future, monitoring changes in iron storage and content may serve as sensitive biomarker for diagnosis as well as treatment monitoring.

Age-related differences in iron content of subcortical nuclei observed in vivo: a meta-analysis

Accumulation of non-heme iron in the brain has been proposed as a biomarker of the progressive neuroanatomical and cognitive declines in healthy adult aging. Postmortem studies indicate that iron content and lifespan differences therein are regionally specific, with a predilection for the basal ganglia. However, the reported in vivo estimates of adult age differences in iron content within subcortical nuclei are highly variable. We present a meta-analysis of 20 in vivo magnetic resonance imaging (MRI) studies that estimated iron content in the caudate nucleus, globus pallidus, putamen, red nucleus, and substantia nigra. The results of the analyses support a robust association between advanced age and high iron content in the substantia nigra and striatum, with a smaller effect noted in the globus pallidus. The magnitude of age differences in estimated iron content of the caudate nucleus and putamen partially depended on the method of estimation, but not on the type of design (continuous age vs. extreme age groups).

Bilateral pre- and postcentral gyrus volume positively correlates with T2-SNR of putamen in healthy adults

INTRODUCTION

The aim of the present study was to investigate the correlation between local gray matter volume and signal-to-noise ratio on T2-weighted imaging (T2-SNR) of putamen in healthy adults using two tools: voxel-based morphometry (VBM) treating age as a confounding covariate to control for age-related gray matter volume changes and high spatial resolution T1-weighted imaging acquired with a 3.0-T magnetic resonance (3T-MR) scanner.

METHODS

Contiguous sagittal T1-weighted images and axial T2-weighted images of the brain were obtained from 1,380 healthy participants. T2-SNR of putamen was defined as A/B, where A is the mean T2-weighted signal intensity (T2-SI) in the right and left sides of putamen, and B is the background noise. The software Statistical Parametric Mapping 5 was used for image segmentation. The association between T2-SNR of putamen and gray matter volume was assessed with VBM, treating age as a confounding covariate.

RESULTS

A significant positive correlation was obtained between T2-SNR of putamen and bilateral pre- and postcentral gyrus volume.

CONCLUSION

To the best of our knowledge, this is the first VBM study to show an age-independent relationship between T2-SNR of putamen and bilateral pre- and postcentral gyrus volumes in healthy adults.

Detecting microstructural properties of white matter based on compartmentalization of magnetic susceptibility

The microscopic structure of neuronal tissue is crucial to brain function, with axon diameter, axonal density and myelination directly influencing signal conduction in the white matter. There is increasing evidence that these microstructural properties alter signal in magnetic resonance imaging (MRI) driven by magnetic susceptibility of different compartments (e.g., myelin sheaths and iron-laden cells). To explain these observations, we have developed a multi-compartmental geometric model of whitematter microstructure. Using a single set of literature parameters, this forward model predicts experimentally observed orientation dependence and temporal evolution of the MRI signal. Where previous models have aimed to explain only the orientation dependence of signal phase, the proposed approach encapsulates the full repertoire of signal behavior. The frequency distribution underlying signal behavior is predicted to be a rich source of microstructural information with relevance to neuronal pathology.

NMR imaging of cell phone radiation absorption in brain tissue

A method is described for measuring absorbed electromagnetic energy radiated from cell phone antennae into ex vivo brain tissue. NMR images the 3D thermal dynamics inside ex vivo bovine brain tissue and equivalent gel under exposure to power and irradiation time-varying radio frequency (RF) fields. The absorbed RF energy in brain tissue converts into Joule heat and affects the nuclear magnetic shielding and the Larmor precession. The resultant temperature increase is measured by the resonance frequency shift of hydrogen protons in brain tissue. This proposed application of NMR thermometry offers sufficient spatial and temporal resolution to characterize the hot spots from absorbed cell phone radiation in aqueous media and biological tissues. Specific absorption rate measurements averaged over 1 mg and 10 s in the brain tissue cover the total absorption volume. Reference measurements with fiber optic temperature sensors confirm the accuracy of the NMR thermometry.

Development and application of STEM for the biological sciences

The design of the scanning transmission electron microscope (STEM), as conceived originally by Crewe and coworkers, enables the highly efficient and flexible collection of different elastic and inelastic signals resulting from the interaction of a focused probe of incident electrons with a specimen. In the present paper we provide a brief review for how the STEM today can be applied towards a range of different problems in the biological sciences, emphasizing four main areas of application. (1) For three decades, the most widely used STEM technique has been the mass determination of proteins and other macromolecular assemblies. Such measurements can be performed at low electron dose by collecting the high-angle dark-field signal using an annular detector. STEM mass mapping has proven valuable for characterizing large protein assemblies such as filamentous proteins with a well-defined mass per length. (2) The annular dark-field signal can also be used to image ultrasmall, functionalized nanoparticles of heavy atoms for labeling specific amino-acid sequences in protein assemblies. (3) By acquiring electron energy loss spectra (EELS) at each pixel in a hyperspectral image, it is possible to map the distributions of specific bound elements like phosphorus, calcium and iron in isolated macromolecular assemblies or in compartments within sectioned cells. Near single atom sensitivity is feasible provided that the specimen can tolerate a very high incident electron dose. (4) Electron tomography is a new application of STEM that enables three-dimensional reconstruction of micrometer-thick sections of cells. In this technique a probe of small convergence angle gives a large depth of field throughout the thickness of the specimen while maintaining a probe diameter of <2 nm; and the use of an on-axis bright-field detector reduces the effects of beam broadening and thus improves the spatial resolution compared to that attainable by STEM dark-field tomography.

Toward in vivo histology: a comparison of quantitative susceptibility mapping (QSM) with magnitude-, phase-, and R2*-imaging at ultra-high magnetic field strength

Quantitative magnetic susceptibility mapping (QSM) has recently been introduced to provide a novel quantitative and local MRI contrast. However, the anatomical contrast represented by in vivo susceptibility maps has not yet been compared systematically and comprehensively with gradient (recalled) echo (GRE) magnitude, frequency, and R(2)(*) images. Therefore, this study compares high-resolution quantitative susceptibility maps with conventional GRE imaging approaches (magnitude, frequency, R(2)(*)) in healthy individuals at 7 T with respect to anatomic tissue contrast. Volumes-of-interest were analyzed in deep and cortical gray matter (GM) as well as in white matter (WM) on R(2)(*) and susceptibility maps. High-resolution magnetic susceptibility maps of the human brain exhibited superb contrast that allowed the identification of substructures of the thalamus, midbrain and basal ganglia, as well as of the cerebral cortex. These were consistent with histology but not generally visible on magnitude, frequency or R(2)(*)-maps. Common target structures for deep brain stimulation, including substantia nigra pars reticulata, ventral intermediate nucleus, subthalamic nucleus, and the substructure of the internal globus pallidus, were clearly distinguishable from surrounding tissue on magnetic susceptibility maps. The laminar substructure of the cortical GM differed depending on the anatomical region, i.e., a cortical layer with increased magnetic susceptibility, corresponding to the Stria of Gennari, was found in the GM of the primary visual cortex, V1, whereas a layer with reduced magnetic susceptibility was observed in the GM of the temporal cortex. Both magnetic susceptibility and R(2)(*) values differed substantially in cortical GM depending on the anatomic regions. Regression analysis between magnetic susceptibility and R(2)(*) values of WM and GM structures suggested that variations in myelin content cause the overall contrast between gray and white matter on susceptibility maps and that both R(2)(*) and susceptibility values provide linear measures for iron content in GM. In conclusion, quantitative magnetic susceptibility mapping provides a non-invasive and spatially specific contrast that opens the door to the assessment of diseases characterized by variation in iron and/or myelin concentrations. Its ability to reflect anatomy of deep GM structures with superb delineation may be useful for neurosurgical applications.

Predicting the location of human perirhinal cortex, Brodmann's area 35, from MRI

The perirhinal cortex (Brodmann's area 35) is a multimodal area that is important for normal memory function. Specifically, perirhinal cortex is involved in the detection of novel objects and manifests neurofibrillary tangles in Alzheimer's disease very early in disease progression. We scanned ex vivo brain hemispheres at standard resolution (1 mm × 1 mm × 1 mm) to construct pial/white matter surfaces in FreeSurfer and scanned again at high resolution (120 μm × 120 μm × 120 μm) to determine cortical architectural boundaries. After labeling perirhinal area 35 in the high resolution images, we mapped the high resolution labels to the surface models to localize area 35 in fourteen cases. We validated the area boundaries determined using histological Nissl staining. To test the accuracy of the probabilistic mapping, we measured the Hausdorff distance between the predicted and true labels and found that the median Hausdorff distance was 4.0mm for the left hemispheres (n=7) and 3.2mm for the right hemispheres (n=7) across subjects. To show the utility of perirhinal localization, we mapped our labels to a subset of the Alzheimer's Disease Neuroimaging Initiative dataset and found decreased cortical thickness measures in mild cognitive impairment and Alzheimer's disease compared to controls in the predicted perirhinal area 35. Our ex vivo probabilistic mapping of the perirhinal cortex provides histologically validated, automated and accurate labeling of architectonic regions in the medial temporal lobe, and facilitates the analysis of atrophic changes in a large dataset for earlier detection and diagnosis.

Biophysical mechanisms of MRI signal frequency contrast in multiple sclerosis

Phase images obtained with gradient echo MRI provide image contrast distinct from T1- and T2-weighted images. It is commonly assumed that the local contribution to MRI signal phase directly relates to local bulk tissue magnetic susceptibility. Here, we use Maxwell's equations and Monte Carlo simulations to provide theoretical background to the hypothesis that the local contribution to MRI signal phase does not depend on tissue bulk magnetic susceptibility but tissue magnetic architecture--distribution of magnetic susceptibility inclusions (lipids, proteins, iron, etc.) at the cellular and subcellular levels. Specifically, we show that the regular longitudinal structures forming cylindrical axons (myelin sheaths and neurofilaments) can be locally invisible in phase images. Contrary to an expectation that the phase contrast in multiple sclerosis lesions should always increase in degree along with worsening of lesion severity (which happens for all known MR magnitude-based contrast mechanisms), we show that phase contrast can actually disappear with extreme tissue destruction. We also show that the phase contrast in multiple sclerosis lesions could be altered without loss of nervous system tissue, which happens in mild injury to the myelin sheaths or axonal neurofilaments. Moreover, we predict that the sign of phase contrast in multiple sclerosis lesions indicates the predominant type of tissue injury-myelin damage (positive sign) vs. axonal neurofilament damage (negative sign). Therefore, our theoretical and experimental results shed light on understanding the relationship between gradient echo MRI signal phase and multiple sclerosis pathology.

Imaging of stroke: a comparison between X-ray fluorescence and magnetic resonance imaging methods

A dual imaging approach, combining magnetic resonance imaging to localize lesions and synchrotron rapid scanning X-ray fluorescence (XRF) mapping to localize and quantify calcium, iron and zinc was used to examine one case of recent stroke with hemorrhage and two cases of ischemia 3 and 7 years before death with the latter showing superficial necrosis. In hemorrhagic lesions, more Fe is found accompanied with less Zn. In chronic ischemic lesions, Fe, Zn and Ca are lower indicating that these elements are removed as the normal tissue dies and scar tissue forms. Both susceptibility and T2* maps were calculated to visualize iron in hemorrhages and validated by XRF Ca and Fe maps. The former was superior for imaging iron in hemorrhagic transformation and necrosis but did not capture ischemic lesions. In contrast, T2* could not differentiate Ca from Fe in necrotic tissue but did capture ischemic lesions, complementing the susceptibility mapping. The spatial localization, accurate quantitative data and elemental differentiation shown here could also be valuable for imaging other brain tissue damage with abnormal Ca and Fe content.

Structure-guided directed evolution of highly selective p450-based magnetic resonance imaging sensors for dopamine and serotonin

New tools that allow dynamic visualization of molecular neural events are important for studying the basis of brain activity and disease. Sensors that permit ligand-sensitive magnetic resonance imaging (MRI) are useful reagents due to the noninvasive nature and good temporal and spatial resolution of MR methods. Paramagnetic metalloproteins can be effective MRI sensors due to the selectivity imparted by the protein active site and the ability to tune protein properties using techniques such as directed evolution. Here, we show that structure-guided directed evolution of the active site of the cytochrome P450-BM3 heme domain produces highly selective MRI probes with submicromolar affinities for small molecules. We report a new, high-affinity dopamine sensor as well as the first MRI reporter for serotonin, with which we demonstrate quantification of neurotransmitter release in vitro. We also present a detailed structural analysis of evolved cytochrome P450-BM3 heme domain lineages to systematically dissect the molecular basis of neurotransmitter binding affinity, selectivity, and enhanced MRI contrast activity in these engineered proteins.

Generalized multiple-layer appearance of the cerebral cortex with 3D FLAIR 7.0-T MR imaging

To examine the multiple-layer appearance of the cerebral cortex with fluid-attenuated inversion recovery (FLAIR) magnetic resonance (MR) imaging at 7.0 T, whole-brain volumetric three-dimensional (3D) magnetization prepared FLAIR images were acquired in 12 volunteers (0.8 3 0.8 3 0.8-mm spatial resolution). Signal intensity profiles were evaluated for the anterior frontal (Brodmann area [BA] 10), posterior frontal (BA 6), parietal (BA 7), precentral (BA 4), postcentral (BA 3), occipital (BA 18), and calcarine (BA 17) regions. Variance of the normalized profile was used as the metric for the multiple-layer appearance. Wilcoxon signed-rank tests were performed to compare variances of the profiles between all areas. All cortical areas showed multiple-layered appearances, with a prominent hyperintense band at the external surface of the cortex, a hypointense band deeper in the cortex, and a hyperintense third band. The ranking from least- to most-pronounced layer appearance was as follows: postcentral (variance, 0.04), posterior frontal (variance, 0.05), calcarine (variance, 0.05), precentral (variance, 0.06), parietal (variance, 0.08), anterior frontal (variance, 0.10), and occipital (variance, 0.11). Each region was significantly different from at least one other region. In conclusion, a multiple-layer appearance of the cerebral cortex was found for all cortical regions with high-spatial-resolution 3D FLAIR MR imaging at 7.0 T.

High-field imaging of neurodegenerative diseases

High-field magnetic resonance (MR) imaging is showing potential for imaging of neurodegenerative diseases. 7 T MR imaging is beginning to be used in a clinical research setting and the theoretical benefits of higher signal-to-noise ratio, sensitivity to iron, improved MR angiography, and increased spectral resolution in spectroscopy are being confirmed. Despite the limited number of studies to date, initial results in patients with multiple sclerosis, Alzheimer disease, and Huntington disease show promising additional features in contrast that may help the diagnosis of these disorders.

Tracking iron in multiple sclerosis: a combined imaging and histopathological study at 7 Tesla

Previous authors have shown that the transverse relaxivity R(2)* and frequency shifts that characterize gradient echo signal decay in magnetic resonance imaging are closely associated with the distribution of iron and myelin in the brain's white matter. In multiple sclerosis, iron accumulation in brain tissue may reflect a multiplicity of pathological processes. Hence, iron may have the unique potential to serve as an in vivo magnetic resonance imaging tracer of disease pathology. To investigate the ability of iron in tracking multiple sclerosis-induced pathology by magnetic resonance imaging, we performed qualitative histopathological analysis of white matter lesions and normal-appearing white matter regions with variable appearance on gradient echo magnetic resonance imaging at 7 Tesla. The samples used for this study derive from two patients with multiple sclerosis and one non-multiple sclerosis donor. Magnetic resonance images were acquired using a whole body 7 Tesla magnetic resonance imaging scanner equipped with a 24-channel receive-only array designed for tissue imaging. A 3D multi-gradient echo sequence was obtained and quantitative R(2)* and phase maps were reconstructed. Immunohistochemical stainings for myelin and oligodendrocytes, microglia and macrophages, ferritin and ferritin light polypeptide were performed on 3- to 5-µm thick paraffin sections. Iron was detected with Perl's staining and 3,3'-diaminobenzidine-tetrahydrochloride enhanced Turnbull blue staining. In multiple sclerosis tissue, iron presence invariably matched with an increase in R(2)*. Conversely, R(2)* increase was not always associated with the presence of iron on histochemical staining. We interpret this finding as the effect of embedding, sectioning and staining procedures. These processes likely affected the histopathological analysis results but not the magnetic resonance imaging that was obtained before tissue manipulations. Several cellular sources of iron were identified. These sources included oligodendrocytes in normal-appearing white matter and activated macrophages/microglia at the edges of white matter lesions. Additionally, in white matter lesions, iron precipitation in aggregates typical of microbleeds was shown by the Perl's staining. Our combined imaging and pathological study shows that multi-gradient echo magnetic resonance imaging is a sensitive technique for the identification of iron in the brain tissue of patients with multiple sclerosis. However, magnetic resonance imaging-identified iron does not necessarily reflect pathology and may also be seen in apparently normal tissue. Iron identification by multi-gradient echo magnetic resonance imaging in diseased tissues can shed light on the pathological processes when coupled with topographical information and patient disease history.

Gradient echo plural contrast imaging--signal model and derived contrasts: T2*, T1, phase, SWI, T1f, FST2*and T2*-SWI

Gradient Echo Plural Contrast Imaging (GEPCI) is a post processing technique that, based on a widely available multiple gradient echo sequence, allows simultaneous generation of naturally co-registered images with various contrasts: T1 weighted, R2*=1/T2* maps and frequency (f) maps. Herein, we present results demonstrating the capability of GEPCI technique to generate image sets with additional contrast characteristics obtained by combing the information from these three basic contrast maps. Specifically, we report its ability to generate GEPCI-susceptibility weighted images (GEPCI-SWI) with improved SWI contrast that is free of T1 weighting and RF inhomogeneities; GEPCI-SWI-like images with the contrast similar to original SWI; T1f images that offer superior GM/WM matter contrast obtained by combining the GEPCI T1 and frequency map data; Fluid Suppressed T2* (FST2*) images that utilize GEPCI T1 data to suppress CSF signal in T2* maps and provide contrast similar to FLAIR T2 weighted images; and T2*-SWI images that combine SWI contrast with quantitative T2* map and offer advantages of visualizing venous structure with hyperintense T2* lesions (e.g. MS lesions). To analyze GEPCI images we use an improved algorithm for combining data from multi-channel RF coils and a method for unwrapping phase/frequency maps that takes advantage of the information on phase evolution as a function of gradient echo time in GEPCI echo train.

High field magnetic resonance microscopy of the human hippocampus in Alzheimer's disease: quantitative imaging and correlation with iron

We report R(2) and R(2) in human hippocampus from five unfixed post-mortem Alzheimer's disease (AD) and three age-matched control cases. Formalin-fixed tissues from opposing hemispheres in a matched AD and control were included for comparison. Imaging was performed in a 600MHz (14T) vertical bore magnet at MR microscopy resolution to obtain R(2) and R(2) (62 μm×62 μm in-plane, 80 μm slice thickness), and R(1) at 250 μm isotropic resolution. R(1), R(2) and R(2) maps were computed for individual slices in each case, and used to compare subfields between AD and controls. The magnitudes of R(2) and R(2) changed very little between AD and control, but their variances in the Cornu Ammonis and dentate gyrus were significantly higher in AD compared for controls (p<0.001). To investigate the relationship between tissue iron and MRI parameters, each tissue block was cryosectioned at 30 μm in the imaging plane, and iron distribution was mapped using synchrotron microfocus X-ray fluorescence spectroscopy. A positive correlation of R(2) and R(2)* with iron was demonstrated. While studies with fixed tissues are more straightforward to conduct, fixation can alter iron status in tissues, making measurement of unfixed tissue relevant. To our knowledge, these data represent an advance in quantitative imaging of hippocampal subfields in unfixed tissue, and the methods facilitate direct analysis of the relationship between MRI parameters and iron. The significantly increased variance in AD compared for controls warrants investigation at lower fields and in-vivo, to determine if this parameter is clinically relevant.

Susceptibility induced gray-white matter MRI contrast in the human brain

MR phase images have shown significantly improved contrast between cortical gray and white matter regions compared to magnitude images obtained with gradient echo sequences. A variety of underlying biophysical mechanisms (including iron, blood, myelin content, macromolecular chemical exchange, and fiber orientation) have been suggested to account for this observation but assessing the individual contribution of these factors is limited in vivo. For a closer investigation of iron and myelin induced susceptibility changes, postmortem MRI of six human corpses (age range at death: 56-80 years) was acquired in situ. Following autopsy, the iron concentrations in the frontal and occipital cortex as well as in white matter regions were chemically determined. The magnetization transfer ratio (MTR) was used as an indirect measure for myelin content. Susceptibility effects were assessed separately by determining R2* relaxation rates and quantitative phase shifts. Contributions of myelin and iron to local variations of the susceptibility were assessed by univariate and multivariate linear regression analysis. Mean iron concentration was lower in the frontal cortex than in frontal white matter (26 ± 6 vs. 45 ± 6 mg/kg wet tissue) while an inverse relation was found in the occipital lobe (cortical gray matter: 41 ± 10 vs. white matter: 34 ± 10mg/kg wet tissue). Multiple regression analysis revealed iron and MTR as independent predictors of the effective transverse relaxation rate R2 but solely MTR was identified as source of MR phase contrast. R2 was correlated with iron concentrations in cortical gray matter only (r=0.42, p<0.05). In conclusion, MR phase contrast between cortical gray and white matter can be mainly attributed to variations in myelin content, but not to iron concentration. Both, myelin and iron impact the effective transverse relaxation rate R2 significantly. Magnitude contrast is limited because it only reflects the extent but not the direction of the susceptibility shift.

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.

The future of susceptibility contrast for assessment of anatomy and function

The magnetic properties of tissues affect MR images and differences in magnetic susceptibility can be utilized to provide impressive image contrast. Specifically, phase images acquired with gradient echo MRI provide unique and superb contrast which reflects variations in the underlying tissue composition. There is great interest in extracting tissue susceptibility from image data since magnetic susceptibility is an intrinsic tissue property that reflects tissue composition much more closely than MRI phase. Still, this major tissue contrast mechanism is largely unexplored in magnetic resonance imaging because non-conventional reconstruction and dipole deconvolution are required to quantitatively map tissue susceptibility properly. This short review summarizes the current state of susceptibility contrast and susceptibility mapping and aims to identify future directions.

Development of Electron Energy Loss Spectroscopy in the Biological Sciences

The high sensitivity of electron energy loss spectroscopy (EELS) for detecting light elements at the nanoscale makes it a valuable technique for application to biological systems. In particular, EELS provides quantitative information about elemental distributions within subcellular compartments, specific atoms bound to individual macromolecular assemblies, and the composition of bionanoparticles. The EELS data can be acquired either in the fixed beam energy-filtered transmission electron microscope (EFTEM) or in the scanning transmission electron microscope (STEM), and recent progress in the development of both approaches has greatly expanded the range of applications for EELS analysis. Near single atom sensitivity is now achievable for certain elements bound to isolated macromolecules, and it becomes possible to obtain three-dimensional compositional distributions from sectioned cells through EFTEM tomography.

Measuring brain oxygenation in humans using a multiparametric quantitative blood oxygenation level dependent MRI approach

Quantitative blood oxygenation level dependent approaches have been designed to obtain quantitative oxygenation information using MRI. A mathematical model is usually fitted to the time signal decay of a gradient-echo and spin-echo measurements to derive hemodynamic parameters such as the blood oxygen saturation or the cerebral blood volume. Although the results in rats and human brain have been encouraging, recent studies have pointed out the need for independent estimation of one or more variables to increase the accuracy of the method. In this study, a multiparametric quantitative blood oxygenation level dependent approach is proposed. A combination of arterial spin labeling and dynamic susceptibility contrast methods were used to obtain quantitative estimates of cerebral blood volume and cerebral blood flow. These results were combined with T 2 and T(2) measurements to derive maps of blood oxygen saturation or cerebral metabolic rate of oxygen. In 12 normal subjects, a mean cerebral blood volume of 4.33 ± 0.7%, cerebral blood flow of 43.8 ± 5.7 mL/min/100 g, blood oxygen saturation of 60 ± 6% and cerebral metabolic rate of oxygen 157 ± 23 μmol/100 g/min were found, which are in agreement with literature values. The results obtained in this study suggest that this methodology could be applied to study brain hypoxia in the setting of pathology.

Chronic multiple sclerosis lesions: characterization with high-field-strength MR imaging

PURPOSE

To elucidate the mechanism of magnetic resonance (MR) imaging contrast in multiple sclerosis (MS) lesion appearance by using susceptibility-weighted imaging and to assess with histologic correlation the role of iron and myelin in generating this MR imaging contrast.

MATERIALS AND METHODS

Each patient provided written consent to a human subject protocol approved by an institutional review board. High-spatial-resolution susceptibility-weighted 7.0-T MR images were obtained in 21 patients with MS. Contrast patterns in quantitative phase and R2* images, derived from 7.0-T data, were investigated in 220 areas defined as chronic MS lesions on conventional T2-weighted fluid-attenuated inversion recovery, T2-weighted, and T1-weighted spin-echo images. The presence of positive or negative phase shifts (ie, decreased or increased MR frequency, respectively) was assessed in each lesion. In addition, postmortem MR imaging was performed at 7.0 T and 11.7 T, and its results were correlated with those of immunohistochemical staining specific for myelin, iron, and ferritin.

RESULTS

The majority (133 [60.5%] of 220) of the identified lesions had a normal phase and reduced R2*. A substantial fraction of the lesions (84 [38.2%] of 220) had negative phase shift, either uniformly or at their rim, and a variety of appearances on R2* maps. These two lesion contrast patterns were reproduced in the postmortem MR imaging study. Comparison with histologic findings showed that, while R2* reduction corresponded to severe loss of both iron and myelin, negative phase shift corresponded to focal iron deposits with myelin loss.

CONCLUSION

Combined analysis of 7.0-T R2* and phase data may help in characterizing the pathologic features of MS lesions. The observed R2* decreases suggest profound myelin loss, whereas negative phase shifts suggest a focal iron accumulation.

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.

The contribution of myelin to magnetic susceptibility-weighted contrasts in high-field MRI of the brain

T(2)*-weighted gradient-echo MRI images at high field (≥ 7T) have shown rich image contrast within and between brain regions. The source for these contrast variations has been primarily attributed to tissue magnetic susceptibility differences. In this study, the contribution of myelin to both T(2)* and frequency contrasts is investigated using a mouse model of demyelination based on a cuprizone diet. The demyelinated brains showed significantly increased T(2)* in white matter and a substantial reduction in gray-white matter frequency contrast, suggesting that myelin is a primary source for these contrasts. Comparison of in-vivo and in-vitro data showed that, although tissue T(2)* values were reduced by formalin fixation, gray-white matter frequency contrast was relatively unaffected and fixation had a negligible effect on cuprizone-induced changes in T(2)* and frequency contrasts.

The future of ultra-high field MRI and fMRI for study of the human brain

MRI and fMRI have been used for about three and two decades respectively and much has changed over this time period, both in the quality of the data and in the range of applications for studying the brain. Apart from resolution improvements from around 4mm in the early days to below 0.5mm with modern technology, novel uses of contrast have led to the ability to sensitize images to some of the brain's structural properties at the cellular scale as well as study the localization and organization of brain function at the level of cortical columns. These developments have in part been facilitated by a continuing drive to increase the magnetic field strength. Will the next few decades see similar improvements? Here we will discuss current state of high field MRI, expected further increases in field strength, and improvements expected with these increases.

Recent progress in high-resolution functional MRI

PURPOSE OF REVIEW

For functional MRI (fMRI), as for any imaging technique, the higher the spatial resolution, the more the details it can reveal. This review will discuss the factors restricting the spatial resolution of fMRI, describe high-resolution fMRI (HR-fMRI) applications in neuroscience and outline a few research areas for future HR-fMRI studies.

RECENT FINDINGS

HR-fMRI has been successfully used to map fine cortical architectures and reveal cortical laminar structures and subcortical structures. HR-fMRI has also played important roles in resolving controversies regarding modular representations in the ventral visual pathway and interpretations of multivariate pattern analysis results.

SUMMARY

Real-time HR-fMRI as well as high-resolution anatomical MRI may emerge as indispensable tools for surgical planning, diagnosis of neurological diseases and targeting of deep brain stimulation.

Novel frontiers in ultra-structural and molecular MRI of the brain

PURPOSE OF REVIEW

Recent developments in the MRI of the brain continue to expand its use in basic and clinical neuroscience. This review highlights some areas of recent progress.

RECENT FINDINGS

Higher magnetic field strengths and improved signal detectors have allowed improved visualization of the various properties of the brain, facilitating the anatomical definition of function-specific areas and their connections. For example, by sensitizing the MRI signal to the magnetic susceptibility of tissue, it is starting to become possible to reveal the laminar structure of the cortex and identify millimeter-scale fiber bundles. Using exogenous contrast agents, and innovative ways to manipulate contrast, it is becoming possible to highlight specific fiber tracts and cell populations. These techniques are bringing us closer to understanding the evolutionary blueprint of the brain, improving the detection and characterization of disease, and help to guide treatment.

SUMMARY

Recent MRI techniques are leading to more detailed and more specific contrast in the study of the brain.

Mapping human cortical areas in vivo based on myelin content as revealed by T1- and T2-weighted MRI

Noninvasively mapping the layout of cortical areas in humans is a continuing challenge for neuroscience. We present a new method of mapping cortical areas based on myelin content as revealed by T1-weighted (T1w) and T2-weighted (T2w) MRI. The method is generalizable across different 3T scanners and pulse sequences. We use the ratio of T1w/T2w image intensities to eliminate the MR-related image intensity bias and enhance the contrast to noise ratio for myelin. Data from each subject were mapped to the cortical surface and aligned across individuals using surface-based registration. The spatial gradient of the group average myelin map provides an observer-independent measure of sharp transitions in myelin content across the surface--i.e., putative cortical areal borders. We found excellent agreement between the gradients of the myelin maps and the gradients of published probabilistic cytoarchitectonically defined cortical areas that were registered to the same surface-based atlas. For other cortical regions, we used published anatomical and functional information to make putative identifications of dozens of cortical areas or candidate areas. In general, primary and early unimodal association cortices are heavily myelinated and higher, multimodal, association cortices are more lightly myelinated, but there are notable exceptions in the literature that are confirmed by our results. The overall pattern in the myelin maps also has important correlations with the developmental onset of subcortical white matter myelination, evolutionary cortical areal expansion in humans compared with macaques, postnatal cortical expansion in humans, and maps of neuronal density in non-human primates.