High-field MRI of brain cortical substructure based on signal phase

A 128-channel receive array with enhanced signal-to-noise ratio performance for 10.5T brain imaging

PURPOSE

To develop and characterize a 128-channel head array for brain imaging at 10.5 T, evaluate signal-to-noise ratio (SNR) relative to ultimate intrinsic SNR (uiSNR) and lower field strengths, and demonstrate human brain anatomical and functional imaging with this unique magnetic field and high-channel-count array.

METHODS

The coil consists of a 16-channel self-decoupled loop transmit/receive (16Tx/Rx) array with a 112-loop receive-only (Rx) insert. Interactions between the 16Tx/Rx array and the 112Rx insert were mitigated using coaxial cable traps placed every 1/16 of a wavelength on each feed cable, locating most preamplifier boards outside the transmitter field, and miniaturizing those placed directly on individual coils.

RESULTS

The effect of the 112Rx insert on the circumscribing 16Tx/Rx array was minimized, leading to similar transmit field maps obtained experimentally with and without the 112Rx array in place and by electromagnetic simulations of the 16Tx/Rx array alone. The 128-channel array captured 77% of uiSNR centrally. Significantly higher 1/g-factor values across the whole brain was achieved compared with 7 T. Excellent SNR, high parallel-imaging performance, and minimal Tx-Rx interactions collectively facilitated acquisition of high-quality, high-resolution, proof-of-concept functional and anatomical images, including with power-demanding sequences in the human brain.

CONCLUSIONS

Counterintuitive to expectations based on magnetic fields less than or equal to 7 T, the higher channel counts provided SNR gains centrally, capturing about 80% uiSNR. The fraction of uiSNR achieved centrally in 64Rx, 80Rx, and 128Rx arrays suggested that a plateau was being reached at 80%. At this plateau, B0-dependent SNR gains for 10.5 T relative to 7 T were approximately linear to quadratic for the periphery and the center, respectively.

Conventional and Advanced Magnetic Resonance Imaging Biomarkers of Multiple Sclerosis in the Brain

Multiple sclerosis (MS) is a heterogeneous disease, and each MS patient exhibits different clinical symptoms that are reflected in their magnetic resonance imaging (MRI) results. Each MS lesion should be interpreted carefully and evaluated in conjunction with a clinical examination. MRI plays a major role in evaluating how MS lesions are aggregated in the central nervous system and how they change over time. There are several conventional MRI biomarkers of MS that could be utilized to evaluate each MS phenotype. MRI is useful for clinical decisions, aiding in the determination of disease-modifying treatment or disease prognosis. Despite its higher sensitivity, MRI provides low specificity due to the heterogeneity of MS lesions. However, advanced MRI biomarkers show promise in terms of defining MS lesions, as each imaging biomarker correlates differently with the clinical scenario of each MS phenotype. The aim of this review is to summarise the current state of MRI biomarkers for MS in the brain and how they relate to neurological disabilities.

In-vivo high-resolution χ-separation at 7T

A recently introduced quantitative susceptibility mapping (QSM) technique, χ-separation, offers the capability to separate paramagnetic (χpara) and diamagnetic (χdia) susceptibility distribution within the brain. In-vivo high-resolution mapping of iron and myelin distribution, estimated by χ-separation, could provide a deeper understanding of brain substructures, assisting the investigation of their functions and alterations. This can be achieved using 7T MRI, which benefits from a high signal-to-noise ratio and susceptibility effects. However, applying χ-separation at 7T presents difficulties due to the requirement of an R2 map, coupled with issues such as high specific absorption rate (SAR), large B1 transmit field inhomogeneities, and prolonged scan time. To address these challenges, we developed a novel deep neural network, R2PRIMEnet7T, designed to convert a 7T R2* map into a 3T R2' map. Building on this development, we present a new pipeline for χ-separation at 7T, enabling us to generate high-resolution χ-separation maps from multi-echo gradient-echo data. The proposed method is compared with alternative pipelines, such as an end-to-end network and linearly-scaled R2', and is validated against χ-separation maps at 3T, demonstrating its accuracy. The 7T χ-separation maps generated by the proposed method exhibit similar contrasts to those from 3T, while 7T high-resolution maps offer enhanced clarity and detail. Quantitative analysis confirms that the proposed method surpasses the alternative pipelines. The proposed method results well delineate the detailed brain structures associated with iron and myelin. This new pipeline holds promise for analyzing iron and myelin concentration changes in various neurodegenerative diseases through precise structural examination.

WAND: A multi-modal dataset integrating advanced MRI, MEG, and TMS for multi-scale brain analysis

This paper introduces the Welsh Advanced Neuroimaging Database (WAND), a multi-scale, multi-modal imaging dataset comprising in vivo brain data from 170 healthy volunteers (aged 18-63 years), including 3 Tesla (3 T) magnetic resonance imaging (MRI) with ultra-strong (300 mT/m) magnetic field gradients, structural and functional MRI and nuclear magnetic resonance spectroscopy at 3 T and 7 T, magnetoencephalography (MEG), and transcranial magnetic stimulation (TMS), together with trait questionnaire and cognitive data. Data are organised using the Brain Imaging Data Structure (BIDS). In addition to raw data, we provide brain-extracted T1-weighted images, and quality reports for diffusion, T1- and T2-weighted structural data, and blood-oxygen level dependent functional tasks. Reasons for participant exclusion are also included. Data are available for download through our GIN repository, a data access management system designed to reduce storage requirements. Users can interact with and retrieve data as needed, without downloading the complete dataset. Given the depth of neuroimaging phenotyping, leveraging ultra-high-gradient, high-field MRI, MEG and TMS, this dataset will facilitate multi-scale and multi-modal investigations of the healthy human brain.

Myelin water imaging of in vivo and ex vivo human brains using multi-echo gradient echo at 3 T and 7 T

PURPOSE

To compare the myelin water fraction (MWF) measurements between 3 T and 7 T and between in vivo and ex vivo human brains, and to investigate the relationship between multi-echo gradient-echo (mGRE)-based 3D MWF and myelin content using histological staining, which has not been validated in the human brain.

METHODS

In this study, we performed 3D mGRE-based MWF measurements on five ex vivo human brain hemispheres and five healthy volunteers at 3 T and 7 T with 1 mm isotropic resolution. The data were fitted with theT 2 * $$ {\mathrm{T}}_2^{\ast } $$ based on a three compartment complex-valued model to estimate MWF. We obtained myelin basic protein (MBP) staining from two tissue blocks and co-registered the MWF map and histology image for voxel-wise correlation between the two.

RESULTS

The MWF values measured from 7 T were overall higher than 7 T, but data between the two field strength demonstrated high correlations both in vivo (r = 0.88) and ex vivo (r = 0.83) across 19 white matter regions. Moreover, the MWF measurements showed a good agreement between in vivo and ex vivo assessments at 3 T (r = 0.61) and 7 T (r = 0.54). Based on MBP staining, the MWF values exhibited strong positive correlations with myelin content on both 3 T (r = 0.68 and r = 0.78 for the two tissue blocks) and 7 T (r = 0.64 and r = 0.82 for the two tissue blocks).

CONCLUSION

The findings demonstrated that the mGRE-based MWF mapping can be used to quantify myelin content in the human brain, despite the field-strength dependency of the measurements.

Quantitative susceptibility mapping at 7 T in COVID-19: brainstem effects and outcome associations

Post-mortem studies have shown that patients dying from severe acute respiratory syndrome coronavirus (SARS-CoV-2) infection frequently have pathological changes in their CNS, particularly in the brainstem. Many of these changes are proposed to result from para-infectious and/or post-infection immune responses. Clinical symptoms such as fatigue, breathlessness, and chest pain are frequently reported in post-hospitalized coronavirus disease 2019 (COVID-19) patients. We propose that these symptoms are in part due to damage to key neuromodulatory brainstem nuclei. While brainstem involvement has been demonstrated in the acute phase of the illness, the evidence of long-term brainstem change on MRI is inconclusive. We therefore used ultra-high field (7 T) quantitative susceptibility mapping (QSM) to test the hypothesis that brainstem abnormalities persist in post-COVID patients and that these are associated with persistence of key symptoms. We used 7 T QSM data from 30 patients, scanned 93-548 days after hospital admission for COVID-19 and compared them to 51 age-matched controls without prior history of COVID-19 infection. We correlated the patients' QSM signals with disease severity (duration of hospital admission and COVID-19 severity scale), inflammatory response during the acute illness (C-reactive protein, D-dimer and platelet levels), functional recovery (modified Rankin scale), depression (Patient Health Questionnaire-9) and anxiety (Generalized Anxiety Disorder-7). In COVID-19 survivors, the MR susceptibility increased in the medulla, pons and midbrain regions of the brainstem. Specifically, there was increased susceptibility in the inferior medullary reticular formation and the raphe pallidus and obscurus. In these regions, patients with higher tissue susceptibility had worse acute disease severity, higher acute inflammatory markers, and significantly worse functional recovery. This study contributes to understanding the long-term effects of COVID-19 and recovery. Using non-invasive ultra-high field 7 T MRI, we show evidence of brainstem pathophysiological changes associated with inflammatory processes in post-hospitalized COVID-19 survivors.

Single-point mutated lanmodulin as a high-performance MRI contrast agent for vascular and kidney imaging

Magnetic resonance imaging contrast agents can enhance diagnostic precision but often face limitations such as short imaging windows, low tissue specificity, suboptimal contrast enhancement, or potential toxicity, which affect resolution and long-term monitoring. Here, we present a protein contrast agent based on lanmodulin, engineered with a single-point mutation at position 108 from N to D to yield maximum gadolinium binding sites. After loading with Gd3+ ions, the resulting protein complex, LanND-Gd, exhibits efficient renal clearance, high relaxivity, and prolonged renal retention compared to commercial agents. LanND-Gd enables high-performance visualization of whole-body structures and brain vasculature in male mice at a resolution finer than one hundred micrometers. In male ischemia mouse models, LanND-Gd also improves kidney dysfunction monitoring while minimizing risks of neural toxicity or immunogenic reactions. This protein-based contrast agent offers superior image quality, improved biocompatibility, and extended imaging timeframes, promising significant advancements in magnetic resonance-based diagnostics and patient outcomes.

Leveraging ultra-high field (7T) MRI in psychiatric research

Non-invasive brain imaging has played a critical role in establishing our understanding of the neural properties that contribute to the emergence of psychiatric disorders. However, characterizing core neurobiological mechanisms of psychiatric symptomatology requires greater structural, functional, and neurochemical specificity than is typically obtainable with standard field strength MRI acquisitions (e.g., 3T). Ultra-high field (UHF) imaging at 7 Tesla (7T) provides the opportunity to identify neurobiological systems that confer risk, determine etiology, and characterize disease progression and treatment outcomes of major mental illnesses. Increases in scanner availability, regulatory approval, and sequence availability have made the application of UHF to clinical cohorts more feasible than ever before, yet the application of UHF approaches to the study of mental health remains nascent. In this technical review, we describe core neuroimaging methodologies which benefit from UHF acquisition, including high resolution structural and functional imaging, single (1H) and multi-nuclear (e.g., 31P) MR spectroscopy, and quantitative MR techniques for assessing brain tissue iron and myelin. We discuss advantages provided by 7T MRI, including higher signal- and contrast-to-noise ratio, enhanced spatial resolution, increased test-retest reliability, and molecular and neurochemical specificity, and how these have begun to uncover mechanisms of psychiatric disorders. Finally, we consider current limitations of UHF in its application to clinical cohorts, and point to ongoing work that aims to overcome technical hurdles through the continued development of UHF hardware, software, and protocols.

A 128-channel receive array with enhanced SNR performance for 10.5 tesla brain imaging

Purpose

To develop and characterize the performance of a 128-channel head array for brain imaging at 10.5 tesla and evaluate the potential of brain imaging at this unique, >10 tesla magnetic field.

Methods

The coil is composed of a 16-channel self-decoupled loop transmit/receive array with a 112-loop receive-only (Rx) insert. Interactions between the outer transmitter and the inner 112Rx insert were mitigated using coaxial cable traps placed every 1/16 of a wavelength on each feed cable, locating most preamplifier boards outside the transmitter field and miniaturizing those placed directly on individual coils.

Results

The 128-channel array described herein achieved 77% of ultimate intrinsic SNR in the center of the brain. Transmit field maps obtained experimentally on a phantom with and without the receive array were similar and matched EM simulations, leading to FDA approval for human imaging. Anatomical and functional data, including with power demanding sequences, were acquired successfully on human volunteers.

Conclusions

Counterintuitive to expectations based on magnetic fields ≤7T, the higher channel counts provided SNR gains centrally, capturing ∼80% uiSNR. Fraction of uiSNR achieved centrally in 64Rx, 80Rx, and 128Rx arrays suggested that a plateau was being reached at 80%. At this plateau, linear to approximately quadratic B 0 dependent SNR gains for the periphery and the center, respectively, were observed for 10.5T relative 7T.

Direct segmentation of cortical cytoarchitectonic domains using ultra-high-resolution whole-brain diffusion MRI

We assess the potential of detecting cortical laminar patterns and areal borders by directly clustering voxel values of microstructural parameters derived from high-resolution mean apparent propagator (MAP) magnetic resonance imaging (MRI), as an alternative to conventional template-warping-based cortical parcellation methods. We acquired MAP-MRI data with 200μm resolution in a fixed macaque monkey brain. To improve the sensitivity to cortical layers, we processed the data with a local anisotropic Gaussian filter determined voxel-wise by the plane tangent to the cortical surface. We directly clustered all cortical voxels using only the MAP-derived microstructural imaging biomarkers, with no information regarding their relative spatial location or dominant diffusion orientations. MAP-based 3D cytoarchitectonic segmentation revealed laminar patterns similar to those observed in the corresponding histological images. Moreover, transition regions between these laminar patterns agreed more accurately with histology than the borders between cortical areas estimated using conventional atlas/template-warping cortical parcellation. By cross-tabulating all cortical labels in the atlas- and MAP-based segmentations, we automatically matched the corresponding MAP-derived clusters (i.e., cytoarchitectonic domains) across the left and right hemispheres. Our results demonstrate that high-resolution MAP-MRI biomarkers can effectively delineate three-dimensional cortical cytoarchitectonic domains in single individuals. Their intrinsic tissue microstructural contrasts enable the construction of whole-brain mesoscopic cortical atlases.

The use of 7T MRI in multiple sclerosis: review and consensus statement from the North American Imaging in Multiple Sclerosis Cooperative

The use of ultra-high-field 7-Tesla (7T) MRI in multiple sclerosis (MS) research has grown significantly over the past two decades. With recent regulatory approvals of 7T scanners for clinical use in 2017 and 2020, the use of this technology for routine care is poised to continue to increase in the coming years. In this context, the North American Imaging in MS Cooperative (NAIMS) convened a workshop in February 2023 to review the previous and current use of 7T technology for MS research and potential future research and clinical applications. In this workshop, experts were tasked with reviewing the current literature and proposing a series of consensus statements, which were reviewed and approved by the NAIMS. In this review and consensus paper, we provide background on the use of 7T MRI in MS research, highlighting this technology's promise for identification and quantification of aspects of MS pathology that are more difficult to visualize with lower-field MRI, such as grey matter lesions, paramagnetic rim lesions, leptomeningeal enhancement and the central vein sign. We also review the promise of 7T MRI to study metabolic and functional changes to the brain in MS. The NAIMS provides a series of consensus statements regarding what is currently known about the use of 7T MRI in MS, and additional statements intended to provide guidance as to what work is necessary going forward to accelerate 7T MRI research in MS and translate this technology for use in clinical practice and clinical trials. This includes guidance on technical development, proposals for a universal acquisition protocol and suggestions for research geared towards assessing the utility of 7T MRI to improve MS diagnostics, prognostics and therapeutic efficacy monitoring. The NAIMS expects that this article will provide a roadmap for future use of 7T MRI in MS.

A method to image brain tissue frozen at autopsy

Magnetic Resonance Imaging (MRI) can provide the location and signal characteristics of pathological regions within a postmortem tissue block, thereby improving the efficiency of histopathological studies. However, such postmortem-MRI guided histopathological studies have so far only been performed on fixed samples as imaging tissue frozen at the time of extraction, while preserving its integrity, is significantly more challenging. Here we describe the development of cold-postmortem-MRI, which can preserve tissue integrity and help target techniques such as transcriptomics. As a first step, RNA integrity number (RIN) was used to determine the rate of tissue biomolecular degradation in mouse brains placed at various temperatures between -20 °C and +20 °C for up to 24 h. Then, human tissue frozen at the time of autopsy was immersed in 2-methylbutane, sealed in a bio-safe tissue chamber, and cooled in the MRI using a recirculating chiller to determine MRI signal characteristics. The optimal imaging temperature, which did not show significant RIN deterioration for over 12 h, at the same time giving robust MRI signal and contrast between brain tissue types was deemed to be -7 °C. Finally, MRI was performed on human tissue blocks at this optimal imaging temperatures using a magnetization-prepared rapid gradient echo (MPRAGE, isotropic resolution between 0.3-0.4 mm) revealing good gray-white matter contrast and revealing subpial, subcortical, and deep white matter lesions. RINs measured before and after imaging revealed no significant changes (n = 3, p = 0.18, paired t-test). In addition to improving efficiency of downstream processes, imaging tissue at sub-zero temperatures may also improve our understanding of compartment specificity of MRI signal.

Quantitative susceptibility mapping in the brain reflects spatial expression of genes involved in iron homeostasis and myelination

Quantitative susceptibility mapping (QSM) is an MRI modality used to non-invasively measure iron content in the brain. Iron exhibits a specific anatomically varying pattern of accumulation in the brain across individuals. The highest regions of accumulation are the deep grey nuclei, where iron is stored in paramagnetic molecule ferritin. This form of iron is considered to be what largely contributes to the signal measured by QSM in the deep grey nuclei. It is also known that QSM is affected by diamagnetic myelin contents. Here, we investigate spatial gene expression of iron and myelin related genes, as measured by the Allen Human Brain Atlas, in relation to QSM images of age-matched subjects. We performed multiple linear regressions between gene expression and the average QSM signal within 34 distinct deep grey nuclei regions. Our results show a positive correlation (p < .05, corrected) between expression of ferritin and the QSM signal in deep grey nuclei regions. We repeated the analysis for other genes that encode proteins thought to be involved in the transport and storage of iron in the brain, as well as myelination. In addition to ferritin, our findings demonstrate a positive correlation (p < .05, corrected) between the expression of ferroportin, transferrin, divalent metal transporter 1, several gene markers of myelinating oligodendrocytes, and the QSM signal in deep grey nuclei regions. Our results suggest that the QSM signal reflects both the storage and active transport of iron in the deep grey nuclei regions of the brain.

Value of Quantitative Susceptibility Mapping in Clinical Neuroradiology

Quantitative susceptibility mapping (QSM) is a unique technique for providing quantitative information on tissue magnetic susceptibility using phase image data. QSM can provide valuable information regarding physiological and pathological processes such as iron deposition, hemorrhage, calcification, and myelin. QSM has been considered for use as an imaging biomarker to investigate physiological status and pathological changes. Although various studies have investigated the clinical applications of QSM, particularly regarding the use of QSM in clinical practice, have not been examined well. This review provides on an overview of the basics of QSM and its clinical applications in neuroradiology. LEVEL OF EVIDENCE: 2 TECHNICAL EFFICACY: Stage 2.

MR Imaging in Ataxias: Consensus Recommendations by the Ataxia Global Initiative Working Group on MRI Biomarkers

With many viable strategies in the therapeutic pipeline, upcoming clinical trials in hereditary and sporadic degenerative ataxias will benefit from non-invasive MRI biomarkers for patient stratification and the evaluation of therapies. The MRI Biomarkers Working Group of the Ataxia Global Initiative therefore devised guidelines to facilitate harmonized MRI data acquisition in clinical research and trials in ataxias. Recommendations are provided for a basic structural MRI protocol that can be used for clinical care and for an advanced multi-modal MRI protocol relevant for research and trial settings. The advanced protocol consists of modalities with demonstrated utility for tracking brain changes in degenerative ataxias and includes structural MRI, magnetic resonance spectroscopy, diffusion MRI, quantitative susceptibility mapping, and resting-state functional MRI. Acceptable ranges of acquisition parameters are provided to accommodate diverse scanner hardware in research and clinical contexts while maintaining a minimum standard of data quality. Important technical considerations in setting up an advanced multi-modal protocol are outlined, including the order of pulse sequences, and example software packages commonly used for data analysis are provided. Outcome measures most relevant for ataxias are highlighted with use cases from recent ataxia literature. Finally, to facilitate access to the recommendations by the ataxia clinical and research community, examples of datasets collected with the recommended parameters are provided and platform-specific protocols are shared via the Open Science Framework.

Improved test-retest reliability of R 2 * $$ {\mathrm{R}}_2^{\ast } $$ and susceptibility quantification using multishot multi-echo 3D EPI

PURPOSE

This study aimed to evaluate the potential of 3D EPI for improving the reliability ofT 2 * $$ {\mathrm{T}}_2^{\ast } $$ -weighted data and quantification ofR 2 * $$ {\mathrm{R}}_2^{\ast } $$ decay rate and susceptibility (χ) compared with conventional gradient-echo (GRE)-based acquisition.

METHODS

Eight healthy subjects in a wide age range were recruited. Each subject received repeated scans for both GRE and EPI acquisitions with an isotropic 1 mm resolution at 3 T. Maps ofR 2 * $$ {\mathrm{R}}_2^{\ast } $$ and χ were quantified, and their interscan differences were used to evaluate the test-retest reliability. Interprotocol differences ofR 2 * $$ {\mathrm{R}}_2^{\ast } $$ and χ between GRE and EPI were also measured voxel by voxel and in selected regions of interest to test the consistency between the two acquisition methods.

RESULTS

The quantifications ofR 2 * $$ {\mathrm{R}}_2^{\ast } $$ and χ using EPI protocols showed increased test-retest reliability with higher EPI factors up to 5 as performed in the experiment and were consistent with those based on GRE.

CONCLUSION

The result suggests that multishot multi-echo 3D EPI can be a useful alternative acquisition method forT 2 * $$ {\mathrm{T}}_2^{\ast } $$ -weighted MRI and quantification ofR 2 * $$ {\mathrm{R}}_2^{\ast } $$ and χ with reduced scan time, improved test-retest reliability, and similar accuracy compared with commonly used 3D GRE.

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.

Exploiting gradient-echo frequency evolution: Probing white matter microstructure and extracting bulk susceptibility-induced frequency for quantitative susceptibility mapping

PURPOSE

This work is to investigate the microstructure-induced frequency shift in white matter (WM) with crossing fibers and to separate the microstructure-related frequency shift from the bulk susceptibility-induced frequency shift by model fitting the gradient-echo (GRE) frequency evolution for potentially more accurate quantitative susceptibility mapping (QSM).

METHODS

A hollow-cylinder fiber model (HCFM) with two fiber populations was developed to investigate GRE frequency evolutions in WM voxels with microstructural orientation dispersion. The simulated and experimentally measured TE-dependent local frequency shift was then fitted to a simplified frequency evolution model to obtain a microstructure-related frequency difference parameter (∆ f $$ \Delta f $$ ) and a TE-independent bulk susceptibility-induced frequency shift (C f $$ {C}_f $$ ). The obtainedC f $$ {C}_f $$ was then used for QSM reconstruction. Reconstruction performances were evaluated using a numerical head phantom and in vivo data and then compared to other multi-echo combination methods.

RESULTS

GRE frequency evolutions and∆ f $$ \Delta f $$ -based tissue parameters in both parallel and crossing fibers determined from our simulations were comparable to those observed in vivo. The TE-dependent frequency fitting method outperformed other multi-echo combination methods in estimatingC f $$ {C}_f $$ in simulations. The fitted∆ f $$ \Delta f $$ ,C f $$ {C}_f $$ , and QSM could be improved further by navigator-based B0 fluctuation correction.

CONCLUSION

A HCFM with two fiber populations can be used to characterize microstructure-induced frequency shifts in WM regions with crossing fibers. HCFM-based TE-dependent frequency fitting provides tissue contrast related to microstructure (∆ f $$ \Delta f $$ ) and in addition may help improve the quantification accuracy ofC f $$ {C}_f $$ and the corresponding QSM.

Clustering the cortical laminae: in vivo parcellation

The laminar microstructure of the cerebral cortex has distinct anatomical characteristics of the development, function, connectivity, and even various pathologies of the brain. In recent years, multiple neuroimaging studies have utilized magnetic resonance imaging (MRI) relaxometry to visualize and explore this intricate microstructure, successfully delineating the cortical laminar components. Despite this progress, T1 is still primarily considered a direct measure of myeloarchitecture (myelin content), rather than a probe of tissue cytoarchitecture (cellular composition). This study aims to offer a robust, whole-brain validation of T1 imaging as a practical and effective tool for exploring the laminar composition of the cortex. To do so, we cluster complex microstructural cortical datasets of both human (N = 30) and macaque (N = 1) brains using an adaptation of an algorithm for clustering cell omics profiles. The resulting cluster patterns are then compared to established atlases of cytoarchitectonic features, exhibiting significant correspondence in both species. Lastly, we demonstrate the expanded applicability of T1 imaging by exploring some of the cytoarchitectonic features behind various unique skillsets, such as musicality and athleticism.

A Complex Quasi-Newton Proximal Method for Image Reconstruction in Compressed Sensing MRI

Model-based methods are widely used for reconstruction in compressed sensing (CS) magnetic resonance imaging (MRI), using regularizers to describe the images of interest. The reconstruction process is equivalent to solving a composite optimization problem. Accelerated proximal methods (APMs) are very popular approaches for such problems. This paper proposes a complex quasi-Newton proximal method (CQNPM) for the wavelet and total variation based CS MRI reconstruction. Compared with APMs, CQNPM requires fewer iterations to converge but needs to compute a more challenging proximal mapping called weighted proximal mapping (WPM). To make CQNPM more practical, we propose efficient methods to solve the related WPM. Numerical experiments on reconstructing non-Cartesian MRI data demonstrate the effectiveness and efficiency of CQNPM.

Incorporating the effect of white matter microstructure in the estimation of magnetic susceptibility in ex vivo mouse brain

PURPOSE

To extend quantitative susceptibility mapping to account for microstructure of white matter (WM) and demonstrate its effect on ex vivo mouse brain at 16.4T.

THEORY AND METHODS

Previous studies have shown that the MRI measured Larmor frequency also depends on local magnetic microstructure at the mesoscopic scale. Here, we include effects from WM microstructure using our previous results for the mesoscopic Larmor frequencyΩ ‾ Meso $$ {\overline{\Omega}}^{\mathrm{Meso}} $$ of cylinders with arbitrary orientations. We scrutinize the validity of our model and QSM in a digital brain phantom includingΩ ‾ Meso $$ {\overline{\Omega}}^{\mathrm{Meso}} $$ from a WM susceptibility tensor and biologically stored iron with scalar susceptibility. We also apply susceptibility tensor imaging to the phantom and investigate how the fitted tensors are biased fromΩ ‾ Meso $$ {\overline{\Omega}}^{\mathrm{Meso}} $$ . Last, we demonstrate how to combine multi-gradient echo and diffusion MRI images of ex vivo mouse brains acquired at 16.4T to estimate an apparent scalar susceptibility without sample rotations.

RESULTS

Our new model improves susceptibility estimation compared to QSM for the brain phantom. Applying susceptibility tensor imaging to the phantom withΩ ‾ Meso $$ {\overline{\Omega}}^{\mathrm{Meso}} $$ from WM axons with scalar susceptibility produces a highly anisotropic susceptibility tensor that mimics results from previous susceptibility tensor imaging studies. For the ex vivo mouse brain we find theΩ ‾ Meso $$ {\overline{\Omega}}^{\mathrm{Meso}} $$ due to WM microstructure to be substantial, changing susceptibility in WM up to 25% root-mean-squared-difference.

CONCLUSION

Ω ‾ Meso $$ {\overline{\Omega}}^{\mathrm{Meso}} $$ impacts susceptibility estimates and biases susceptibility tensor imaging fitting substantially. Hence, it should not be neglected when imaging structurally anisotropic tissue such as brain WM.

Postmortem MRI of Tissue Frozen at Autopsy

Introduction

Postmortem MRI provides insight into location of pathology within tissue blocks, enabling efficient targeting of histopathological studies. While postmortem imaging of fixed tissue is gaining popularity, imaging tissue frozen at the time of extraction is significantly more challenging.

Methods

Tissue integrity was examined using RNA integrity number (RIN), in mouse brains placed between -20 °C and 20 °C for up to 24 hours, to determine the highest temperature that could potentially be used for imaging without tissue degeneration. Human tissue frozen at the time of autopsy was sealed in a tissue chamber filled with 2-methylbutane to prevent contamination of the MRI components. The tissue was cooled to a range of temperatures in a 9.4T MRI using a recirculating aqueous ethylene glycol solution. MRI was performed using a magnetization-prepared rapid gradient echo (MPRAGE) sequence with inversion time of 1400 ms to null the signal from 2-methylbutane bath, isotropic resolution between 0.3-0.4 mm, and scan time of about 4 hours was used to study the anatomical details of the tissue block.

Results and Discussion

A temperature of -7 °C was chosen for imaging as it was below the highest temperature that did not show significant RIN deterioration for over 12 hours, at the same time gave robust imaging signal and contrast between brain tissue types. Imaging performed on various human tissue blocks revealed good gray-white matter contrast and revealing subpial, subcortical, and deep white matter lesions typical of multiple sclerosis enabling further spatially targeted studies.

Conclusion

Here, we describe a new method to image cold tissue, while maintaining tissue integrity and biosafety during scanning. In addition to improving efficiency of downstream processes, imaging tissue at sub-zero temperatures may also improve our understanding of compartment specificity of MRI signal.

Analyzing the cortical fine structure as revealed by ex-vivo anatomical MRI

The human cortex has a rich fiber structure as revealed by myelin-staining of histological slices. Myelin also contributes to the image contrast in Magnetic Resonance Imaging (MRI). Recent advances in Magnetic Resonance (MR) scanner and imaging technology allowed the acquisition of an ex-vivo data set at an isotropic resolution of 100 µm. This study focused on a computational analysis of this data set with the aim of bridging between histological knowledge and MRI-based results. This work highlights: (1) the design and implementation of a processing chain that extracts intracortical features from a high-resolution MR image; (2) a demonstration of the correspondence between MRI-based cortical intensity profiles and the myelo-architectonic layering of the cortex; (3) the characterization and classification of four basic myelo-architectonic profile types; (4) the distinction of cortical regions based on myelo-architectonic features; and (5) the segmentation of cortical modules in the entorhinal cortex.

Mapping the individual human cortex using multidimensional MRI and unsupervised learning

Human evolution has seen the development of higher-order cognitive and social capabilities in conjunction with the unique laminar cytoarchitecture of the human cortex. Moreover, early-life cortical maldevelopment has been associated with various neurodevelopmental diseases. Despite these connections, there is currently no noninvasive technique available for imaging the detailed cortical laminar structure. This study aims to address this scientific and clinical gap by introducing an approach for imaging human cortical lamina. This method combines diffusion-relaxation multidimensional MRI with a tailored unsupervised machine learning approach that introduces enhanced microstructural sensitivity. This new imaging method simultaneously encodes the microstructure, the local chemical composition and importantly their correlation within complex and heterogenous tissue. To validate our approach, we compared the intra-cortical layers obtained using our ex vivo MRI-based method with those derived from Nissl staining of postmortem human brain specimens. The integration of unsupervised learning with diffusion-relaxation correlation MRI generated maps that demonstrate sensitivity to areal differences in cytoarchitectonic features observed in histology. Significantly, our observations revealed layer-specific diffusion-relaxation signatures, showing reductions in both relaxation times and diffusivities at the deeper cortical levels. These findings suggest a radial decrease in myelin content and changes in cell size and anisotropy, reflecting variations in both cytoarchitecture and myeloarchitecture. Additionally, we demonstrated that 1D relaxation and high-order diffusion MRI scalar indices, even when aggregated and used jointly in a multimodal fashion, cannot disentangle the cortical layers. Looking ahead, our technique holds the potential to open new avenues of research in human neurodevelopment and the vast array of disorders caused by disruptions in neurodevelopment.

Single-slab 3D double inversion recovery for magnetic resonance brain imaging in clinically healthy dogs

Introduction

In veterinary medicine, magnetic resonance imaging (MRI) is widely utilized for brain imaging. But the complex structures of brain tissues can give rise to artifacts such as partial volume averaging in conventional sequences. To address this issue, several studies about double inversion recovery (DIR) sequences have been conducted in human medicine. However, published clinical studies about brain MRI using DIR sequences in dogs are currently lacking. The purpose of this study was to evaluate the magnetic resonance features of single-slab 3D DIR sequences in the normal canine brain.

Methods

Five healthy Beagle dogs were examined and the following pulse sequences were acquired for each: (1) spin-echo T2-weighted (T2W), (2) fluid attenuated inversion recovery (FLAIR), (3) gray matter (GM) selective, and (4) white matter (WM) selective single-slab 3D DIR sequence. For qualitative analysis, the distinction between gray and white matter of the cerebral cortex, presence and severity of the image artifacts were assessed for each pulse sequence. In addition, reconstructed images of single-slab 3D DIR sequences were qualitatively evaluated. For quantitative analysis, contrast ratios (CRs), signal-to-noise ratios (SNRs), and contrast-to-noise ratios (CNRs) of the GM, WM and cerebrospinal fluid (CSF) were measured for each pulse sequence.

Results and Discussion

GM selective 3D DIR was superior to T2W and FLAIR in delineating the boundaries between GM and WM in the overall brain area. Whereas WM selective 3D DIR provided better gray-white matter distinction of the cerebral cortex than T2W and FLAIR at the level of the medulla oblongata, where T2W and FLAIR images exhibited severe partial volume averaging artifacts. In general, the 3D DIR images demonstrated fewer artifacts compared to other sequences, and the reconstructed sagittal and dorsal images of these sequences maintained same spatial resolution as the original transverse images without any image degradation. Both gray and white matter selective 3D DIR sequences effectively suppressed unwanted signals, thereby providing high contrast between gray and white matter. Findings from this study could serve as a foundation for further studies on DIR sequences for the evaluation of brain diseases in dogs.

Expanding connectomics to the laminar level: A perspective

Despite great progress in uncovering the complex connectivity patterns of the human brain over the last two decades, the field of connectomics still experiences a bias in its viewpoint of the cerebral cortex. Due to a lack of information regarding exact end points of fiber tracts inside cortical gray matter, the cortex is commonly reduced to a single homogenous unit. Concurrently, substantial developments have been made over the past decade in the use of relaxometry and particularly inversion recovery imaging for exploring the laminar microstructure of cortical gray matter. In recent years, these developments have culminated in an automated framework for cortical laminar composition analysis and visualization, followed by studies of cortical dyslamination in epilepsy patients and age-related differences in laminar composition in healthy subjects. This perspective summarizes the developments and remaining challenges of multi-T1 weighted imaging of cortical laminar substructure, the current limitations in structural connectomics, and the recent progress in integrating these fields into a new model-based subfield termed 'laminar connectomics'. In the coming years, we predict an increased use of similar generalizable, data-driven models in connectomics with the purpose of integrating multimodal MRI datasets and providing a more nuanced and detailed characterization of brain connectivity.

Effect of motion, cortical orientation and spatial resolution on quantitative imaging of cortical R2* and magnetic susceptibility at 0.3 mm in-plane resolution at 7 T

MR images of the effective relaxation rate R2* and magnetic susceptibility χ derived from multi-echo T2*-weighted (T2*w) MRI can provide insight into iron and myelin distributions in the brain, with the potential of providing biomarkers for neurological disorders. Quantification of R2* and χ at submillimeter resolution in the cortex in vivo has been difficult because of challenges such as head motion, limited signal to noise ratio, long scan time, and motion related magnetic field fluctuations. This work aimed to improve the robustness for quantifying intracortical R2* and χ and analyze the effects from motion, spatial resolution, and cortical orientation. T2*w data was acquired with a spatial resolution of 0.3 × 0.3 × 0.4 mm3 at 7 T and downsampled to various lower resolutions. A combined correction for motion and B0 changes was deployed using volumetric navigators. Such correction improved the T2*w image quality rated by experienced image readers and test-retest reliability of R2* and χ quantification with reduced median inter-scan differences up to 10 s-1 and 5 ppb, respectively. R2* and χ near the line of Gennari, a cortical layer high in iron and myelin, were as much as 10 s-1 and 10 ppb higher than the region at adjacent cortical depth. In addition, a significant effect due to the cortical orientation relative to the static field (B0) was observed in χ with a peak-to-peak amplitude of about 17 ppb. In retrospectively downsampled data, the capability to distinguish different cortical depth regions based on R2* or χ contrast remained up to isotropic 0.5 mm resolution. This study highlights the unique characteristics of R2* and χ along the cortical depth at submillimeter resolution and the need for motion and B0 corrections for their robust quantification in vivo.

Synthesizing Complex-Valued Multicoil MRI Data from Magnitude-Only Images

Despite the proliferation of deep learning techniques for accelerated MRI acquisition and enhanced image reconstruction, the construction of large and diverse MRI datasets continues to pose a barrier to effective clinical translation of these technologies. One major challenge is in collecting the MRI raw data (required for image reconstruction) from clinical scanning, as only magnitude images are typically saved and used for clinical assessment and diagnosis. The image phase and multi-channel RF coil information are not retained when magnitude-only images are saved in clinical imaging archives. Additionally, preprocessing used for data in clinical imaging can lead to biased results. While several groups have begun concerted efforts to collect large amounts of MRI raw data, current databases are limited in the diversity of anatomy, pathology, annotations, and acquisition types they contain. To address this, we present a method for synthesizing realistic MR data from magnitude-only data, allowing for the use of diverse data from clinical imaging archives in advanced MRI reconstruction development. Our method uses a conditional GAN-based framework to generate synthetic phase images from input magnitude images. We then applied ESPIRiT to derive RF coil sensitivity maps from fully sampled real data to generate multi-coil data. The synthetic data generation method was evaluated by comparing image reconstruction results from training Variational Networks either with real data or synthetic data. We demonstrate that the Variational Network trained on synthetic MRI data from our method, consisting of GAN-derived synthetic phase and multi-coil information, outperformed Variational Networks trained on data with synthetic phase generated using current state-of-the-art methods. Additionally, we demonstrate that the Variational Networks trained with synthetic k-space data from our method perform comparably to image reconstruction networks trained on undersampled real k-space data.

High-resolution magnetization-transfer imaging of post-mortem marmoset brain: Comparisons with relaxometry and histology

Cell membranes and macromolecules or paramagnetic compounds interact with water proton spins, which modulates magnetic resonance imaging (MRI) contrast providing information on tissue composition. For a further investigation, quantitative magnetization transfer (qMT) parameters (at 3T), including the ratio of the macromolecular and water proton pools, F, and the exchange-rate constant as well as the (observed) longitudinal and the effective transverse relaxation rates (at 3T and 7T), R₁^obs and R₂^*, respectively, were measured at high spatial resolution (200 µm) in a slice of fixed marmoset brain and compared to histology results obtained with Gallyas' myelin stain and Perls' iron stain. R₁^obs and R₂^* were linearly correlated with the iron content for the entire slice, whereas distinct differences were obtained between gray and white matter for correlations of relaxometry and qMT parameters with myelin content. The combined results suggest that the macromolecular pool interacting with water consists of myelin and (less efficient) non-myelin contributions. Despite strong correlation of F and R₁^obs, none of these parameters was uniquely specific to myelination. Due to additional sensitivity to iron stores, R₁^obs and R₂^* were more sensitive for depicting microstructural differences between cortical layers than F.

Iron quantitative analysis of motor combined with bulbar region in M1 cortex may improve diagnosis performance in ALS

OBJECTIVES

To explore whether the combined analysis of motor and bulbar region of M1 on susceptibility-weighted imaging (SWI) can be a valid biomarker for amyotrophic lateral sclerosis (ALS).

METHODS

Thirty-two non-demented ALS patients and 35 age- and gender-matched healthy controls (HC) were retrospectively recruited. SWI and 3D-T1-MPRAGE images were obtained from all individuals using a 3.0-T MRI scan. The bilateral posterior band of M1 was manually delineated by three neuroradiologists on phase images and subdivided into the motor and bulbar regions. We compared the phase values in two groups and performed a stratification analysis (ALSFRS-R score, duration, disease progression rate, and onset). Receiver operating characteristic (ROC) curves were also constructed.

RESULTS

ALS group showed significantly increased phase values in M1 and the two subregions than the HC group, on the all and elderly level (p < 0.001, respectively). On all-age level comparison, negative correlations were found between phase values of M1 and clinical score and duration (p < 0.05, respectively). Similar associations were found in the motor region (p < 0.05, respectively). On both the total (p < 0.01) and elderly (p < 0.05) levels, there were positive relationships between disease progression rate and M1 phase values. In comparing ROC curves, the entire M1 showed the best diagnostic performance.

CONCLUSIONS

Combining motor and bulbar analyses as an integral M1 region on SWI can improve ALS diagnosis performance, especially in the elderly. The phase value could be a valuable biomarker for ALS evaluation.

KEY POINTS

• Integrated analysis of the motor and bulbar as an entire M1 region on SWI can improve the diagnosis performance in ALS. • Quantitative analysis of iron deposition by SWI measurement helps the clinical evaluation, especially for the elderly patients. • Phase value, when combined with the disease progression rate, could be a valuable biomarker for ALS.

Microstructural Neurodegeneration of the Entorhinal-Hippocampus Pathway along the Alzheimer's Disease Continuum

BACKGROUND

Conventional neuroimaging biomarkers for the neurodegeneration of Alzheimer's disease (AD) are not sensitive enough to detect neurodegenerative alterations during the preclinical stage of AD individuals.

OBJECTIVE

We examined whether neurodegeneration of the entorhinal-hippocampal pathway could be detected along the AD continuum using ultra-high-field diffusion tensor imaging and tractography for ex vivo brain tissues.

METHODS

Postmortem brain specimens from a cognitively unimpaired individual without AD pathological changes (non-AD), a cognitively unimpaired individual with AD pathological changes (preclinical AD), and a demented individual with AD pathological changes (AD dementia) were scanned with an 11.7T diffusion magnetic resonance imaging. Fractional anisotropy (FA) values of the entorhinal layer II and number of perforant path fibers counted by tractography were compared among the AD continuum. Following the imaging analyses, the status of myelinated fibers and neuronal cells were verified by subsequent serial histological examinations.

RESULTS

At 250μm (zipped to 125μm) isotropic resolution, the entorhinal layer II islands and the perforant path fibers could be identified in non-AD and preclinical AD, but not in AD dementia, followed by histological verification. The FA value of the entorhinal layer II was the highest among the entorhinal laminae in non-AD and preclinical AD, whereas the FA values in the entorhinal laminae were homogeneously low in AD dementia. The FA values and number of perforant path fibers decreased along the AD continuum (non-AD>preclinical AD > AD dementia).

CONCLUSION

We successfully detected neurodegenerative alterations of the entorhinal-hippocampal pathway at the preclinical stage of the AD continuum.

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

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

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.

SWI by 7T MR Imaging for the Microscopic Imaging Diagnosis of Astrocytic and Oligodendroglial Tumors

BACKGROUND AND PURPOSE

Despite advances in molecular imaging, preoperative diagnosis of astrocytomas and oligodendrogliomas can be challenging. In the present study, we assessed whether 7T SWI can be used to distinguish astrocytomas and oligodendrogliomas and whether malignant grading of gliomas is possible.

MATERIALS AND METHODS

7T SWI was performed on 21 patients with gliomas before surgery with optimization for sharp visualization of the corticomedullary junction. Scoring for cortical thickening and displacement of medullary vessels, characteristic of oligodendroglial tumors, and cortical tapering, characteristic of astrocytic tumors, was performed. Additionally, characteristics of malignancy, including thickening of the medullary veins, the presence of microbleeds, and/or necrosis were scored.

RESULTS

Scoring for oligodendroglial (highest possible score, +3) and astrocytic (lowest score possible, -3) characteristics yielded a significant difference between astrocytomas and oligodendrogliomas (mean, -1.93 versus +1.71, P < .01). Scoring for malignancy was significantly different among the World Health Organization grade II (n = 10), grade III (n = 4), and grade IV (n = 7) tumors (mean, 0.20 versus 1.38 versus 2.79). Cortical thickening was observed significantly more frequently in oligodendrogliomas (P < .02), with a sensitivity of 71.4% and specificity of 85.7%; observation of tapering of the cortex was higher in astrocytomas (P < .01) with a sensitivity of 85.7% and specificity of 100%.

CONCLUSIONS

Visualization of the corticomedullary junction by 7T SWI was useful in distinguishing astrocytomas and oligodendrogliomas. Observation of tapering of the cortex was most sensitive and specific for diagnosing astrocytomas. Reliably predicting malignant grade was also possible by 7T SWI.

The design and evaluation of single-channel loopole coils at 7T MRI

Objective. Improving the local uniformity of B 1 + field for awake monkey brain magnetic resonance imaging (MRI) at ultra-high fields while facilitating convenient placement and fixation of MRI-compatible multimodal devices for neuroscience study, can eventually advance our understanding of the primate’s brain organization. Approach. A group of single-channel RF coils including conventional loop coils and loopole coils sharing the same size and shape were designed for comparison; their performance as the transmit coil was quantitatively evaluated through a series of numerical electromagnetic (EM) simulations, and further verified by using 7T MRI over a saline phantom and a monkey in vivo. Main results. Compared to conventional loop coils, the optimized loopole coil brought up to 23.5% B 1 + uniformity improvement for monkey brain imaging in EM simulations, and this performance was further verified over monkey brain imaging at 7T in vivo. Importantly, we have systematically explored the underlying mechanism regarding the relationship between loopole coils’ current density distribution and B 1 + uniformity, observing that it can be approximated as a sinusoidal curve. Significance. The proposed loopole coil design can improve the imaging quality in awake and behaving monkeys, thus benefiting advanced brain research at UHF.

Quantitative susceptibility mapping of basal ganglia iron is associated with cognitive and motor functions that distinguish spinocerebellar ataxia type 6 and type 3

Background

In spinocerebellar ataxia type 3 (SCA3), volume loss has been reported in the basal ganglia, an iron-rich brain region, but iron content has not been examined. Recent studies have reported that patients with SCA6 have markedly decreased iron content in the cerebellar dentate, coupled with severe volume loss. Changing brain iron levels can disrupt cognitive and motor functions, yet this has not been examined in the SCAs, a disease in which iron-rich regions are affected.

Methods

In the present study, we used quantitative susceptibility mapping (QSM) to measure tissue magnetic susceptibility (indicating iron concentration), structural volume, and normalized susceptibility mass (indicating iron content) in the cerebellar dentate and basal ganglia in people with SCA3 (n = 10) and SCA6 (n = 6) and healthy controls (n = 9). Data were acquired using a 7T Philips MRI scanner. Supplemental measures assessed motor, cognitive, and mood domains.

Results

Putamen volume was lower in both SCA groups relative to controls, replicating prior findings. Dentate susceptibility mass and volume in SCA6 was lower than in SCA3 or controls, also replicating prior findings. The novel finding was that higher basal ganglia susceptibility mass in SCA6 correlated with lower cognitive performance and greater motor impairment, an association that was not observed in SCA3. Cerebellar dentate susceptibility mass, however, had the opposite relationship with cognition and motor function in SCA6, suggesting that, as dentate iron is depleted, it relocated to the basal ganglia, which contributed to cognitive and motor decline. By contrast, basal ganglia volume loss, rather than iron content, appeared to drive changes in motor function in SCA3.

Conclusion

The associations of higher basal ganglia iron with lower motor and cognitive function in SCA6 but not in SCA3 suggest the potential for using brain iron deposition profiles beyond the cerebellar dentate to assess disease states within the cerebellar ataxias. Moreover, the role of the basal ganglia deserves greater attention as a contributor to pathologic and phenotypic changes associated with SCA.

Modelling Cortical Laminar Connectivity in the Macaque Brain

In 1991, Felleman and Van Essen published their seminal study regarding hierarchical processing in the primate cerebral cortex. Their work encompassed a widescale analysis of connections reported through tracing between 35 regions in the macaque visual cortex, extending from cortical regions to the laminar level. In this work, we revisit laminar-level connectivity in the macaque brain using a whole-brain MRI-based approach. We use multimodal ex-vivo MRI imaging of the macaque brain in both white and grey matter, which are then integrated via a simple model of laminar connectivity. This model uses a granularity-based approach to define a set of rules that expands cortical connections to the laminar level. Different fiber tracking routines are then examined in order to explore the ability of our model to infer laminar connectivity. The network of macaque cortical laminar connectivity resulting from the chosen routine is then validated in the visual cortex by comparison to findings from Felleman and Van Essen with an 83% accuracy level. By using a more comprehensive definition of the cortex that addresses its heterogenous laminar composition, we can explore a new avenue of structural connectivity on the laminar level.

Neuroimaging at 7 Tesla: a pictorial narrative review

Neuroimaging using the 7-Tesla (7T) human magnetic resonance (MR) system is rapidly gaining popularity after being approved for clinical use in the European Union and the USA. This trend is the same for functional MR imaging (MRI). The primary advantages of 7T over lower magnetic fields are its higher signal-to-noise and contrast-to-noise ratios, which provide high-resolution acquisitions and better contrast, making it easier to detect lesions and structural changes in brain disorders. Another advantage is the capability to measure a greater number of neurochemicals by virtue of the increased spectral resolution. Many structural and functional studies using 7T have been conducted to visualize details in the white matter and layers of the cortex and hippocampus, the subnucleus or regions of the putamen, the globus pallidus, thalamus and substantia nigra, and in small structures, such as the subthalamic nucleus, habenula, perforating arteries, and the perivascular space, that are difficult to observe at lower magnetic field strengths. The target disorders for 7T neuroimaging range from tumoral diseases to vascular, neurodegenerative, and psychiatric disorders, including Alzheimer's disease, Parkinson's disease, multiple sclerosis, epilepsy, major depressive disorder, and schizophrenia. MR spectroscopy has also been used for research because of its increased chemical shift that separates overlapping peaks and resolves neurochemicals more effectively at 7T than a lower magnetic field. This paper presents a narrative review of these topics and an illustrative presentation of images obtained at 7T. We expect 7T neuroimaging to provide a new imaging biomarker of various brain disorders.

Reliability of quantitative multiparameter maps is high for magnetization transfer and proton density but attenuated for R1 and R2 * in healthy young adults

We investigate the reliability of individual differences of four quantities measured by magnetic resonance imaging‐based multiparameter mapping (MPM): magnetization transfer saturation (MT), proton density (PD), longitudinal relaxation rate (R₁), and effective transverse relaxation rate (R₂*). Four MPM datasets, two on each of two consecutive days, were acquired in healthy young adults. On Day 1, no repositioning occurred and on Day 2, participants were repositioned between MPM datasets. Using intraclass correlation effect decomposition (ICED), we assessed the contributions of session‐specific, day‐specific, and residual sources of measurement error. For whole‐brain gray and white matter, all four MPM parameters showed high reproducibility and high reliability, as indexed by the coefficient of variation (CoV) and the intraclass correlation (ICC). However, MT, PD, R₁, and R₂* differed markedly in the extent to which reliability varied across brain regions. MT and PD showed high reliability in almost all regions. In contrast, R₁ and R₂* showed low reliability in some regions outside the basal ganglia, such that the sum of the measurement error estimates in our structural equation model was higher than estimates of between‐person differences. In addition, in this sample of healthy young adults, the four MPM parameters showed very little variability over four measurements but differed in how well they could assess between‐person differences. We conclude that R₁ and R₂* might carry only limited person‐specific information in some regions of the brain in healthy young adults, and, by implication, might be of restricted utility for studying associations to between‐person differences in behavior in those regions.

Imaging white matter microstructure with gradient-echo phase imaging: Is ex vivo imaging with formalin-fixed tissue a good approximation of the in vivo brain?

Purpose

Ex vivo imaging is a commonly used approach to investigate the biophysical mechanism of orientation‐dependent signal phase evolution in white matter. Yet, how phase measurements are influenced by the structural alteration in the tissue after formalin fixation is not fully understood. Here, we study the effects on magnetic susceptibility, microstructural compartmentalization, and chemical exchange measurement with a postmortem formalin‐fixed whole‐brain human tissue.

Methods

A formalin‐fixed, postmortem human brain specimen was scanned with multiple orientations to the main magnetic field direction for robust bulk magnetic susceptibility measurement with conventional quantitative susceptibility imaging models. White matter samples were subsequently excised from the whole‐brain specimen and scanned in multiple rotations on an MRI scanner to measure the anisotropic magnetic susceptibility and microstructure‐related contributions in the signal phase and to validate the findings of the whole‐brain data.

Results

The bulk isotropic magnetic susceptibility of ex vivo whole‐brain imaging is comparable to in vivo imaging, with noticeable enhanced nonsusceptibility contributions. The excised specimen experiment reveals that anisotropic magnetic susceptibility and compartmentalization phase effect were considerably reduced in the formalin‐fixed white matter specimens.

Conclusions

Formalin‐fixed postmortem white matter exhibits comparable isotropic magnetic susceptibility to previous in vivo imaging findings. However, the measured phase and magnitude data of the fixed white matter tissue shows a significantly weaker orientation dependency and compartmentalization effect. Alternatives to formalin fixation are needed to better reproduce the in vivo microstructural effects in postmortem samples.

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%.

A nine-channel transmit/receive array for spine imaging at 10.5 T: Introduction to a nonuniform dielectric substrate antenna

PURPOSE

The purpose of this study is to introduce a new antenna element with improved transmit performance, named the nonuniform dielectric substrate (NODES) antenna, for building transmit arrays at ultrahigh-field.

METHODS

We optimized a dipole antenna at 10.5 Tesla by maximizing the B 1 + -SAR efficiency in a phantom for a human spine target. The optimization parameters included permittivity variation in the substrate, substrate thickness, antenna length, and conductor geometry. We conducted electromagnetic simulations as well as phantom experiments to compare the transmit/receive performance of the proposed NODES antenna design with existing coil elements from the literature.

RESULTS

Single NODES element showed up to 18% and 30% higher B 1 + -SAR efficiency than the fractionated dipole and loop elements, respectively. The new element is substantially shorter than a commonly used dipole, which enables z-stacked array formation; it is additionally capable of providing a relatively uniform current distribution along its conductors. The nine-channel transmit/receive NODES array achieved 7.5% higher B 1 + homogeneity than a loop array with the same number of elements. Excitation with the NODES array resulted in 33% lower peak 10g-averaged SAR and required 34% lower input power than the loop array for the target anatomy of the spine.

CONCLUSION

In this study, we introduced a new RF coil element: the NODES antenna. NODES antenna outperformed the widely used loop and dipole elements and may provide improved transmit/receive performance for future ultrahigh field MRI applications.

New Prospects for Ultra-High-Field Magnetic Resonance Imaging in Multiple Sclerosis

ABSTRACT

There is growing interest in imaging multiple sclerosis (MS) through the ultra-high-field (UHF) lens, which currently means a static magnetic field strength of 7 T or higher. Because of higher signal-to-noise ratio and enhanced susceptibility effects, UHF magnetic resonance imaging improves conspicuity of MS pathological hallmarks, among them cortical demyelination and the central vein sign. This could, in turn, improve confidence in MS diagnosis and might also facilitate therapeutic monitoring of MS patients. Furthermore, UHF imaging offers unique insight into iron-related pathology, leptomeningeal inflammation, and spinal cord pathologies in neuroinflammation. Yet, limitations such as the longer scanning times to achieve improved resolution and incipient safety data on implanted medical devices need to be considered. In this review, we discuss applications of UHF imaging in MS, its advantages and limitations, and practical aspects of UHF in the clinical setting.

7 Tesla and Beyond: Advanced Methods and Clinical Applications in Magnetic Resonance Imaging

ABSTRACT

Ultrahigh magnetic fields offer significantly higher signal-to-noise ratio, and several magnetic resonance applications additionally benefit from a higher contrast-to-noise ratio, with static magnetic field strengths of B0 ≥ 7 T currently being referred to as ultrahigh fields (UHFs). The advantages of UHF can be used to resolve structures more precisely or to visualize physiological/pathophysiological effects that would be difficult or even impossible to detect at lower field strengths. However, with these advantages also come challenges, such as inhomogeneities applying standard radiofrequency excitation techniques, higher energy deposition in the human body, and enhanced B0 field inhomogeneities. The advantages but also the challenges of UHF as well as promising advanced methodological developments and clinical applications that particularly benefit from UHF are discussed in this review article.

A 16-Channel Dipole Antenna Array for Human Head Magnetic Resonance Imaging at 10.5 Tesla

For ultra-high field and frequency (UHF) magnetic resonance imaging (MRI), the associated short wavelengths in biological tissues leads to penetration and homogeneity issues at 10.5 tesla (T) and require antenna transmit arrays for efficiently generated 447 MHz B₁⁺ fields (defined as the transmit radiofrequency (RF) magnetic field generated by RF coils). Previously, we evaluated a 16-channel combined loop + dipole antenna (LD) 10.5 T head array. While the LD array configuration did not achieve the desired B₁⁺ efficiency, it showed an improvement of the specific absorption rate (SAR) efficiency compared to the separate 8-channel loop and separate 8-channel dipole antenna arrays at 10.5 T. Here we compare a 16-channel dipole antenna array with a 16-channel LD array of the same dimensions to evaluate B₁⁺ efficiency, 10 g SAR, and SAR efficiency. The 16-channel dipole antenna array achieved a 24% increase in B₁⁺ efficiency in the electromagnetic simulation and MR experiment compared to the LD array, as measured in the central region of a phantom. Based on the simulation results with a human model, we estimate that a 16-channel dipole antenna array for human brain imaging can increase B₁⁺ efficiency by 15% with similar SAR efficiency compared to a 16-channel LD head array.

Paradoxical paramagnetic calcifications in the globus pallidus: An ex vivo MR investigation and histological validation study

MR images based on phase contrast images have gained clinical interest as an in vivo tool for assessing anatomical and histological findings. The globus pallidus is an area of major iron metabolism and storage in the brain tissue. Calcium, another important metal in the body, is frequently deposited in the globus pallidus as well. Recently, we observed dense paramagnetic deposition with paradoxical calcifications in the globus pallidus and putamen. In this work, we explore detailed MR findings on these structures, and the histological source of the related findings using ex vivo CT and MR images. Ex vivo MR was obtained with a maximum 100 μm³ isotropic resolution using a 15.2 T MR system. 3D gradient echo images and quantitative susceptibility mapping were used because of their good sensitivity to metallic deposition, high signal-to-noise ratio, and excellent contrast to iron and calcium. We found dense paramagnetic deposition along the perforating arteries in the globus pallidus. This paramagnetic deposition was hyperdense on ex vivo CT scans. Histological studies confirmed this finding, and simultaneous deposition of iron and calcium, although more iron dominant, was observed along the vessel walls of the globus pallidus. This was an exclusive finding for the penetrating arteries of the globus pallidus. Thus, our results suggest that several strong and paradoxical paramagnetic sources at the globus pallidus can be associated with vascular degeneration.

Evaluation of 8-Channel Radiative Antenna Arrays for Human Head Imaging at 10.5 Tesla

For human head magnetic resonance imaging at 10.5 tesla (T), we built an 8-channel transceiver dipole antenna array and evaluated the influence of coaxial feed cables. The influence of coaxial feed cables was evaluated in simulation and compared against a physically constructed array in terms of transmit magnetic field (B₁⁺) and specific absorption rate (SAR) efficiency. A substantial drop (23.1% in simulation and 20.7% in experiment) in B₁⁺ efficiency was observed with a tight coaxial feed cable setup. For the investigation of the feed location, the center-fed dipole antenna array was compared to two 8-channel end-fed arrays: monopole and sleeve antenna arrays. The simulation results with a phantom indicate that these arrays achieved ~24% higher SAR efficiency compared to the dipole antenna array. For a human head model, we observed 30.8% lower SAR efficiency with the 8-channel monopole antenna array compared to the phantom. Importantly, our simulation with the human model indicates that the sleeve antenna arrays can achieve 23.8% and 21% higher SAR efficiency compared to the dipole and monopole antenna arrays, respectively. Finally, we obtained high-resolution human cadaver images at 10.5 T with the 8-channel sleeve antenna array.

Quantitative MRI susceptibility mapping reveals cortical signatures of changes in iron, calcium and zinc in malformations of cortical development in children with drug-resistant epilepsy

OBJECTIVE

Malformations of cortical development (MCD), including focal cortical dysplasia (FCD), are the most common cause of drug-resistant focal epilepsy in children. Histopathological lesion characterisation demonstrates abnormal cell types and lamination, alterations in myelin (typically co-localised with iron), and sometimes calcification. Quantitative susceptibility mapping (QSM) is an emerging MRI technique that measures tissue magnetic susceptibility (χ) reflecting it's mineral composition. We used QSM to investigate abnormal tissue composition in a group of children with focal epilepsy with comparison to effective transverse relaxation rate (R2*) and Synchrotron radiation X-ray fluorescence (SRXRF) elemental maps. Our primary hypothesis was that reductions in χ would be found in FCD lesions, resulting from alterations in their iron and calcium content. We also evaluated deep grey matter nuclei for changes in χ with age.

METHODS

QSM and R2* maps were calculated for 40 paediatric patients with suspected MCD (18 histologically confirmed) and 17 age-matched controls. Patients' sub-groups were defined based on concordant electro-clinical or histopathology data. Quantitative investigation of QSM and R2* was performed within lesions, using a surface-based approach with comparison to homologous regions, and within deep brain regions using a voxel-based approach with regional values modelled with age and epilepsy as covariates. Synchrotron radiation X-ray fluorescence (SRXRF) was performed on brain tissue resected from 4 patients to map changes in iron, calcium and zinc and relate them to MRI parameters.

RESULTS

Compared to fluid-attenuated inversion recovery (FLAIR) or T1-weighted imaging, QSM improved lesion conspicuity in 5% of patients. In patients with well-localised lesions, quantitative profiling demonstrated decreased χ, but not R2*, across cortical depth with respect to the homologous regions. Contra-lateral homologous regions additionally exhibited increased χ at 2-3 mm cortical depth that was absent in lesions. The iron decrease measured by the SRXRF in FCDIIb lesions was in agreement with myelin reduction observed by Luxol Fast Blue histochemical staining. SRXRF analysis in two FCDIIb tissue samples showed increased zinc and calcium in one patient, and decreased iron in the brain region exhibiting low χ and high R2* in both patients. QSM revealed expected age-related changes in the striatum nuclei, substantia nigra, sub-thalamic and red nucleus.

CONCLUSION

QSM non-invasively revealed cortical/sub-cortical tissue alterations in MCD lesions and in particular that χ changes in FCDIIb lesions were consistent with reduced iron, co-localised with low myelin and increased calcium and zinc content. These findings suggest that measurements of cortical χ could be used to characterise tissue properties non-invasively in epilepsy lesions.