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

Seven-tesla magnetic resonance imaging in Wilson disease using quantitative susceptibility mapping for measurement of copper accumulation

OBJECTIVES

In Wilson disease (WD), the copper content of cerebral tissue is increased, particularly in the basal ganglia. This study investigated whether a change in magnetic susceptibility can be detected using quantitative susceptibility mapping of the brain in patients with WD compared with healthy controls.

MATERIALS AND METHODS

Eleven patients with WD (6 with the neurological form, 5 with the hepatic form) and 10 age-matched healthy controls who gave informed consent were examined at 7 T in a whole-body scanner (MAGNETOM; Siemens Medical Solutions, Erlangen, Germany) using a 24-channel phased array coil (Nova Medical). For imaging, a 3-dimensional spoiled gradient multiecho sequence (repetition time, 40 milliseconds; echo time, 9.76/19.19/28.62 milliseconds; bandwidth, 150 hertz per pixel; voxel size, 0.6 × 0.6 × 0.8 mm) was used. The susceptibility of selected regions (substantia nigra, red nucleus, pallidum, putamen, caudate nucleus) was analyzed in susceptibility maps.

RESULTS

The patients with WD showed significantly increased susceptibility (P value, 0.001-0.05) in all analyzed regions compared with healthy controls. This was evident not only in patients with a neurological syndrome but also, with lower values, in patients with isolated hepatic manifestations. The distribution patterns of copper accumulation were different between the patients with neurological and non-neurological manifestations of the disease.

CONCLUSIONS

In neurologically symptomatic and asymptomatic patients with WD, we found increased magnetic susceptibility in the brain tissue using quantitative susceptibility mapping.

Multi-modal ultra-high resolution structural 7-Tesla MRI data repository

Structural brain data is key for the understanding of brain function and networks, i.e., connectomics. Here we present data sets available from the 'atlasing of the basal ganglia (ATAG)' project, which provides ultra-high resolution 7 Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. The ATAG data set includes whole-brain and reduced field-of-view MP2RAGE and T2*-weighted scans of the subcortex and brainstem with ultra-high resolution at a sub-millimeter scale. The data can be used to develop new algorithms that help building high-resolution atlases both relevant for the basic and clinical neurosciences. Importantly, the present data repository may also be used to inform the exact positioning of electrodes used for deep-brain-stimulation in patients with Parkinson's disease and neuropsychiatric diseases.

Phase-corrected bipolar gradients in multi-echo gradient-echo sequences for quantitative susceptibility mapping

OBJECTIVE

Large echo spacing of unipolar readout gradients in current multi-echo gradient-echo (GRE) sequences for mapping fields in quantitative susceptibility mapping (QSM) can be reduced using bipolar readout gradients thereby improving acquisition efficiency.

MATERIALS AND METHODS

Phase discrepancies between odd and even echoes in the bipolar readout gradients caused by non-ideal gradient behaviors were measured, modeled as polynomials in space and corrected for accordingly in field mapping. The bipolar approach for multi-echo GRE field mapping was compared with the unipolar approach for QSM.

RESULTS

The odd-even-echo phase discrepancies were approximately constant along the phase encoding direction and linear along the readout and slice-selection directions. A simple linear phase correction in all three spatial directions was shown to enable accurate QSM of the human brain using a bipolar multi-echo GRE sequence. Bipolar multi-echo acquisition provides QSM in good quantitative agreement with unipolar acquisition while also reducing noise.

CONCLUSION

With a linear phase correction between odd-even echoes, bipolar readout gradients can be used in multi-echo GRE sequences for QSM.

Reproducibility of T2 * mapping in the human cerebral cortex in vivo at 7 tesla MRI

BACKGROUND

To assess the test-retest reproducibility of cortical mapping of T2 * relaxation rates at 7 Tesla (T) MRI. T2 * maps have been used for studying cortical myelo-architecture patterns in vivo and for characterizing conditions associated with changes in iron and/or myelin concentration.

METHODS

T2 * maps were calculated from 7T multi-echo T2 *-weighted images acquired during separate scanning sessions on 8 healthy subjects. The reproducibility of surface-based cortical T2 * mapping was assessed at different depths of the cortex; from pial surface (0% depth) towards gray/white matter boundary (100% depth), across cortical regions and hemispheres, using coefficients of variation (COVs = SD/mean) between each couple (scan-rescan) of average T2 * measurements.

RESULTS

Average cortical T2 * was significantly different among 25%, 50%, and 75% depths (analysis of variance, P < 0.001). Coefficient of variations were very low within cortical regions, and whole cortex (average COV = 0.83-1.79%), indicating a high degree of reproducibility in T2 * measures.

CONCLUSION

Surface-based mapping of T2 * relaxation rates as a function of cortical depth is reproducible and could prove useful for studying the laminar architecture of the cerebral cortex in vivo, and for investigating physiological and pathological states associated with changes in iron and/or myelin concentration.

Ultra-high field magnetic resonance imaging of the basal ganglia and related structures

Deep brain stimulation is a treatment for Parkinson's disease and other related disorders, involving the surgical placement of electrodes in the deeply situated basal ganglia or thalamic structures. Good clinical outcome requires accurate targeting. However, due to limited visibility of the target structures on routine clinical MR images, direct targeting of structures can be challenging. Non-clinical MR scanners with ultra-high magnetic field (7T or higher) have the potential to improve the quality of these images. This technology report provides an overview of the current possibilities of visualizing deep brain stimulation targets and their related structures with the aid of ultra-high field MRI. Reviewed studies showed improved resolution, contrast- and signal-to-noise ratios at ultra-high field. Sequences sensitive to magnetic susceptibility such as T2^* and susceptibility weighted imaging and their maps in general showed the best visualization of target structures, including a separation between the subthalamic nucleus and the substantia nigra, the lamina pallidi medialis and lamina pallidi incompleta within the globus pallidus and substructures of the thalamus, including the ventral intermediate nucleus (Vim). This shows that the visibility, identification, and even subdivision of the small deep brain stimulation targets benefit from increased field strength. Although ultra-high field MR imaging is associated with increased risk of geometrical distortions, it has been shown that these distortions can be avoided or corrected to the extent where the effects are limited. The availability of ultra-high field MR scanners for humans seems to provide opportunities for a more accurate targeting for deep brain stimulation in patients with Parkinson's disease and related disorders.

Quantitative susceptibility mapping: current status and future directions

Quantitative susceptibility mapping (QSM) is a new technique for quantifying magnetic susceptibility. It has already found various applications in quantifying in vivo iron content, calcifications and changes in venous oxygen saturation. The accuracy of susceptibility mapping is dependent on several factors. In this review, we evaluate the entire process of QSM from data acquisition to individual data processing steps. We also show preliminary results of several new concepts introduced in this review in an attempt to improve the quality and accuracy for certain steps. The uncertainties in estimating susceptibility differences using susceptibility maps, phase images, and T2* maps are analyzed and compared. Finally, example clinical applications are presented. We conclude that QSM holds great promise in quantifying iron and becoming a standard clinical tool.

Quantitative susceptibility mapping of human brain at 3T: a multisite reproducibility study

BACKGROUND AND PURPOSE

Quantitative susceptibility mapping of the human brain has demonstrated strong potential in examining iron deposition, which may help in investigating possible brain pathology. This study assesses the reproducibility of quantitative susceptibility mapping across different imaging sites.

MATERIALS AND METHODS

In this study, the susceptibility values of 5 regions of interest in the human brain were measured on 9 healthy subjects following calibration by using phantom experiments. Each of the subjects was imaged 5 times on 1 scanner with the same procedure repeated on 3 different 3T systems so that both within-site and cross-site quantitative susceptibility mapping precision levels could be assessed. Two quantitative susceptibility mapping algorithms, similar in principle, one by using iterative regularization (iterative quantitative susceptibility mapping) and the other with analytic optimal solutions (deterministic quantitative susceptibility mapping), were implemented, and their performances were compared.

RESULTS

Results show that while deterministic quantitative susceptibility mapping had nearly 700 times faster computation speed, residual streaking artifacts seem to be more prominent compared with iterative quantitative susceptibility mapping. With quantitative susceptibility mapping, the putamen, globus pallidus, and caudate nucleus showed smaller imprecision on the order of 0.005 ppm, whereas the red nucleus and substantia nigra, closer to the skull base, had a somewhat larger imprecision of approximately 0.01 ppm. Cross-site errors were not significantly larger than within-site errors. Possible sources of estimation errors are discussed.

CONCLUSIONS

The reproducibility of quantitative susceptibility mapping in the human brain in vivo is regionally dependent, and the precision levels achieved with quantitative susceptibility mapping should allow longitudinal and multisite studies such as aging-related changes in brain tissue magnetic susceptibility.

Association between increased magnetic susceptibility of deep gray matter nuclei and decreased motor function in healthy adults

In the human brain, iron is more prevalent in gray matter than in white matter, and deep gray matter structures, particularly the globus pallidus, putamen, caudate nucleus, substantia nigra, red nucleus, and dentate nucleus, exhibit especially high iron content. Abnormally elevated iron levels have been found in various neurodegenerative diseases. Additionally, iron overload and related neurodegeneration may also occur during aging, but the functional consequences are not clear. In this study, we explored the correlation between magnetic susceptibility--a surrogate marker of brain iron--of these gray matter structures with behavioral measures of motor and cognitive abilities, in 132 healthy adults aged 40-83 years. Latent variables corresponding to manual dexterity and executive functions were obtained using factor analysis. The factor scores for manual dexterity declined significantly with increasing age. Independent of gender, age, and global cognitive function, increasing magnetic susceptibility in the globus pallidus and red nuclei was associated with decreasing manual dexterity. This finding suggests the potential value of magnetic susceptibility, a non-invasive quantitative imaging marker of iron, for the study of iron-related brain function changes.

Quantification of iron in the non-human primate brain with diffusion-weighted magnetic resonance imaging

Pathological iron deposits in the brain, especially within basal ganglia, are linked to severe neurodegenerative disorders like Parkinson's disease. As iron induces local changes in magnetic susceptibility, its presence can be visualized with magnetic resonance imaging (MRI). The usual approach, based on iron induced changes in magnetic relaxation (T2/T2'), is often prone, however, to confounding artifacts and lacks specificity. Here, we propose a new method to quantify and map iron deposits using water diffusion MRI. This method is based on the differential sensitivity of two image acquisition schemes to the local magnetic field gradients induced by iron deposits and their cross-term with gradient pulses used for diffusion encoding. Iron concentration could be imaged and estimated with high accuracy in the brain cortex, the thalamus, the substantia nigra and the globus pallidus of macaques, showing iron distributions in agreement with literature. Additionally, iron maps could clearly show a dramatic increase in iron content upon injection of an UltraSmall Particle Iron Oxide (USPIO) contrast agent, notably in the cortex and the thalamus, reflecting regional differences in blood volume. The method will benefit clinical investigations on the effect of iron deposits in the brain or other organs, as iron deposits are increasingly seen as a biomarker for a wide range of diseases, notably, neurodegenerative diseases in the pre-symptomatic stage. It also has the potential for quantifying variations in blood volume induced by brain activation in fMRI studies using USPIOs.

A gradual increase of iron toward the medial-inferior tip of the subthalamic nucleus

The subthalamic nucleus (STN) is an important node of the cortico-basal ganglia network and the main target of deep brain stimulation (DBS) in Parkinson's disease. Histological studies have revealed an inhomogeneous iron distribution within the STN, which has been related to putative subdivisions within this nucleus. Here, we investigate the iron distribution in more detail using quantitative susceptibility mapping (QSM), a novel magnetic resonance imaging (MRI) contrast mechanism. QSM allows for detailed assessment of iron content in both in vivo and postmortem tissue. Twelve human participants and 7 postmortem brain samples containing the STN were scanned using ultra-high field 7 Tesla (T) MRI. Iron concentrations were found to be higher in the medial-inferior tip of the STN. Using quantitative methods we show that the increase of iron concentration towards the medial-inferior tip is of a gradual rather than a discrete nature.

Cerebellar pathology in Friedreich's ataxia: atrophied dentate nuclei with normal iron content

BACKGROUND

In Friedreich's ataxia (FA) the genetically decreased expression of the mitochondrial protein frataxin leads to disturbance of the mitochondrial iron metabolism. Within the cerebellum the dentate nuclei (DN) are primarily affected. Histopathological studies show atrophy and accumulation of mitochondrial iron in DN. Dentate iron content has been suggested as a biomarker to measure the effects of siderophores/antioxidant treatment of FA. We assessed the iron content and the volume of DN in FA patients and controls based on ultra-high-field MRI (7 Tesla) images.

METHODS

Fourteen FA patients (mean age 38.1 yrs) and 14 age- and gender-matched controls participated. Multi-echo gradient echo and susceptibility weighted imaging (SWI) sequences were acquired on a 7 T whole-body scanner. For comparison SWI images were acquired on a 1.5 T MR scanner. Volumes of the DN and cerebellum were assessed at 7 and 1.5 T, respectively. Parametric maps of T2 and T2* sequences were created and proton transverse relaxation rates were estimated as a measure of iron content.

RESULTS

In FA, the DN and the cerebellum were significantly smaller compared to controls. However, proton transverse relaxation rates of the DN were not significantly different between both groups.

CONCLUSIONS

Applying in vivo MRI methods we could demonstrate significant atrophy of the DN in the presence of normal iron content. The findings suggest that relaxation rates are not reliable biomarkers in clinical trials evaluating the potential effect of FA therapy.

Mean magnetic susceptibility regularized susceptibility tensor imaging (MMSR-STI) for estimating orientations of white matter fibers in human brain

PURPOSE

An increasing number of studies show that magnetic susceptibility in white matter fibers is anisotropic and may be described by a tensor. However, the limited head rotation possible for in vivo human studies leads to an ill-conditioned inverse problem in susceptibility tensor imaging (STI). Here we suggest the combined use of limiting the susceptibility anisotropy to white matter and imposing morphology constraints on the mean magnetic susceptibility (MMS) for regularizing the STI inverse problem.

METHODS

The proposed MMS regularized STI (MMSR-STI) method was tested using computer simulations and in vivo human data collected at 3T. The fiber orientation estimated from both the STI and MMSR-STI methods was compared to that from diffusion tensor imaging (DTI).

RESULTS

Computer simulations show that the MMSR-STI method provides a more accurate estimation of the susceptibility tensor than the conventional STI approach. Similarly, in vivo data show that use of the MMSR-STI method leads to a smaller difference between the fiber orientation estimated from STI and DTI for most selected white matter fibers.

CONCLUSION

The proposed regularization strategy for STI can improve estimation of the susceptibility tensor in white matter.

Joint estimation of chemical shift and quantitative susceptibility mapping (chemical QSM)

PURPOSE

The purpose of this work is to address the unsolved problem of quantitative susceptibility mapping (QSM) of tissue with fat where both fat and susceptibility change the MR signal phase.

THEORY AND METHODS

The chemical shift of fat was treated as an additional unknown and was estimated jointly with susceptibility to provide the best data fitting using an automated and iterative algorithm. A simplified susceptibility model was used to calculate an updated value of the chemical shift based on the local magnetic field in each iteration. Numerical simulation, phantom experiments and in vivo imaging were performed. Artifacts were assessed by measuring the susceptibility variance in uniform regions. Accuracy was assessed by comparison with ground truth in simulation, and using a susceptibility matching approach in phantom.

RESULTS

Using the proposed method, artifacts on the QSM image were markedly suppressed in all tested datasets compared with results generated using fixed chemical shifts. Accuracy of the estimated susceptibility was also improved in numerical simulation and phantom experiments.

CONCLUSION

A joint estimation of fat content and magnetic susceptibility using an iterative chemical shift update was shown to improve image quality and accuracy on QSM images.

Direct visualization of anatomic subfields within the superior aspect of the human lateral thalamus by MRI at 7T

BACKGROUND AND PURPOSE

The morphology of the human thalamus shows high interindividual variability. Therefore, direct visualization of landmarks within the thalamus is essential for an improved definition of electrode positions for deep brain stimulation. The aim of this study was to provide anatomic detail in the thalamus by using inversion recovery TSE imaging at 7T.

MATERIALS AND METHODS

The MR imaging protocol was optimized on 1 healthy subject to segment thalamic nuclei from one another. Final images, acquired with 0.5(2)-mm2 in-plane resolution and 3-mm section thickness, were compared with stereotactic brain atlases to assign visualized details to known anatomy. The robustness of the visualization of thalamic nuclei was assessed with 4 healthy subjects at lower image resolution.

RESULTS

Thalamic subfields were successfully delineated in the dorsal aspect of the lateral thalamus. T1-weighting was essential. MR images had an appearance very similar to that of myelin-stained sections seen in brain atlases. Visualized intrathalamic structures were, among others, the lamella medialis, the external medullary lamina, the reticulatum thalami, the nucleus centre médian, the boundary between the nuclei dorso-oralis internus and externus, and the boundary between the nuclei dorso-oralis internus and zentrolateralis intermedius internus.

CONCLUSIONS

Inversion recovery-prepared TSE imaging at 7T has a high potential to reveal fine anatomic detail in the thalamus, which may be helpful in enhancing the planning of stereotactic neurosurgery in the future.

Multiple sclerosis: improved identification of disease-relevant changes in gray and white matter by using susceptibility-based MR imaging

PURPOSE

To evaluate the potential of quantitative susceptibility (QS) and R2* mapping as surrogate biomarkers of clinically relevant, age-adjusted demyelination and iron deposition in multiple sclerosis (MS).

MATERIALS AND METHODS

All study participants gave written informed consent, and the study was approved by the institutional review board. Quantitative maps of the magnetic resonance imaging susceptibility parameters (R2* and QS) were computed for 25 patients with either clinically isolated syndrome (CIS) or relapsing-remitting MS, as well as for 15 age- and sex-matched control subjects imaged at 7 T. The candidate MR imaging biomarkers were correlated with Extended Disability Status Scale (EDSS), time since CIS diagnosis, time since MS diagnosis, and age.

RESULTS

QS maps aided identification of significant, voxel-level increases in iron deposition in subcortical gray matter (GM) of patients with MS compared with control subjects. These voxel-level increases were not observed on R2* maps. Region-of-interest analysis of mean R2* and QS in subcortical GM demonstrated that R2* (R ≥ 0.39, P < .01) and QS (R ≥ 0.44, P < .01) were strongly correlated with EDSS. In white matter (WM), the volume of total WM damage (defined by a z score of less than -2.0 criterion, indicating demyelination) on QS maps correlated significantly with EDSS (R = 0.46, P = .02). Voxelwise QS also supported a significant contribution of age to demyelination in patients with MS, suggesting that age-adjusted clinical scores may provide more robust measures of MS disease severity compared with non-age-adjusted scores.

CONCLUSION

Using QS and R2* mapping, evidence of both significant increases in iron deposition in subcortical GM and myelin degeneration along the WM skeleton of patients with MS was identified. Both effects correlated strongly with EDSS.

Quantification of cerebral perfusion using dynamic quantitative susceptibility mapping

PURPOSE

The purpose of this study is to develop a dynamic quantitative susceptibility mapping (QSM) technique with sufficient temporal resolution to map contrast agent concentration in cerebral perfusion imaging.

METHODS

The dynamic QSM used a multiecho three-dimensional (3D) spoiled gradient echo golden angle interleaved spiral sequence during contrast bolus injection. Four-dimensional (4D) space-time resolved magnetic field reconstruction was performed using the temporal resolution acceleration with constrained evolution reconstruction method. Deconvolution of the gadolinium-induced field was performed at each time point with the morphology enabled dipole inversion method to generate a 4D gadolinium concentration map, from which three-dimensional spatial distributions of cerebral blood volume and cerebral blood flow were computed.

RESULTS

Initial in vivo brain imaging demonstrated the feasibility of using dynamic QSM for generating quantitative 4D contrast agent maps and imaging three-dimensional perfusion. The cerebral blood flow obtained with dynamic QSM agreed with that obtained using arterial spin labeling.

CONCLUSION

Dynamic QSM can be used to perform 4D mapping of contrast agent concentration in contrast-enhanced magnetic resonance imaging. The perfusion parameters derived from this 4D contrast agent concentration map were in good agreement with those obtained using arterial spin labeling.

Quantifying inter-individual anatomical variability in the subcortex using 7 T structural MRI

Functional magnetic resonance imaging (MRI) data are usually registered into standard anatomical space. However, standard atlases, such as LPBA40, the Harvard-Oxford atlas, FreeSurfer, and the Jülich cytoarchitectonic maps all lack important detailed information about small subcortical structures like the substantia nigra and subthalamic nucleus. Here we introduce a new subcortical probabilistic atlas based on ultra-high resolution in-vivo anatomical imaging from 7 T MRI. The atlas includes six important but elusive subcortical nuclei: the striatum, the globus pallidus internal and external segment (GPi/e), the subthalamic nucleus, the substantia nigra, and the red nucleus. With a sample of 30 young subjects and carefully cross-validated delineation protocols, our atlas is able to capture the anatomical variability within healthy populations for each of the included structures at an unprecedented level of detail. All the generated probabilistic atlases are registered to MNI standard space and are publicly available.

Do we need to revise the tripartite subdivision hypothesis of the human subthalamic nucleus (STN)?

The exciting development of ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) has made it possible to clearly visualize and delineate the subthalamic nucleus (STN). Ultra-high resolution MRI provides a first step in the ongoing improvement of imaging techniques rendering it likely that in the near future specific subareas of small brain nuclei such as the STN can be visualized. These developments can contribute to improve clinical imaging, allowing even more accurate targeting of the STN. This is interesting in view of putative limbic, associative, and sensomotoric subdivisions within the STN. The concept of anatomically distinct subdivisions is attractive, both from an anatomical as well as a clinical perspective. However, we argue that the current leading hypothesis of three STN subdivisions is based on low numbers of clinical observations and primate tracing studies. 7T imaging provides us with markers that could potentially help us to distinguish subdivisions, but our preliminary findings do not indicate the existence of subdivisions. In our opinion additional research is needed. As a consequence the tripartite hypothesis should therefore still be a topic of debate. In view of the possible clinical implications, we would like to raise the question whether anatomical evidence on the topological organization within the STN points towards delineated subdivisions, or an organization without strict anatomical boundaries or septa. The latter would require a revision of the current tripartite hypothesis of the human STN.

Background field removal by solving the Laplacian boundary value problem

The removal of the background magnetic field is a critical step in generating phase images and quantitative susceptibility maps, which have recently been receiving increasing attention. Although it is known that the background field satisfies Laplace's equation, the boundary values of the background field for the region of interest have not been explicitly addressed in the existing methods, and they are not directly available from MRI measurements. In this paper, we assume simple boundary conditions and remove the background field by explicitly solving the boundary value problems of Laplace's or Poisson's equation. The proposed Laplacian boundary value (LBV) method for background field removal retains data near the boundary and is computationally efficient. Tests on a numerical phantom and an experimental phantom showed that LBV was more accurate than two existing methods.

Origins of R2* orientation dependence in gray and white matter

Estimates of the apparent transverse relaxation rate (R2*) can be used to quantify important properties of biological tissue. Surprisingly, the mechanism of R2* dependence on tissue orientation is not well understood. The primary goal of this paper was to characterize orientation dependence of R2* in gray and white matter and relate it to independent measurements of two other susceptibility based parameters: the local Larmor frequency shift (fL) and quantitative volume magnetic susceptibility (Δχ). Through this comparative analysis we calculated scaling relations quantifying R2' (reversible contribution to the transverse relaxation rate from local field inhomogeneities) in a voxel given measurements of the local Larmor frequency shift. R2' is a measure of both perturber geometry and density and is related to tissue microstructure. Additionally, two methods (the Generalized Lorentzian model and iterative dipole inversion) for calculating Δχ were compared in gray and white matter. The value of Δχ derived from fitting the Generalized Lorentzian model was then connected to the observed R2* orientation dependence using image-registered optical density measurements from histochemical staining. Our results demonstrate that the R2* and fL of white and cortical gray matter are well described by a sinusoidal dependence on the orientation of the tissue and a linear dependence on the volume fraction of myelin in the tissue. In deep brain gray matter structures, where there is no obvious symmetry axis, R2* and fL have no orientation dependence but retain a linear dependence on tissue iron concentration and hence Δχ.

In vivo normative atlas of the hippocampal subfields using multi-echo susceptibility imaging at 7 Tesla

OBJECTIVES

To generate a high-resolution atlas of the hippocampal subfields using images acquired from 7 T, multi-echo, gradient-echo MRI for the evaluation of epilepsy and neurodegenerative disorders as well as investigating R2* (apparent transverse relaxation rate) and quantitative volume magnetic susceptibility (QS) of the subfields.

EXPERIMENTAL DESIGN

Healthy control subjects (n=17) were scanned at 7 T using a multi-echo gradient-echo sequence and susceptibility-weighted magnitude images, R2* and QS maps were reconstructed. We defined a hippocampal subfield labeling protocol for the magnitude image produced from the average of all echoes and assessed reproducibility through volume and shape metrics. A group-wise diffeomorphic registration procedure was used to generate an average atlas of the subfields for the whole subject cohort. The quantitative MRI maps and subfield labels were then warped to the average atlas space and used to measure mean values of R2* and QS characterizing each subfield.

PRINCIPAL OBSERVATIONS

We were able to reliably label hippocampal subfields on the multi-echo susceptibility images. The group-averaged atlas accurately aligns these structures to produce a high-resolution depiction of the subfields, allowing assessment of both quantitative susceptibility and R2* across subjects. Our analysis of variance demonstrates that there are more apparent differences between the subfields on these quantitative maps than the normalized magnitude images.

CONCLUSION

We constructed a high-resolution atlas of the hippocampal subfields for use in voxel-based studies and demonstrated in vivo quantification of susceptibility and R2* in the subfields. This work is the first in vivo quantification of susceptibility values within the hippocampal subfields at 7 T.

In vivo quantitative susceptibility mapping (QSM) in Alzheimer's disease

Background

This study explores the magnetostatic properties of the Alzheimer's disease brain using a recently proposed, magnetic resonance imaging, postprocessed contrast mechanism. Quantitative susceptibility mapping (QSM) has the potential to monitor in vivo iron levels by reconstructing magnetic susceptibility sources from field perturbations. However, with phase data acquired at a single head orientation, the technique relies on several theoretical approximations and requires fast-evolving regularisation strategies.

Methods

In this context, the present study describes a complete methodological framework for magnetic susceptibility measurements with a review of its theoretical foundations.

Findings and Significance

The regional and whole-brain cross-sectional comparisons between Alzheimer's disease subjects and matched controls indicate that there may be significant magnetic susceptibility differences for deep brain nuclei – particularly the putamen – as well as for posterior grey and white matter regions. The methodology and findings described suggest that the QSM method is ready for larger-scale clinical studies.

An iterative spherical mean value method for background field removal in MRI

PURPOSE

The sophisticated harmonic artifact reduction for phase data (SHARP) method has been proposed for the removal of background field in MRI phase data. It relies on the spherical mean value (SMV) property of harmonic functions, and its accuracy depends on the radius of the sphere used for computing the SMV and truncation threshold needed for deconvolution. The goal of this study was to develop an alternative SMV-based background field removal method with reduced dependences on these parameters.

METHODS

The proposed background field removal method, termed iterative SMV (iSMV), consists of applying the SMV operation repeatedly on the field map. It was validated in a phantom and in vivo brain data of five healthy volunteers.

RESULTS

The iSMV method demonstrates accurate background field removal in the phantom. Compared with SHARP, the iSMV method shows a significantly reduced dependence on the SMV radius both in phantom and in human data. Because a smaller radius can be chosen, the iSMV method allows retaining a larger part of the region of interest compared with SHARP.

CONCLUSION

The iSMV method is an effective background field removal method with a reduced dependence on method parameters. Magn Reson Med 72:1065-1071, 2014. © 2013 Wiley Periodicals, Inc.

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

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

Differential developmental trajectories of magnetic susceptibility in human brain gray and white matter over the lifespan

As indicated by several recent studies, magnetic susceptibility of the brain is influenced mainly by myelin in the white matter and by iron deposits in the deep nuclei. Myelination and iron deposition in the brain evolve both spatially and temporally. This evolution reflects an important characteristic of normal brain development and ageing. In this study, we assessed the changes of regional susceptibility in the human brain in vivo by examining the developmental and ageing process from 1 to 83 years of age. The evolution of magnetic susceptibility over this lifespan was found to display differential trajectories between the gray and the white matter. In both cortical and subcortical white matter, an initial decrease followed by a subsequent increase in magnetic susceptibility was observed, which could be fitted by a Poisson curve. In the gray matter, including the cortical gray matter and the iron-rich deep nuclei, magnetic susceptibility displayed a monotonic increase that can be described by an exponential growth. The rate of change varied according to functional and anatomical regions of the brain. For the brain nuclei, the age-related changes of susceptibility were in good agreement with the findings from R2* measurement. Our results suggest that magnetic susceptibility may provide valuable information regarding the spatial and temporal patterns of brain myelination and iron deposition during brain maturation and ageing.

Visualization of intra-thalamic nuclei with optimized white-matter-nulled MPRAGE at 7T

Novel MR image acquisition strategies have been investigated to elicit contrast within the thalamus, but direct visualization of individual thalamic nuclei remains a challenge because of their small size and the low intrinsic contrast between adjacent nuclei. We present a step-by-step specific optimization of the 3D MPRAGE pulse sequence at 7T to visualize the intra-thalamic nuclei. We first measured T1 values within different sub-regions of the thalamus at 7T in 5 individuals. We used these to perform simulations and sequential experimental measurements (n=17) to tune the parameters of the MPRAGE sequence. The optimal set of parameters was used to collect high-quality data in 6 additional volunteers. Delineation of thalamic nuclei was performed twice by one rater and MR-defined nuclei were compared to the classic Morel histological atlas. T1 values within the thalamus ranged from 1400ms to 1800ms for adjacent nuclei. Using these values for theoretical evaluations combined with in vivo measurements, we showed that a short inversion time (TI) close to the white matter null regime (TI=670ms) enhanced the contrast between the thalamus and the surrounding tissues, and best revealed intra-thalamic contrast. At this particular nulling regime, lengthening the time between successive inversion pulses (TS=6000ms) increased the thalamic signal and contrast and lengthening the α pulse train time (N*TR) further increased the thalamic signal. Finally, a low flip angle during the gradient echo acquisition (α=4°) was observed to mitigate the blur induced by the evolution of the magnetization along the α pulse train. This optimized set of parameters enabled the 3D delineation of 15 substructures in all 6 individuals; these substructures corresponded well with the known anatomical structures of the thalamus based on the classic Morel atlas. The mean Euclidean distance between the centers of mass of MR- and Morel atlas-defined nuclei was 2.67mm (±1.02mm). The reproducibility of the MR-defined nuclei was excellent with intraclass correlation coefficient measured at 0.997 and a mean Euclidean distance between corresponding centers of mass found at first versus second readings of 0.69mm (±0.38mm). This 7T strategy paves the way to better identification of thalamic nuclei for neurosurgical planning and investigation of regional changes in neurological disorders.

Susceptibility map-weighted imaging (SMWI) for neuroimaging

PURPOSE

To propose a susceptibility map-weighted imaging (SMWI) method by combining a magnitude image with a quantitative susceptibility mapping (QSM) -based weighting factor thereby providing an alternative contrast compared with magnitude image, susceptibility-weighted imaging, and QSM.

METHODS

A three-dimensional multi-echo gradient echo sequence is used to obtain the data. The QSM was transformed to a susceptibility mask that varies in amplitude between zero and unity. This mask was multiplied several times with the original magnitude image to create alternative contrasts between tissues with different susceptibilities. A temporal domain denoising method to enhance the signal-to-noise ratio was further applied. Optimal reconstruction processes of the SMWI were determined from simulations.

RESULTS

Temporal domain denoising enhanced the signal-to-noise ratio, especially at late echoes without spatial artifacts. From phantom simulations, the optimal number of multiplication and threshold values was chosen. Reconstructed SMWI created different contrasts based on its weighting factors made from paramagnetic or diamagnetic susceptibility tissue and provided an excellent delineation of microhemorrhage without blooming artifacts typically caused by the nonlocal property of phase.

CONCLUSION

SMWI presents an alternative contrast for susceptibility-based imaging. The validity of this method was demonstrated using in vivo data. This proposed method together with denoising allows high-quality reconstruction of susceptibility-weighted image of human brain in vivo.

Quantitative oxygenation venography from MRI phase

PURPOSE

To demonstrate acquisition and processing methods for quantitative oxygenation venograms that map in vivo oxygen saturation (SvO2 ) along cerebral venous vasculature.

METHODS

Regularized quantitative susceptibility mapping (QSM) is used to reconstruct susceptibility values and estimate SvO2 in veins. QSM with ℓ1 and ℓ2 regularization are compared in numerical simulations of vessel structures with known magnetic susceptibility. Dual-echo, flow-compensated phase images are collected in three healthy volunteers to create QSM images. Bright veins in the susceptibility maps are vectorized and used to form a three-dimensional vascular mesh, or venogram, along which to display SvO2 values from QSM.

RESULTS

Quantitative oxygenation venograms that map SvO2 along brain vessels of arbitrary orientation and geometry are shown in vivo. SvO2 values in major cerebral veins lie within the normal physiological range reported by (15) O positron emission tomography. SvO2 from QSM is consistent with previous MR susceptometry methods for vessel segments oriented parallel to the main magnetic field. In vessel simulations, ℓ1 regularization results in less than 10% SvO2 absolute error across all vessel tilt orientations and provides more accurate SvO2 estimation than ℓ2 regularization.

CONCLUSION

The proposed analysis of susceptibility images enables reliable mapping of quantitative SvO2 along venograms and may facilitate clinical use of venous oxygenation imaging.

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.

Comparison of susceptibility weighted imaging and TOF-angiography for the detection of Thrombi in acute stroke

BACKGROUND AND PURPOSE

Time-of-flight (TOF) angiography detects embolic occlusion of arteries in patients with acute ischemic stroke due to the absence of blood flow in the occluded vessel. In contrast, susceptibility weighted imaging (SWI) directly enables intravascular clot visualization due to hypointense susceptibility vessel signs (SVS) in the occluded vessel. The aim of this study was to compare the diagnostic accuracy of both methods to determine vessel occlusion in patients with acute stroke.

METHODS

94 patients were included who presented with clinical symptoms for acute stroke and displayed a delay on the time-to-peak perfusion map in the territory of the anterior (ACA), middle (M1, M1/M2, M2/M3) or posterior (PCA) cerebral artery. The frequency of SVS on SWI and vessel occlusion or stenosis on TOF-angiography was compared using the McNemar-Test.

RESULTS

87 of 94 patients displayed a clearly definable SVS on SWI. In 72 patients the SVS was associated with occlusion or stenosis on TOF-angiography. Fifteen patients exclusively displayed SVS on SWI (14 M2/M3, 1 M1), whereas no patient revealed exclusively occlusion or stenosis on TOF-angiography. Sensitivity for detection of embolic occlusion within major vessel segments (M1, M1/M2, ACA, and PCA) did not show any significant difference between both techniques (97% for SWI versus 96% for TOF-angiography) while the sensitivity for detection of embolic occlusion within M2/M3 was significantly different (84% for SWI versus 39% for TOF-angiography, p<0.00012).

CONCLUSIONS

SWI and TOF-angiography provide similar sensitivity for central thrombi while SWI is superior for the detection of peripheral thrombi in small arterial vessel segments.

A computational framework for ultra-high resolution cortical segmentation at 7Tesla

This paper presents a computational framework for whole brain segmentation of 7Tesla magnetic resonance images able to handle ultra-high resolution data. The approach combines multi-object topology-preserving deformable models with shape and intensity atlases to encode prior anatomical knowledge in a computationally efficient algorithm. Experimental validation on simulated and real brain images shows accuracy and robustness of the method and demonstrates the benefits of an increased processing resolution.

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.