Incorporating a-priori information in deep learning models for quantitative susceptibility mapping via adaptive convolution

Quantitative susceptibility mapping (QSM) has attracted considerable interest for tissue characterization (e.g., iron and calcium accumulation, myelination, venous vasculature) in the human brain and relies on extensive data processing of gradient-echo MRI phase images. While deep learning-based field-to-susceptibility inversion has shown great potential, the acquisition parameters applied in clinical settings such as image resolution or image orientation with respect to the magnetic field have not been fully accounted for. Furthermore, the lack of comprehensive training data covering a wide range of acquisition parameters further limits the current QSM deep learning approaches. Here, we propose the integration of a priori information of imaging parameters into convolutional neural networks with our approach, adaptive convolution, that learns the mapping between the additional presented information (acquisition parameters) and the changes in the phase images associated with these varying acquisition parameters. By associating a-priori information with the network parameters itself, the optimal set of convolution weights is selected based on data-specific attributes, leading to generalizability towards changes in acquisition parameters. Moreover, we demonstrate the feasibility of pre-training on synthetic data and transfer learning to clinical brain data to achieve substantial improvements in the computation of susceptibility maps. The adaptive convolution 3D U-Net demonstrated generalizability in acquisition parameters on synthetic and in-vivo data and outperformed models lacking adaptive convolution or transfer learning. Further experiments demonstrate the impact of the side information on the adaptive model and assessed susceptibility map computation on simulated pathologic data sets and measured phase data.

Genotype-specific spinal cord damage in spinocerebellar ataxias: an ENIGMA-Ataxia study

BACKGROUND

Spinal cord damage is a feature of many spinocerebellar ataxias (SCAs), but well-powered in vivo studies are lacking and links with disease severity and progression remain unclear. Here we characterise cervical spinal cord morphometric abnormalities in SCA1, SCA2, SCA3 and SCA6 using a large multisite MRI dataset.

METHODS

Upper spinal cord (vertebrae C1-C4) cross-sectional area (CSA) and eccentricity (flattening) were assessed using MRI data from nine sites within the ENIGMA-Ataxia consortium, including 364 people with ataxic SCA, 56 individuals with preataxic SCA and 394 nonataxic controls. Correlations and subgroup analyses within the SCA cohorts were undertaken based on disease duration and ataxia severity.

RESULTS

Individuals in the ataxic stage of SCA1, SCA2 and SCA3, relative to non-ataxic controls, had significantly reduced CSA and increased eccentricity at all examined levels. CSA showed large effect sizes (d>2.0) and correlated with ataxia severity (r<-0.43) and disease duration (r<-0.21). Eccentricity correlated only with ataxia severity in SCA2 (r=0.28). No significant spinal cord differences were evident in SCA6. In preataxic individuals, CSA was significantly reduced in SCA2 (d=1.6) and SCA3 (d=1.7), and the SCA2 group also showed increased eccentricity (d=1.1) relative to nonataxic controls. Subgroup analyses confirmed that CSA and eccentricity are abnormal in early disease stages in SCA1, SCA2 and SCA3. CSA declined with disease progression in all, whereas eccentricity progressed only in SCA2.

CONCLUSIONS

Spinal cord abnormalities are an early and progressive feature of SCA1, SCA2 and SCA3, but not SCA6, which can be captured using quantitative MRI.

Ultra-short echo time (UTE) MR imaging: A brief review on technical considerations and clinical applications

BACKGROUND

 With the availability of MRI sequences with ultrashort echo times (UTE sequences), a signal can be gained from tissue, which was formerly only indirectly accessible. While already extensively employed in various research settings, the widespread transition of UTE imaging to clinical practice is just starting.

METHODS

 Based on a systematic literature search as well as knowledge gained through annual participation in conferences dedicated to advances in MRI, this review aims to give a brief overview of technical considerations and challenges of UTE imaging and summarizes the major areas of application of UTE imaging.

RESULTS

 UTE is already employed in clinical practice for structural lung imaging as well as the characterization of tissue composition and its alterations in selected musculoskeletal, cardiovascular, or neurodegenerative diseases. In specific contexts it can replace CT examinations with ionizing radiation and is especially attractive for pediatric patients and longitudinal monitoring of disease progression and treatment.

CONCLUSION

 UTE imaging provides an interesting and very valuable tool for various clinical purposes and promises a multitude of new insights into tissue properties. While some challenges remain, ongoing adoption in the clinical routine can be expected, as UTE approaches provide a new contrast and capture a signal in tissue formerly invisible on MR imaging.

KEY POINTS

  · UTE imaging gains relevance in clinical settings. · UTE imaging is employed for the characterization of tissue composition and its alterations in selected musculoskeletal, cardiovascular, or neurodegenerative diseases. · UTE imaging is employed in the clinical routine for structural lung imaging. · UTE imaging promises a multitude of new insights into tissue properties.

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.

Age-related differences of cerebellar cortex and nuclei: MRI findings in healthy controls and its application to spinocerebellar ataxia (SCA6) patients

Understanding cerebellar alterations due to healthy aging provides a reference point against which pathological findings in late-onset disease, for example spinocerebellar ataxia type 6 (SCA6), can be contrasted. In the present study, we investigated the impact of aging on the cerebellar nuclei and cerebellar cortex in 109 healthy controls (age range: 16 - 78 years) using 3 Tesla magnetic resonance imaging (MRI). Findings were compared with 25 SCA6 patients (age range: 38 - 78 years). A subset of 16 SCA6 (included: 14) patients and 50 controls (included: 45) received an additional MRI scan at 7 Tesla and were re-scanned after one year. MRI included T1-weighted, T2-weighted FLAIR, and multi-echo T2*-weighted imaging. The T2*-weighted phase images were converted to quantitative susceptibility maps (QSM). Since the cerebellar nuclei are characterized by elevated iron content with respect to their surroundings, two independent raters manually outlined them on the susceptibility maps. T1-weighted images acquired at 3T were utilized to automatically identify the cerebellar gray matter (GM) volume. Linear correlations revealed significant atrophy of the cerebellum due to tissue loss of cerebellar cortical GM in healthy controls with increasing age. Reduction of the cerebellar GM was substantially stronger in SCA6 patients. The volume of the dentate nuclei did not exhibit a significant relationship with age, at least in the age range between 18 and 78 years, whereas mean susceptibilities of the dentate nuclei increased with age. As previously shown, the dentate nuclei volumes were smaller and magnetic susceptibilities were lower in SCA6 patients compared to age- and sex-matched controls. The significant dentate volume loss in SCA6 patients could also be confirmed with 7T MRI. Linear mixed effects models and individual paired t-tests accounting for multiple comparisons revealed no statistical significant change in volume and susceptibility of the dentate nuclei after one year in neither patients nor controls. Importantly, dentate volumes were more sensitive to differentiate between SCA6 (Cohen's d = 3.02) and matched controls than the cerebellar cortex volume (d = 2.04). In addition to age-related decline of the cerebellar cortex and atrophy in SCA6 patients, age-related increase of susceptibility of the dentate nuclei was found in controls, whereas dentate volume and susceptibility was significantly decreased in SCA6 patients. Because no significant changes of any of these parameters was found at follow-up, these measures do not allow to monitor disease progression at short intervals.

Individualized treatment of congenital vascular malformations of the tongue

BACKGROUND/OBJECTIVE

Oral malformations of the tongue are exceedingly rare. The aim of this study was to evaluate the effectiveness of individualized treatment for patients with vascular malformations of the tongue.

METHODS

This retrospective study is based on a consecutive local registry at a tertiary care Interdisciplinary Center for Vascular Anomalies. Patients with vascular malformations of the tongue were included. Indications for therapy of the vascular malformation were macroglossia with the impossibility to close the mouth, bleeding, recurrent infection and dysphagia. Size regression of the malformation (volume measurement) and symptom improvement were investigated.

RESULTS

Out of 971 consecutive patients with vascular malformations, 16 patients suffered from a vascular malformation of the tongue. Twelve patients had slow-flow malformations and 4 fast-flow malformations. Indications for interventions were bleeding (4/16, 25%), macroglossia (6/16, 37.5%), and recurrent infections (4/16, 25%). For two patients (2/16, 12.5%), there was no indication for intervention due to absence of symptoms. Four patients received sclerotherapy, 7 patients Bleomycin-electrosclerotherapy (BEST) and 3 patients embolization. Median follow-up was 16 months (IQR 7-35.5). In all patients, symptoms had decreased after two interventions at a median (IQR 1-3.75). Volume reduction of the malformation of the tongue was 13.3%(from median 27.9 cm3 to median 24.2 cm3, p = 0.0039), and even more pronounced when considering only patients with BEST (from 86 cm3 to 59.1 cm3, p = 0.001).

CONCLUSION

Symptoms of vascular malformations of the tongue are improved after a median of two interventions with significantly increased volume reduction after Bleomycin-electrosclerotherapy.

Progressive Spinal Cord Degeneration in Friedreich's Ataxia: Results from ENIGMA-Ataxia

BACKGROUND

Spinal cord damage is a hallmark of Friedreich's ataxia (FRDA), but its progression and clinical correlates remain unclear.

OBJECTIVE

The objective of this study was to perform a characterization of cervical spinal cord structural damage in a large multisite FRDA cohort.

METHODS

We performed a cross-sectional analysis of cervical spinal cord (C1-C4) cross-sectional area (CSA) and eccentricity using magnetic resonance imaging data from eight sites within the ENIGMA-Ataxia initiative, including 256 individuals with FRDA and 223 age- and sex-matched control subjects. Correlations and subgroup analyses within the FRDA cohort were undertaken based on disease duration, ataxia severity, and onset age.

RESULTS

Individuals with FRDA, relative to control subjects, had significantly reduced CSA at all examined levels, with large effect sizes (d > 2.1) and significant correlations with disease severity (r < -0.4). Similarly, we found significantly increased eccentricity (d > 1.2), but without significant clinical correlations. Subgroup analyses showed that CSA and eccentricity are abnormal at all disease stages. However, although CSA appears to decrease progressively, eccentricity remains stable over time.

CONCLUSIONS

Previous research has shown that increased eccentricity reflects dorsal column (DC) damage, while decreased CSA reflects either DC or corticospinal tract (CST) damage, or both. Hence our data support the hypothesis that damage to the DC and damage to CST follow distinct courses in FRDA: developmental abnormalities likely define the DC, while CST alterations may be both developmental and degenerative. These results provide new insights about FRDA pathogenesis and indicate that CSA of the cervical spinal cord should be investigated further as a potential biomarker of disease progression. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Development of hemodynamically relevant acquired arterio-venous fistulae in patients with venous malformations

BACKGROUND

Venous malformations tend to retain their slow-flow behavior, even in progressive disease or regression following therapy.

OBJECTIVE

The aim of this study is to analyze the development of acquired hemodynamic relevant arterio-venous fistulae in patients with slow-flow malformations.

METHODS

This study is a retrospective analysis based on a consecutive local registry at a tertiary care Interdisciplinary Center for Vascular Anomalies. Patients with venous malformations and development of secondary arterio-venous fistulae were included. Indications for therapy of the vascular malformation were based on patients' symptoms and complications. The following endpoints were of clinical interest and were assessed: origin of development of arteriovenous fistula, development of secondary comorbidities as a result of the vascular malformation. For analysis we focused on descriptive statistics.

RESULTS

Out of 1213 consecutive patients with vascular malformations, in 6 patients perfusion changed from slow flow to arterio-venous fast-flow patterns. Four patients developed the fistula after local trauma in the area of the malformation, the other 2 patients developed the fistula due to progression of the disease and recurrent thrombophlebitis. These 2 patients had no trauma or interventions at the time of arterio-venous fistula development.

CONCLUSIONS

Acquired arterio-venous fast-flow fistula in patients with slow flow vascular malformation is very rare and might be a result of local trauma or the progression of the disease with recurrent thrombophlebitis. Specific evidence-based treatment options for these patients do not exist.

Magnetic susceptibility anisotropy in normal appearing white matter in multiple sclerosis from single-orientation acquisition

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Orientation dependence of QSM is studied in a large cohort of MS patients.

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Apparent magnetic susceptibility anisotropy (MSA) obtained from single-orientation QSM.

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Apparent MSA found decreased in optic radiation (OR) of MS patients.

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Apparent MSA decreases with lesion load in OR and with disease duration in splenium.

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Negative apparent MSA observed in SLF indicates limitations of the proposed method.

Quantitative susceptibility mapping (QSM) has been successfully applied to study changes in deep grey matter nuclei as well as in lesional tissue, but its application to white matter has been complicated by the observed orientation dependence of gradient echo signal. The anisotropic susceptibility tensor is thought to be at the origin of this orientation dependence, and magnetic susceptibility anisotropy (MSA) derived from this tensor has been proposed as a marker of the state and integrity of the myelin sheath and may therefore be of particular interest for the study of demyelinating pathologies such as multiple sclerosis (MS). Reconstruction of the susceptibility tensor, however, requires repeated measurements with multiple head orientations, rendering the approach impractical for clinical applications.

In this study, we combined single-orientation QSM with fibre orientation information to assess apparent MSA in three white matter tracts, i.e., optic radiation (OR), splenium of the corpus callosum (SCC), and superior longitudinal fascicle (SLF), in two cohorts of 64 healthy controls and 89 MS patients. The apparent MSA showed a significant decrease in optic radiation in the MS cohort compared with healthy controls. It decreased in the MS cohort with increasing lesion load in OR and with disease duration in the splenium. All of this suggests demyelination in normal appearing white matter. However, the apparent MSA observed in the SLF pointed to potential systematic issues that require further exploration to realize the full potential of the presented approach. Despite the limitations of such single-orientation ROI-specific estimation, we believe that our clinically feasible approach to study degenerative changes in WM is worthy of further investigation.

Quantitative susceptibility mapping reveals alterations of dentate nuclei in common types of degenerative cerebellar ataxias

The cerebellar nuclei are a brain region with high iron content. Surprisingly, little is known about iron content in the cerebellar nuclei and its possible contribution to pathology in cerebellar ataxias, with the only exception of Friedreich’s ataxia. In the present exploratory cross-sectional study, quantitative susceptibility mapping was used to investigate volume, iron concentration and total iron content of the dentate nuclei in common types of hereditary and non-hereditary degenerative ataxias. Seventy-nine patients with spinocerebellar ataxias of types 1, 2, 3 and 6; 15 patients with Friedreich’s ataxia; 18 patients with multiple system atrophy, cerebellar type and 111 healthy controls were also included. All underwent 3 T MRI and clinical assessments. For each specific ataxia subtype, voxel-based and volumes-of-interest-based group analyses were performed in comparison with a corresponding age- and sex-matched control group, both for volume, magnetic susceptiblity (indicating iron concentration) and susceptibility mass (indicating total iron content) of the dentate nuclei. Spinocerebellar ataxia of type 1 and multiple system atrophy, cerebellar type patients showed higher susceptibilities in large parts of the dentate nucleus but unaltered susceptibility masses compared with controls. Friedreich’s ataxia patients and, only on a trend level, spinocerebellar ataxia of type 2 patients showed higher susceptibilities in more circumscribed parts of the dentate. In contrast, spinocerebellar ataxia of type 6 patients revealed lower susceptibilities and susceptibility masses compared with controls throughout the dentate nucleus. Spinocerebellar ataxia of type 3 patients showed no significant changes in susceptibility and susceptibility mass. Lower volume of the dentate nuclei was found to varying degrees in all ataxia types. It was most pronounced in spinocerebellar ataxia of type 6 patients and least prominent in spinocerebellar ataxia of type 3 patients. The findings show that alterations in susceptibility revealed by quantitative susceptibility mapping are common in the dentate nuclei in different types of cerebellar ataxias. The most striking changes in susceptibility were found in spinocerebellar ataxia of type 1, multiple system atrophy, cerebellar type and spinocerebellar ataxia of type 6. Because iron content is known to be high in glial cells but not in neurons of the cerebellar nuclei, the higher susceptibility in spinocerebellar ataxia of type 1 and multiple system atrophy, cerebellar type may be explained by a reduction of neurons (increase in iron concentration) and/or an increase in iron-rich glial cells, e.g. microgliosis. Hypomyelination also leads to higher susceptibility and could also contribute. The lower susceptibility in SCA6 suggests a loss of iron-rich glial cells. Quantitative susceptibility maps warrant future studies of iron content and iron-rich cells in ataxias to gain a more comprehensive understanding of the pathogenesis of these diseases.

Motor training-related brain reorganization in patients with cerebellar degeneration

Cerebellar degeneration progressively impairs motor function. Recent research showed that cerebellar patients can improve motor performance with practice, but the optimal feedback type (visual, proprioceptive, verbal) for such learning and the underlying neuroplastic changes are unknown. Here, patients with cerebellar degeneration (N = 40) and age‐ and sex‐matched healthy controls (N = 40) practiced single‐joint, goal‐directed forearm movements for 5 days. Cerebellar patients improved performance during visuomotor practice, but a training focusing on either proprioceptive feedback, or explicit verbal feedback and instruction did not show additional benefits. Voxel‐based morphometry revealed that after training gray matter volume (GMV) was increased prominently in the visual association cortices of controls, whereas cerebellar patients exhibited GMV increase predominantly in premotor cortex. The premotor cortex as a recipient of cerebellar efferents appears to be an important hub in compensatory remodeling following damage of the cerebro‐cerebellar motor system.

Brain Structure and Degeneration Staging in Friedreich Ataxia: Magnetic Resonance Imaging Volumetrics from the ENIGMA-Ataxia Working Group

Objective

Friedreich ataxia (FRDA) is an inherited neurological disease defined by progressive movement incoordination. We undertook a comprehensive characterization of the spatial profile and progressive evolution of structural brain abnormalities in people with FRDA.

Methods

A coordinated international analysis of regional brain volume using magnetic resonance imaging data charted the whole‐brain profile, interindividual variability, and temporal staging of structural brain differences in 248 individuals with FRDA and 262 healthy controls.

Results

The brainstem, dentate nucleus region, and superior and inferior cerebellar peduncles showed the greatest reductions in volume relative to controls (Cohen d = 1.5–2.6). Cerebellar gray matter alterations were most pronounced in lobules I–VI (d = 0.8), whereas cerebral differences occurred most prominently in precentral gyri (d = 0.6) and corticospinal tracts (d = 1.4). Earlier onset age predicted less volume in the motor cerebellum (r_max = 0.35) and peduncles (r_max = 0.36). Disease duration and severity correlated with volume deficits in the dentate nucleus region, brainstem, and superior/inferior cerebellar peduncles (r_max = −0.49); subgrouping showed these to be robust and early features of FRDA, and strong candidates for further biomarker validation. Cerebral white matter abnormalities, particularly in corticospinal pathways, emerge as intermediate disease features. Cerebellar and cerebral gray matter loss, principally targeting motor and sensory systems, preferentially manifests later in the disease course.

Interpretation

FRDA is defined by an evolving spatial profile of neuroanatomical changes beyond primary pathology in the cerebellum and spinal cord, in line with its progressive clinical course. The design, interpretation, and generalization of research studies and clinical trials must consider neuroanatomical staging and associated interindividual variability in brain measures. ANN NEUROL 2021;90:570–583

Quantitative susceptibility mapping in ischemic stroke patients after successful recanalization

Quantitative susceptibility mapping (QSM) is a novel processing method for gradient-echo magnetic resonance imaging (MRI). Higher magnetic susceptibility in cortical veins have been observed on susceptibility maps in the ischemic hemisphere of stroke patients, indicating an increased oxygen extraction fraction (OEF). Our goal was to investigate susceptibility in veins of stroke patients after successful recanalization in order to analyze the value of QSM in predicting tissue prognosis and clinical outcome. We analyzed MR images of 23 patients with stroke due to unilateral middle cerebral artery (MCA)-M1/M2 occlusion acquired 24–72 h after successful thrombectomy. The susceptibilities of veins were obtained from QSM and compared between the stroke territory, the ipsilateral non-ischemic MCA territory and the contralateral MCA territory. As outcome variables, early infarct size and functional disability (modified Rankin Scale, mRS) after 3–5 months was used. The median susceptibility value of cortical veins in the ischemic core was 41% lower compared to the ipsilateral non-ischemic MCA territory and 38% lower than on the contralateral MCA territory. Strikingly, in none of the patients prominent vessels with high susceptibility signal were found after recanalization. Venous susceptibility values within the infarct did not correlate with infarct volume or functional disability after 3–5 months. Low venous susceptibility within the infarct core after successful recanalization of the occluded vessel likely indicates poor oxygen extraction arising from tissue damage. We did not identify peri-infarct tissue with increased susceptibility values as potential surrogate of former penumbral areas. We found no correlation of QSM parameters with infarct size or outcome.

Vascular malformations of the female and male genitalia: type and distribution patterns revealed by magnetic resonance imaging

BACKGROUND

Vascular malformations of the genitalia often go undetected in clinical examination. These vascular malformations can cause a variety of clinical symptoms such as swelling, pain and bleeding.

AIM

To characterize the distribution patterns of genital vascular malformations using magnetic resonance imaging (MRI) and to correlate these patterns with clinical findings in order to guide diagnostic decisions.

METHODS

A retrospective analysis of MRIs of the pelvis and legs in 370 patients with vascular malformation was performed to determine the involvement of the internal and external genitalia.

RESULTS

In 71 patients (19%), genital involvement could be identified by MRI. Of these, 11.3% (8 of 71) presented with internal involvement, 36.6% (26 of 71) with external involvement and 52.1% (37 of 71) with both internal and external involvement. Over half (57.1%) of the 49 patients with visible external genital signs detected during a clinical examination had additional internal genital involvement.

CONCLUSIONS

Genital involvement is a common finding in patients with vascular malformation of the legs and/or pelvis. Based on our data, we recommend MRI of the legs and pelvic region in patients with externally visible signs of a vascular malformation of the external genitalia in order to exclude additional internal involvement.

Superficial white matter imaging: Contrast mechanisms and whole-brain in vivo mapping

Superficial white matter (SWM) contains the most cortico-cortical white matter connections in the human brain encompassing the short U-shaped association fibers. Despite its importance for brain connectivity, very little is known about SWM in humans, mainly due to the lack of noninvasive imaging methods. Here, we lay the groundwork for systematic in vivo SWM mapping using ultrahigh resolution 7 T magnetic resonance imaging. Using biophysical modeling informed by quantitative ion beam microscopy on postmortem brain tissue, we demonstrate that MR contrast in SWM is driven by iron and can be linked to the microscopic iron distribution. Higher SWM iron concentrations were observed in U-fiber-rich frontal, temporal, and parietal areas, potentially reflecting high fiber density or late myelination in these areas. Our SWM mapping approach provides the foundation for systematic studies of interindividual differences, plasticity, and pathologies of this crucial structure for cortico-cortical connectivity in humans.

Characterization of Iron Accumulation in Deep Gray Matter in Myotonic Dystrophy Type 1 and 2 Using Quantitative Susceptibility Mapping and R2* Relaxometry: A Magnetic Resonance Imaging Study at 3 Tesla

Quantitative mapping of the magnetic susceptibility and the effective transverse relaxation rate (R2^*) are suitable to assess the iron content in distinct brain regions. In this prospective, explorative study the iron accumulation in deep gray matter nuclei (DGM) in myotonic dystrophy type 1 (DM1) and 2 (DM2) and its clinical and neuro-cognitive relevance using susceptibility and R2^* mapping was examined. Twelve classical DM1, four childhood-onset DM1 (DM1_c.o.), twelve DM2 patients and twenty-nine matched healthy controls underwent MRI at 3 Tesla, neurological and neuro-cognitive tests. Susceptibility, R2^* and volumes were determined for eleven DGM structures and compared between patients and controls. Twelve classical DM1, four childhood-onset DM1, and 12 DM2 patients as well as 29 matched healthy controls underwent MRI at 3 Tesla, and neurological and neuro-cognitive tests. Susceptibility, R2^* and volumes were determined for 11 DGM structures and compared between patients and controls. Iron accumulation in DGM reflected by R2^* or susceptibility was found in the putamen and accumbens of DM1 and in DM2, but was more widespread in DM1 (caudate, pallidum, hippocampus, subthalamic nucleus, thalamus, and substantia nigra). Opposed changes of R2^* or susceptibility were detected in caudate, putamen and accumbens in the childhood-onset DM1 patients compared to classical DM1. R2^* or susceptibility alterations in DGM were significantly associated with clinical symptoms including muscular weakness (DM1), daytime sleepiness (DM1), depression (DM2), and with specific cognitive deficits in DM1 and DM2.

A new framework for assessing subject-specific whole brain circulation and perfusion using MRI-based measurements and a multi-scale continuous flow model

A large variety of severe medical conditions involve alterations in microvascular circulation. Hence, measurements or simulation of circulation and perfusion has considerable clinical value and can be used for diagnostics, evaluation of treatment efficacy, and for surgical planning. However, the accuracy of traditional tracer kinetic one-compartment models is limited due to scale dependency. As a remedy, we propose a scale invariant mathematical framework for simulating whole brain perfusion. The suggested framework is based on a segmentation of anatomical geometry down to imaging voxel resolution. Large vessels in the arterial and venous network are identified from time-of-flight (ToF) and quantitative susceptibility mapping (QSM). Macro-scale flow in the large-vessel-network is accurately modelled using the Hagen-Poiseuille equation, whereas capillary flow is treated as two-compartment porous media flow. Macro-scale flow is coupled with micro-scale flow by a spatially distributing support function in the terminal endings. Perfusion is defined as the transition of fluid from the arterial to the venous compartment. We demonstrate a whole brain simulation of tracer propagation on a realistic geometric model of the human brain, where the model comprises distinct areas of grey and white matter, as well as large vessels in the arterial and venous vascular network. Our proposed framework is an accurate and viable alternative to traditional compartment models, with high relevance for simulation of brain perfusion and also for restoration of field parameters in clinical brain perfusion applications.

An accurate simulation of blood-flow in the human brain can be used for improved diagnostics and assignment of personalized treatment regimes. However, current algorithms are limited to simulation of blood flow within tumours only, and in terms of parameter estimation, traditional compartment models have limited accuracy due to lack of spatial connectivity within the models. As a remedy, we propose a data-driven computational fluid dynamics model where the geometric domains for simulation are defined from state-of-the art MR acquisitions enabling a segmentation of large arteries and veins. In the capillary tissue we apply a two-compartment porous media model, where the perfusion is pressure-driven and is defined as the transition of blood from arterial to venous side. In addition, we propose a model for dealing with the intermediate scale problem where the vessels are undetectable and the flow does not adhere to requirements of porous media flow. For this scale, we propose a support function distributing the fluid in a nearby region around the vessel terminals. Combining these elements, we have developed a novel full human brain blood-flow simulator.

Analysis of intensity normalization for optimal segmentation performance of a fully convolutional neural network

INTRODUCTION

Convolutional neural networks have begun to surpass classical statistical- and atlas based machine learning techniques in medical image segmentation in recent years, proving to be superior in performance and speed. However, a major challenge that the community faces are mismatch between variability within training and evaluation datasets and therefore a dependency on proper data pre-processing. Intensity normalization is a widely applied technique for reducing the variance of the data for which there are several methods available ranging from uniformity transformation to histogram equalization. The current study analyses the influence of intensity normalization on cerebellum segmentation performance of a convolutional neural network (CNN).

METHOD

The study included three population samples with a total number of 218 datasets, all including a T1w MRI data set acquired at 3T and a ground truth segmentation delineating the cerebellum. A 12 layer deep 3D fully convolutional neural network was trained using 150 datasets from one of the population samples. Four different intensity normalization methods were separately applied to pre-process the data, and the CNN was correspondingly trained four times with respect to the different normalization techniques. A quantitative analysis of the segmentation performance, assessed via the Sørensen-Dice similarity coefficient (DSC) of all four CNNs, was performed to investigate the intensity sensitivity of the CNNs. Additionally, the optimal network performance was determined by identifying the best parameter set for intensity normalization.

RESULTS

All four normalization methods led to excellent (mean DSC score=0.96) segmentation results when evaluated using known data; however, the segmentation performance differed depending on the applied intensity normalization method when testing with formerly unseen data, in which case the histogram equalization methods outperformed the unit distribution methods. A detailed, systematic analysis of intensity manipulations revealed, that the distribution of input intensities clearly affected the segmentation performance and that for each input dataset a linear intensity modification (shifting and scaling) existed leading to optimal segmentation results. This was further proven by an optimization analysis to find the optimal adjustment for an individual input evaluation sample within each normalization configuration.

DISCUSSION

The findings suggest that proper preparation of the evaluation data is more crucial than the exact choice of normalization method to prepare the training data. The histogram equalization methods tested in this study were found to perform this task best, although leaving room for further improvements, as shown by the optimization analysis.

Vascular and Tissue Changes of Magnetic Susceptibility in the Mouse Brain After Transient Cerebral Ischemia

Quantitative susceptibility mapping (QSM) has been recently introduced as a novel MRI post-processing technique of gradient recalled echo (GRE) data. QSM is useful in depicting both brain anatomy and for detecting abnormalities. Its utility in the context of ischemic stroke has, however, not been extensively characterized so far. In this study, we explored the potential of QSM to characterize vascular and tissue changes in the transient middle cerebral artery occlusion (tMCAO) mouse model of cerebral ischemia. We acquired GRE data of mice brains at different time points after tMCAO, from which we computed QSM and MR frequency maps, and compared these maps with diffusion imaging and multi-slice multi-echo imaging data acquired in the same animals. Prominent vessels with increased magnetic susceptibility were visible surrounding the lesion on both frequency and magnetic susceptibility maps at all time points (mostly visible at > 12 h after reperfusion). Immunohistochemistry revealed the presence of compressed capillaries and dilated larger vessels, suggesting that the appearance of prominent vessels after reestablishment of reperfusion may serve compensatory purposes. In addition, on both contrast maps, tissue regions of decreased magnetic susceptibility were observed at 24 and 48 h after reperfusion that were distinctly different from the lesions seen on maps of the apparent diffusion coefficient and T₂ relaxation time constant. Since QSM can be extracted as an add-on from GRE data and thus requires no additional acquisition time in the course of acute stroke MRI examination, it may provide unique and complementary information during the course of acute stroke MRI examinations.

Quantitative susceptibility mapping (QSM) and R2* in the human brain at 3T: Evaluation of intra-scanner repeatability

Quantitative susceptibility mapping (QSM) and the effective transverse relaxation rate (R₂*) can be used to monitor iron and myelin content in brain tissue, which are both subject to changes in many neurological diseases but also during healthy aging. In this study, we quantitatively assessed the repeatability of QSM and R₂* by applying four independent scans in eight young healthy, female subjects on a 3T MRI scanner. Since QSM does not yield absolute values for bulk magnetic susceptibilities, we additionally investigated the influence of the choice of a reference brain region for susceptibility by computing susceptibility differences with respect to five different brain structures (whole brain, frontal white matter (fWM), internal capsule (IC), cerebrospinal fluid (CSF) in the lateral ventricle, cortical gray matter (cGM)). The intra-class correlation coefficient (ICC), variance ratio (VR) and repeatability coefficient (RC) were used to evaluate the repeatability of the calculated susceptibility differences and the R₂* values in six different subcortical brain structures. Linear regression was used to analyze the correlation between susceptibility differences and R₂*. We found that the susceptibility differences with respect to each investigated reference region (0.868≤mean ICC≤0.914) and the R₂* values (mean ICC=0.923) were highly repeatable across the four times repeated scans. With consistently higher ICC, higher VR and lower RC, whole brain and cGM appeared to be the two most suitable reference regions for QSM with respect to repeatability.

Changes of deep gray matter magnetic susceptibility over 2 years in multiple sclerosis and healthy control brain

In multiple sclerosis, pathological changes of both tissue iron and myelin occur, yet these factors have not been characterized in a longitudinal fashion using the novel iron- and myelin-sensitive quantitative susceptibility mapping (QSM) MRI technique. We investigated disease-relevant tissue changes associated with myelin loss and iron accumulation in multiple sclerosis deep gray matter (DGM) over two years. One-hundred twenty (120) multiple sclerosis patients and 40 age- and sex-matched healthy controls were included in this prospective study. Written informed consent and local IRB approval were obtained from all participants. Clinical testing and QSM were performed both at baseline and at follow-up. Brain magnetic susceptibility was measured in major DGM structures. Temporal (baseline vs. follow-up) and cross-sectional (multiple sclerosis vs. controls) differences were studied using mixed factorial ANOVA analysis and appropriate t-tests. At either time-point, multiple sclerosis patients had significantly higher susceptibility in the caudate and globus pallidus and lower susceptibility in the thalamus. Over two years, susceptibility increased significantly in the caudate of both controls and multiple sclerosis patients. Inverse thalamic findings among MS patients suggest a multi-phase pathology explained by simultaneous myelin loss and/or iron accumulation followed by iron depletion and/or calcium deposition at later stages.

A comprehensive numerical analysis of background phase correction with V-SHARP

Sophisticated harmonic artifact reduction for phase data (SHARP) is a method to remove background field contributions in MRI phase images, which is an essential processing step for quantitative susceptibility mapping (QSM). To perform SHARP, a spherical kernel radius and a regularization parameter need to be defined. In this study, we carried out an extensive analysis of the effect of these two parameters on the corrected phase images and on the reconstructed susceptibility maps. As a result of the dependence of the parameters on acquisition and processing characteristics, we propose a new SHARP scheme with generalized parameters. The new SHARP scheme uses a high-pass filtering approach to define the regularization parameter. We employed the variable-kernel SHARP (V-SHARP) approach, using different maximum radii (R_m ) between 1 and 15 mm and varying regularization parameters (f) in a numerical brain model. The local root-mean-square error (RMSE) between the ground-truth, background-corrected field map and the results from SHARP decreased towards the center of the brain. RMSE of susceptibility maps calculated with a spatial domain algorithm was smallest for R_m between 6 and 10 mm and f between 0 and 0.01 mm^-1 , and for maps calculated with a Fourier domain algorithm for R_m between 10 and 15 mm and f between 0 and 0.0091 mm^-1 . We demonstrated and confirmed the new parameter scheme in vivo. The novel regularization scheme allows the use of the same regularization parameter irrespective of other imaging parameters, such as image resolution. Copyright © 2016 John Wiley & Sons, Ltd.

Overview of quantitative susceptibility mapping

Magnetic susceptibility describes the magnetizability of a material to an applied magnetic field and represents an important parameter in the field of MRI. With the recently introduced method of quantitative susceptibility mapping (QSM) and its conceptual extension to susceptibility tensor imaging (STI), the non-invasive assessment of this important physical quantity has become possible with MRI. Both methods solve the ill-posed inverse problem to determine the magnetic susceptibility from local magnetic fields. Whilst QSM allows the extraction of the spatial distribution of the bulk magnetic susceptibility from a single measurement, STI enables the quantification of magnetic susceptibility anisotropy, but requires multiple measurements with different orientations of the object relative to the main static magnetic field. In this review, we briefly recapitulate the fundamental theoretical foundation of QSM and STI, as well as computational strategies for the characterization of magnetic susceptibility with MRI phase data. In the second part, we provide an overview of current methodological and clinical applications of QSM with a focus on brain imaging. Copyright © 2016 John Wiley & Sons, Ltd.

An improved FSL-FIRST pipeline for subcortical gray matter segmentation to study abnormal brain anatomy using quantitative susceptibility mapping (QSM)

Accurate and robust segmentation of subcortical gray matter (SGM) nuclei is required in many neuroimaging applications. FMRIB's Integrated Registration and Segmentation Tool (FIRST) is one of the most popular software tools for automated subcortical segmentation based on T₁-weighted (T1w) images. In this work, we demonstrate that FIRST tends to produce inaccurate SGM segmentation results in the case of abnormal brain anatomy, such as present in atrophied brains, due to a poor spatial match of the subcortical structures with the training data in the MNI space as well as due to insufficient contrast of SGM structures on T1w images. Consequently, such deviations from the average brain anatomy may introduce analysis bias in clinical studies, which may not always be obvious and potentially remain unidentified. To improve the segmentation of subcortical nuclei, we propose to use FIRST in combination with a special Hybrid image Contrast (HC) and Non-Linear (nl) registration module (HC-nlFIRST), where the hybrid image contrast is derived from T1w images and magnetic susceptibility maps to create subcortical contrast that is similar to that in the Montreal Neurological Institute (MNI) template. In our approach, a nonlinear registration replaces FIRST's default linear registration, yielding a more accurate alignment of the input data to the MNI template. We evaluated our method on 82 subjects with particularly abnormal brain anatomy, selected from a database of >2000 clinical cases. Qualitative and quantitative analyses revealed that HC-nlFIRST provides improved segmentation compared to the default FIRST method.

Simulation of MR angiography imaging for validation of cerebral arteries segmentation algorithms

BACKGROUND AND OBJECTIVE

Accurate vessel segmentation of magnetic resonance angiography (MRA) images is essential for computer-aided diagnosis of cerebrovascular diseases such as stenosis or aneurysm. The ability of a segmentation algorithm to correctly reproduce the geometry of the arterial system should be expressed quantitatively and observer-independently to ensure objectivism of the evaluation.

METHODS

This paper introduces a methodology for validating vessel segmentation algorithms using a custom-designed MRA simulation framework. For this purpose, a realistic reference model of an intracranial arterial tree was developed based on a real Time-of-Flight (TOF) MRA data set. With this specific geometry blood flow was simulated and a series of TOF images was synthesized using various acquisition protocol parameters and signal-to-noise ratios. The synthesized arterial tree was then reconstructed using a level-set segmentation algorithm available in the Vascular Modeling Toolkit (VMTK). Moreover, to present versatile application of the proposed methodology, validation was also performed for two alternative techniques: a multi-scale vessel enhancement filter and the Chan-Vese variant of the level-set-based approach, as implemented in the Insight Segmentation and Registration Toolkit (ITK). The segmentation results were compared against the reference model.

RESULTS

The accuracy in determining the vessels centerline courses was very high for each tested segmentation algorithm (mean error rate = 5.6% if using VMTK). However, the estimated radii exhibited deviations from ground truth values with mean error rates ranging from 7% up to 79%, depending on the vessel size, image acquisition and segmentation method.

CONCLUSIONS

We demonstrated the practical application of the designed MRA simulator as a reliable tool for quantitative validation of MRA image processing algorithms that provides objective, reproducible results and is observer independent.

Quantitative Susceptibility Mapping in Parkinson's Disease

BACKGROUND

Quantitative susceptibility mapping (QSM) and R2* relaxation rate mapping have demonstrated increased iron deposition in the substantia nigra of patients with idiopathic Parkinson's disease (PD). However, the findings in other subcortical deep gray matter nuclei are converse and the sensitivity of QSM and R2* for morphological changes and their relation to clinical measures of disease severity has so far been investigated only sparsely.

METHODS

The local ethics committee approved this study and all subjects gave written informed consent. 66 patients with idiopathic Parkinson's disease and 58 control subjects underwent quantitative MRI at 3T. Susceptibility and R2* maps were reconstructed from a spoiled multi-echo 3D gradient echo sequence. Mean susceptibilities and R2* rates were measured in subcortical deep gray matter nuclei and compared between patients with PD and controls as well as related to clinical variables.

RESULTS

Compared to control subjects, patients with PD had increased R2* values in the substantia nigra. QSM also showed higher susceptibilities in patients with PD in substantia nigra, in the nucleus ruber, thalamus, and globus pallidus. Magnetic susceptibility of several of these structures was correlated with the levodopa-equivalent daily dose (LEDD) and clinical markers of motor and non-motor disease severity (total MDS-UPDRS, MDS-UPDRS-I and II). Disease severity as assessed by the Hoehn & Yahr scale was correlated with magnetic susceptibility in the substantia nigra.

CONCLUSION

The established finding of higher R2* rates in the substantia nigra was extended by QSM showing superior sensitivity for PD-related tissue changes in nigrostriatal dopaminergic pathways. QSM additionally reflected the levodopa-dosage and disease severity. These results suggest a more widespread pathologic involvement and QSM as a novel means for its investigation, more sensitive than current MRI techniques.

Quantitative assessment of microvasculopathy in arcAβ mice with USPIO-enhanced gradient echo MRI

Magnetic resonance imaging employing administration of iron oxide-based contrast agents is widely used to visualize cellular and molecular processes in vivo. In this study, we investigated the ability of [Formula: see text] and quantitative susceptibility mapping to quantitatively assess the accumulation of ultrasmall superparamagnetic iron oxide (USPIO) particles in the arcAβ mouse model of cerebral amyloidosis. Gradient-echo data of mouse brains were acquired at 9.4 T after injection of USPIO. Focal areas with increased magnetic susceptibility and [Formula: see text] values were discernible across several brain regions in 12-month-old arcAβ compared to 6-month-old arcAβ mice and to non-transgenic littermates, indicating accumulation of particles after USPIO injection. This was concomitant with higher [Formula: see text] and increased magnetic susceptibility differences relative to cerebrospinal fluid measured in USPIO-injected compared to non-USPIO-injected 12-month-old arcAβ mice. No differences in [Formula: see text] and magnetic susceptibility were detected in USPIO-injected compared to non-injected 12-month-old non-transgenic littermates. Histological analysis confirmed focal uptake of USPIO particles in perivascular macrophages adjacent to small caliber cerebral vessels with radii of 2-8 µm that showed no cerebral amyloid angiopathy. USPIO-enhanced [Formula: see text] and quantitative susceptibility mapping constitute quantitative tools to monitor such functional microvasculopathies.

Quantitative Susceptibility Mapping Indicates a Disturbed Brain Iron Homeostasis in Neuromyelitis Optica - A Pilot Study

Dysregulation of brain iron homeostasis is a hallmark of many neurodegenerative diseases and can be associated with oxidative stress. The objective of this study was to investigate brain iron in patients with Neuromyelitis Optica (NMO) using quantitative susceptibility mapping (QSM), a quantitative iron-sensitive MRI technique. 12 clinically confirmed NMO patients (6 female and 6 male; age 35.4y±14.2y) and 12 age- and sex-matched healthy controls (7 female and 5 male; age 33.9±11.3y) underwent MRI of the brain at 3 Tesla. Quantitative maps of the effective transverse relaxation rate (R2*) and magnetic susceptibility were calculated and a blinded ROI-based group comparison analysis was performed. Normality of the data and differences between patients and controls were tested by Kolmogorov-Smirnov and t-test, respectively. Correlation with age was studied using Spearman's rank correlation and an ANCOVA-like analysis. Magnetic susceptibility values were decreased in the red nucleus (p<0.01; d>0.95; between -15 and -22 ppb depending on reference region) with a trend toward increasing differences with age. R2* revealed significantly decreased relaxation in the optic radiations of five of the 12 patients (p<0.0001; -3.136±0.567 s(-1)). Decreased relaxation in the optic radiation is indicative for demyelination, which is in line with previous findings. Decreased magnetic susceptibility in the red nucleus is indicative for a lower brain iron concentration, a chemical redistribution of iron into less magnetic forms, or both. Further investigations are necessary to elucidate the pathological cause or consequence of this finding.

Susceptibility Sensitive Magnetic Resonance Imaging Displays Pallidofugal and Striatonigral Fiber Tracts

BACKGROUND

The pallidofugal and striatonigral fiber tracts form a functional part of the basal ganglionic neuronal networks. For deep brain stimulation, a surgical procedure applied in the treatment of Parkinson disease and dystonia, precise localization of pallidofugal pathways may be of particular clinical relevance for correct electrode positioning.

OBJECTIVE

To investigate whether the pallidofugal and striatonigral pathways can be visualized with magnetic resonance imaging in vivo by exploiting their intrinsic magnetic susceptibility.

METHODS

Three-dimensional gradient-echo imaging of 5 volunteers was performed on a 7 T magnetic resonance imaging system. To demonstrate that the displayed tubular structures in the vicinity of the subthalamic nucleus and substantia nigra truly represent fiber tracts rather than veins, gradient-echo data of a formalin-fixated brain and a volunteer during inhalation of ambient air and carbogen were collected at 3 T. Susceptibility weighted images, quantitative susceptibility maps, and effective transverse relaxation maps were reconstructed and the depiction of fiber tracts was qualitatively assessed.

RESULTS

High-resolution susceptibility-based magnetic resonance imaging contrasts enabled visualization of pallidofugal and striatonigral fiber tracts noninvasively at 3 T and 7 T. We verified that the stripe-like pattern observed on susceptibility-sensitive images is not caused by veins crossing the internal capsule but by fiber tracts traversing the internal capsule.

CONCLUSION

Pallidofugal and striatonigral fiber tracts have been visualized in vivo for the first time by using susceptibility-sensitive image contrasts. Considering the course of pallidofugal pathways, in particular for deep brain stimulation procedures in the vicinity of the subthalamic nucleus, could provide landmarks for optimal targeting during stereotactic planning.

Quantitative Susceptibility Mapping: Concepts and Applications

PURPOSE

To review the fundamental principles of susceptibility-weighted imaging (SWI) and quantitative susceptibility mapping (QSM), and to discuss recent clinical developments.

METHODS

SWI is a magnetic resonance imaging method that takes advantage of magnitude signal loss and phase information to reveal anatomic and physiologic information about tissue and venous vasculature. The method enhances image contrast qualitatively, relying on phase shifts due to differences in magnetic susceptibility between tissues. QSM, extending SWI in an elegant way, is a new sophisticated postprocessing technique that numerically solves the inverse source-effect problem to derive local tissue magnetic susceptibility (source) from the measured magnetic field distribution (effect) as it is reflected in the phase images of gradient-echo sequences.

RESULTS

SWI has meanwhile been established in numerous clinical as well as basic biomedical applications due to its ability to highlight tissue structures and compounds that are difficult to detect by conventional magnetic resonance imaging (MRI), including iron, calcifications, small veins, blood, and bones. The field of QSM has also progressed rapidly, both in terms of optimizing the post-processing strategies and algorithms as well as in gaining ground for new clinical applications that take advantage of its quantitative nature and improved specificity to identify the magnetic signature of lesions.

CONCLUSIONS

Though magnetic susceptibility may be a major nuisance producing image artifacts in MRI, recent work has transformed it into a useful source of image contrast. Both SWI and QSM are gaining increasing acceptance in clinical practice. In particular, QSM provides new insights into tissue composition and organization due to its more direct relation to the actual physical tissue magnetic properties.

Susceptibility-weighted imaging provides insight into white matter damage in amyotrophic lateral sclerosis

Background

Amyotrophic lateral sclerosis (ALS) is a fatal, progressive neurodegenerative disorder, characterised by widespread white matter damage. There is growing evidence that disturbances in iron metabolism contribute to white matter alterations.

Materials & Methods

We analysed the data of susceptibility-weighted imaging (SWI) of white matter in a cohort of 27 patients with ALS and 30 healthy age-matched controls.

Results

Signal alterations were found on SWI in the corpus callosum; along the corticospinal tract (subcortical motor cortex, posterior limb of the internal capsule and brainstem levels) and in the subgyral regions of frontal, parietal, temporal, occipital and limbic lobes. Alterations of white matter in the corpus callosum correlated with disease severity as assessed by the revised ALS functional rating scale.

Conclusion

SWI is capable of indicating iron and myelin disturbances in white matter of ALS patients. The SWI patterns observed in this study suggest that widespread alterations due to iron disturbances occur in patients with ALS and correlate with disease severity.

Brain iron quantification by MRI in mitochondrial membrane protein-associated neurodegeneration under iron-chelating therapy

Therapeutic trials for Neurodegeneration with Brain Iron Accumulation have aimed at a reduction of cerebral iron content. A 13-year-old girl with mitochondrial membrane protein-associated neurodegeneration treated with an iron-chelating agent was monitored by R2 relaxometry, R2* relaxometry, and quantitative susceptibility mapping to estimate the brain iron content. The highly increased brain iron content slowly decreased in the substantia nigra but remained stable for globus pallidus. The estimated iron content was higher by R2* compared to R2 and quantitative susceptibility mapping, a finding not previously observed in the brain of healthy volunteers. A hypothesis explaining this discrepancy is offered.

Effect of age on MRI phase behavior in the subcortical deep gray matter of healthy individuals

BACKGROUND AND PURPOSE

It has been demonstrated that increased levels of iron in the brain occur with aging. In this study we investigated the nature of the association between age and SWI-filtered phase values, indicative of iron content, in the subcortical deep gray matter of healthy individuals.

MATERIALS AND METHODS

A total of 210 healthy individuals (men: n = 89, women: n = 121), mean age, 39.8 years (standard deviation = 15.5; range = 6-76 years), were imaged on a 3T scanner. Mean MRI phase, mean phase of low-phase voxels, and normalized volumes were determined for total subcortical deep gray matter, caudate, putamen, globus pallidus, thalamus, pulvinar nucleus, hippocampus, amygdala, nucleus accumbens, red nucleus, and substantia nigra. Linear and nonlinear regression models were used to explore the relationship between phase and volume measures, and aging.

RESULTS

Mean phase values of subcortical deep gray matter structures showed a quadratic relationship, with individuals in late middle age (40-59 years) having the lowest mean phase values, followed by a reversal of this trend in the elderly. In contrast, mean phase of low-phase voxel measurements showed strong negative linear relationships with aging. Significantly lower phase values were detected in women compared with men (P < .001), whereas no sex differences were observed for mean phase of low-phase voxels. Normalized volume measurements were also linearly related to aging, and women showed smaller normalized volumes of subcortical deep gray matter structures than men (P < .001). Lower mean phase of low-phase voxels was related to decreased volume measures.

CONCLUSIONS

A strong association between phase (quadratic effect; phase decreases are followed by increases), mean phase of low-phase voxels (linear effect), volume (linear effect), and age was observed. Low phase was related to brain atrophy.

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.

Longitudinal Assessment of Amyloid Pathology in Transgenic ArcAβ Mice Using Multi-Parametric Magnetic Resonance Imaging

Magnetic resonance imaging (MRI) can be used to monitor pathological changes in Alzheimer's disease (AD). The objective of this longitudinal study was to assess the effects of progressive amyloid-related pathology on multiple MRI parameters in transgenic arcAβ mice, a mouse model of cerebral amyloidosis. Diffusion-weighted imaging (DWI), T1-mapping and quantitative susceptibility mapping (QSM), a novel MRI based technique, were applied to monitor structural alterations and changes in tissue composition imposed by the pathology over time. Vascular function and integrity was studied by assessing blood-brain barrier integrity with dynamic contrast-enhanced MRI and cerebral microbleed (CMB) load with susceptibility weighted imaging and QSM. A linear mixed effects model was built for each MRI parameter to incorporate effects within and between groups (i.e. genotype) and to account for changes unrelated to the disease pathology. Linear mixed effects modelling revealed a strong association of all investigated MRI parameters with age. DWI and QSM in addition revealed differences between arcAβ and wt mice over time. CMBs became apparent in arcAβ mice with 9 month of age; and the CMB load reflected disease stage. This study demonstrates the benefits of linear mixed effects modelling of longitudinal imaging data. Moreover, the diagnostic utility of QSM and assessment of CMB load should be exploited further in studies of AD.

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.

Quantitative susceptibility mapping differentiates between blood depositions and calcifications in patients with glioblastoma

OBJECTIVES

The application of susceptibility weighted imaging (SWI) in brain tumor imaging is mainly used to assess tumor-related "susceptibility based signals" (SBS). The origin of SBS in glioblastoma is still unknown, potentially representing calcifications or blood depositions. Reliable differentiation between both entities may be important to evaluate treatment response and to identify glioblastoma with oligodendroglial components that are supposed to present calcifications. Since calcifications and blood deposits are difficult to differentiate using conventional MRI, we investigated whether a new post-processing approach, quantitative susceptibility mapping (QSM), is able to distinguish between both entities reliably.

MATERIALS AND METHODS

SWI, FLAIR, and T1-w images were acquired from 46 patients with glioblastoma (14 newly diagnosed, 24 treated with radiochemotherapy, 8 treated with radiochemotherapy and additional anti-angiogenic medication). Susceptibility maps were calculated from SWI data. All glioblastoma were evaluated for the appearance of hypointense or hyperintense correlates of SBS on the susceptibility maps.

RESULTS

43 of 46 glioblastoma presented only hyperintense intratumoral SBS on susceptibility maps, indicating blood deposits. Additional hypointense correlates of tumor-related SBS on susceptibility maps, indicating calcification, were identified in 2 patients being treated with radiochemotherapy and in one patient being treated with additional anti-angiogenic medication. Histopathologic reports revealed an oligodendroglial component in one patient that presented calcifications on susceptibility maps.

CONCLUSIONS

QSM provides a quantitative, local MRI contrast, which reliably differentiates between blood deposits and calcifications. Thus, quantitative susceptibility mapping appears promising to identify rare variants of glioblastoma with oligodendroglial components non-invasively and may allow monitoring the role of calcification in the context of different therapy regimes.

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

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

Toward online reconstruction of quantitative susceptibility maps: superfast dipole inversion

Magnetic susceptibility is an intrinsic tissue property that recently became measureable in vivo by a magnetic-resonance based technique called quantitative susceptibility mapping (QSM). Although QSM may be performed without additional acquisition time, for example, in the course of the well-established susceptibility weighted imaging, the applicability of QSM is currently hampered by the numerical complexity and computational cost associated with the reconstruction procedure. This work introduces a novel QSM framework called superfast dipole inversion which allows rapid online reconstruction of susceptibility maps from wrapped raw gradient-echo phase data. The algorithm relies on the extension and combination of several recent algorithms involving the precalculation of convolution kernels and the correction of inversion artifacts. Reconstruction of three-dimensional high resolution susceptibility maps of the human brain was achieved with superfast dipole inversion in less than 20 s on a conventional workstation computer. Thus, superfast dipole inversion opens the door to an implementation of QSM on MR scanner hardware as well as to the routine reconstruction of large cohorts of datasets.

Quantitative susceptibility mapping for investigating subtle susceptibility variations in the human brain

Quantitative susceptibility mapping (QSM) is a novel magnetic resonance-based technique that determines tissue magnetic susceptibility from measurements of the magnetic field perturbation. Due to the ill-posed nature of this problem, regularization strategies are generally required to reduce streaking artifacts on the computed maps. The present study introduces a new algorithm for calculating the susceptibility distribution utilizing a priori information on its regional homogeneity derived from gradient echo phase images and analyzes the impact of erroneous a priori information on susceptibility map fidelity. The algorithm, Homogeneity Enabled Incremental Dipole Inversion (HEIDI), was investigated with a special focus on the reconstruction of subtle susceptibility variations in a numerical model and in volunteer data and was compared with two recently published approaches, Thresholded K-space Division (TKD) and Morphology Enabled Dipole Inversion (MEDI). HEIDI resulted in susceptibility maps without streaking artifacts and excellent depiction of subtle susceptibility variations in most regions. By investigating HEIDI susceptibility maps acquired with the volunteers' heads in different orientations, it was demonstrated that the apparent magnetic susceptibility distribution of human brain tissue considerably depends on the direction of the main magnetic field.

Quantitative susceptibility mapping (QSM) as a means to measure brain iron? A post mortem validation study

Quantitative susceptibility mapping (QSM) is a novel technique which allows determining the bulk magnetic susceptibility distribution of tissue in vivo from gradient echo magnetic resonance phase images. It is commonly assumed that paramagnetic iron is the predominant source of susceptibility variations in gray matter as many studies have reported a reasonable correlation of magnetic susceptibility with brain iron concentrations in vivo. Instead of performing direct comparisons, however, all these studies used the putative iron concentrations reported in the hallmark study by Hallgren and Sourander (1958) for their analysis. Consequently, the extent to which QSM can serve to reliably assess brain iron levels is not yet fully clear. To provide such information we investigated the relation between bulk tissue magnetic susceptibility and brain iron concentration in unfixed (in situ) post mortem brains of 13 subjects using MRI and inductively coupled plasma mass spectrometry. A strong linear correlation between chemically determined iron concentration and bulk magnetic susceptibility was found in gray matter structures (r = 0.84, p < 0.001), whereas the correlation coefficient was much lower in white matter (r = 0.27, p < 0.001). The slope of the overall linear correlation was consistent with theoretical considerations of the magnetism of ferritin supporting that most of the iron in the brain is bound to ferritin proteins. In conclusion, iron is the dominant source of magnetic susceptibility in deep gray matter and can be assessed with QSM. In white matter regions the estimation of iron concentrations by QSM is less accurate and more complex because the counteracting contribution from diamagnetic myelinated neuronal fibers confounds the interpretation.

Detection of cerebral microbleeds with quantitative susceptibility mapping in the ArcAbeta mouse model of cerebral amyloidosis

Cerebral microbleeds (CMBs) are findings in patients with neurological disorders such as cerebral amyloid angiopathy and Alzheimer's disease, and are indicative of an underlying vascular pathology. A diagnosis of CMBs requires an imaging method that is capable of detecting iron-containing lesions with high sensitivity and spatial accuracy in the presence of potentially confounding tissue abnormalities. In this study, we investigated the feasibility of quantitative magnetic susceptibility mapping (QSM), a novel technique based on gradient-recalled echo (GRE) phase data, for the detection of CMBs in the arcAβ mouse, a mouse model of cerebral amyloidosis. Quantitative susceptibility maps were generated from phase data acquired with a high-resolution T(2)(*)-weighted GRE sequence at 9.4 T. We examined the influence of different regularization parameters on susceptibility computation; a proper adjustment of the regularization parameter minimizes streaking artifacts and preserves fine structures. In the present study, it is shown that QSM provides increased detection sensitivity of CMBs and improved contrast when compared with GRE magnitude imaging. Furthermore, QSM corrects for the blooming effect observed in magnitude and phase images and depicts both the localization and spatial extent of CMBs with high accuracy. Therefore, QSM may become an important tool for diagnosing CMBs in neurological diseases.

Differentiation between diamagnetic and paramagnetic cerebral lesions based on magnetic susceptibility mapping

PURPOSE

Identification of calcifications and hemorrhages is essential for the etiological diagnosis of cerebral lesions. The purpose of this work was to develop a robust method for characterization of para- and diamagnetic intracerebral lesions based on clinical gradient-echo magnetic resonance phase data acquired at 1.5 Tesla.

METHODS

The magnetic susceptibility distribution of biological tissue produces a distinct magnetic field pattern, which is directly reflected in gradient-echo magnetic resonance phase images. Compared to brain parenchyma, iron-laden tissues are more paramagnetic, whereas mineralized tissues usually possess more diamagnetic susceptibilities. Magnetic resonance phase data were inverted to the underlying susceptibility distribution utilizing additional geometrical information about the lesions, which was obtained from the gradient-echo magnitude signal void corresponding to the lesions. Clinical magnetic resonance exams of three patients with multiple brain lesions (total n = 70) were processed and evaluated. For one patient, the results were validated by an additionally available computed tomography scan. Numerical simulations were conducted to evaluate the robustness of the method.

RESULTS

The obtained susceptibility maps showed impressive delineation of lesions, vessels, and potentially iron-laden tissue. Compensation of the nonlocal field perturbations was clearly discernable on the susceptibility maps. In all cases, discrimination of para- from diamagnetic lesions was achieved and the results were confirmed by the additional computed tomography. The numerical simulations demonstrated that robust determination of the total magnetic moment of lesions is possible. Thus, the proposed method is able to yield quantitative values for the minimum magnetic susceptibility of lesions.

CONCLUSIONS

A method has been developed for noninvasive, semiautomatic characterization of brain lesions based on magnetic resonance imaging data. Initial clinical results demonstrated that the proposed technique can be applied to diagnosis of lesions with calcifications or hemorrhages. If confirmed by larger studies, it bears the potential to obviate the need for confirmation with computed tomography.