Добірка наукової літератури з теми "Brain, Magnetic Resonance Imaging, Neuroscience, Diffusion-weighted MRI"

AbstractWith the increasing size of datasets used in medical imaging research, the need for automated data curation is arising. One important data curation task is the structured organization of a dataset for preserving integrity and ensuring reusability. Therefore, we investigated whether this data organization step can be automated. To this end, we designed a convolutional neural network (CNN) that automatically recognizes eight different brain magnetic resonance imaging (MRI) scan types based on visual appearance. Thus, our method is unaffected by inconsistent or missing scan metadata. It can recognize pre-contrast T1-weighted (T1w),post-contrast T1-weighted (T1wC), T2-weighted (T2w), proton density-weighted (PDw) and derived maps (e.g. apparent diffusion coefficient and cerebral blood flow). In a first experiment,we used scans of subjects with brain tumors: 11065 scans of 719 subjects for training, and 2369 scans of 192 subjects for testing. The CNN achieved an overall accuracy of 98.7%. In a second experiment, we trained the CNN on all 13434 scans from the first experiment and tested it on 7227 scans of 1318 Alzheimer’s subjects. Here, the CNN achieved an overall accuracy of 98.5%. In conclusion, our method can accurately predict scan type, and can quickly and automatically sort a brain MRI dataset virtually without the need for manual verification. In this way, our method can assist with properly organizing a dataset, which maximizes the shareability and integrity of the data.

Magnetic resonance imaging (MRI) has been used to investigate migraine pathophysiology because it is a non-invasive technique. The main aim of clinical imaging for patients with headaches is to exclude secondary headaches due to organic lesions. Conventional structural imaging techniques such as routine MRI demonstrate white matter lesions, changes in gray matter volume or cortical thickness, and cerebral blood flow in patients with migraine. Changes in metabolite levels are observed by magnetic resonance spectroscopy. Diffusion tensor imaging, neurite orientation dispersion, density imaging, and functional MRI reveal dynamic real-time functional changes in brain microstructures. These analyses have been applied not only for comparing patients with migraine and healthy controls but also for understanding the dynamic changes in brain function during the cyclic migraine ictal phase. Although these analyses have demonstrated migraine pathophysiology, there are still many limitations. Following the improvement in imaging technology, further research on this topic is in progress.

Diffusion-based magnetic resonance imaging (MRI) studies, namely diffusion-weighted imaging (DWI) and diffusion-tensor imaging (DTI), have been performed in the context of systemic lupus erythematosus (SLE), either with or without neuropsychiatric (NP) involvement, to deepen cerebral microstructure alterations. These techniques permit the measurement of the variations in random movement of water molecules in tissues, enabling their microarchitecture analysis. While DWI is recommended as part of the initial MRI assessment of SLE patients suspected for NP involvement, DTI is not routinely part of the instrumental evaluation for clinical purposes, and it has been mainly used for research. DWI and DTI studies revealed less restricted movement of water molecules inside cerebral white matter (WM), expression of a global loss of WM density, occurring in the context of SLE, prevalently, but not exclusively, in case of NP involvement. More advanced studies have combined DTI with other quantitative MRI techniques, to further characterize disease pathogenesis, while brain connectomes analysis revealed structural WM network disruption. In this narrative review, the authors provide a summary of the evidence regarding cerebral microstructure analysis by DWI and DTI studies in SLE, focusing on lessons learned and future research perspectives.

Although both common and crucian carp survived 2 h of anoxia at 18°C, the response of their brains to anoxia was quite different and indicative of the fact that the crucian carp is anoxia tolerant while the common carp is not. Using in vivo T2 and diffusion-weighted magnetic resonance imaging (MRI), we studied anoxia induced changes in brain volume, free water content (T2), and water homeostasis (water diffusion coefficient). The anoxic crucian carp showed no signs of brain swelling or changes in brain water homeostasis even after 24 h except for the optic lobes, where cellular edema was indicated. The entire common carp brain suffered from cellular edema, net water gain, and a volume increase (by 6.5%) that proceeded during 100 min normoxic recovery (by 10%). The common carp recovered from this insult, proving that the changes were reversible and suggesting that the oversized brain cavity allows brain swelling during energy deficiency without a resultant increase in intracranial pressure and global ischemia. It is tempting to suggest that this is a function of the large brain cavity seen in many ectothermic vertebrates.

AbstractExplorations of the relation between brain anatomy and functional connections in the brain are crucial for shedding more light on network connectivity that sustains brain communication. In this study, by means of an integrative approach, we examined both the structural and functional connections of the default mode network (DMN) in a group of sixteen healthy subjects. For each subject, the DMN was extracted from the structural and functional resonance imaging data; the areas that were part of the DMN were defined as the regions of interest. Then, the target network was structurally explored by diffusion-weighted imaging, tested by neurophysiological means, and retested by means of concurrent transcranial magnetic stimulation and electroencephalography (TMS-EEG). A series of correlational analyses were performed to explore the relationship between the amplitude of early-latency TMS-evoked potentials and the indexes of structural connectivity (weighted number of fibres and fractional anisotropy). Stimulation of the left or right parietal nodes of the DMN-induced activation in the contralateral parietal and frontocentral electrodes within 60 ms; this activation correlated with fractional anisotropy measures of the corpus callosum. These results showed that distant secondary activations after target stimulation can be predicted based on the target’s anatomical connections. Interestingly, structural features of the corpus callosum predicted the activation of the directly connected nodes, i.e., parietal-parietal nodes, and of the broader DMN network, i.e., parietal-frontal nodes, as identified with functional magnetic resonance imaging. Our results suggested that the proposed integrated approach would allow us to describe the contributory causal relationship between structural connectivity and functional connectivity of the DMN.

This issue on the genetics of brain imaging phenotypes is a celebration of the happy marriage between two of science's highly interesting fields: neuroscience and genetics. The articles collected here are ample evidence that a good deal of synergy exists in this marriage. A wide selection of papers is presented that provide many different perspectives on how genes cause variation in brain structure and function, which in turn influence behavioral phenotypes (including psychopathology). They are examples of the many different methodologies in contemporary genetics and neuroscience research. Genetic methodology includes genome-wide association (GWA), candidate-gene association, and twin studies. Sources of data on brain phenotypes include cortical gray matter (GM) structural/volumetric measures from magnetic resonance imaging (MRI); white matter (WM) measures from diffusion tensor imaging (DTI), such as fractional anisotropy; functional- (activity-) based measures from electroencephalography (EEG), and functional MRI (fMRI). Together, they reflect a combination of scientific fields that have seen great technological advances, whether it is the single-nucleotide polymorphism (SNP) array in genetics, the increasingly high-resolution MRI imaging, or high angular resolution diffusion imaging technique for measuring WM connective properties.

Abstract Wilson’s disease (WD) is an inherited disorder of copper metabolism. Multimodal magnetic resonance imaging (MRI) has been reported to provide evidence of the extent and severity of brain lesions. However, there are few studies related to the diagnosis of WD with multimodal MRI. Here, we reported a WD patient who was subjected to Sanger sequencing, conventional MRI, and multimodal MRI examinations, including susceptibility-weighted imaging (SWI) and arterial spin labeling (ASL). Sanger sequencing demonstrated two pathogenic mutations in exon 8 of the ATP7B gene. Slit-lamp examination revealed the presence of Kayser–Fleischer rings in both eyes, as well as low serum ceruloplasmin and high 24-h urinary copper excretion on admission. Although the substantia nigra, red nucleus, and lenticular nucleus on T1-weighted imaging and T2-weighted imaging were normal, SWI and ASL showed hypointensities in these regions. Besides, decreased cerebral blood flow was found in the lenticular nucleus and the head of caudate nucleus. The patient recovered well after 1 year and 9 months of follow-up, with only a Unified Wilson Disease Rating Scale score of 1 for neurological symptom. Brain multimodal MRI provided a thorough insight into the WD, which might make up for the deficiency of conventional MRI.

Abstract Background Hypoxic–ischemic encephalopathy (HIE) is the most commonly diagnosed neurological abnormality affecting children leading to severe neurological deficits and a cause of neonatal mortality. HIE constitutes a diagnostic challenge in the prematurely born and full-term neonates. HIE causes severe neurological deficit in children and many a times goes unnoticed in early stages. The various patterns of central nervous system (CNS) involvement in HIE are dependent on factors, such as severity and duration of hypoxia, and brain maturity in preterm and full-term patients. Magnetic resonance imaging (MRI) has prognostic significance in detecting patterns of HIE secondary to mild-to-moderate and severe hypoxias and the imaging findings are highly dependent on the time at which imaging is done. MRI helps determine the prognosis of brain development in patients with HIE. Objective This retrospective study elucidates the spectrum of MRI findings in preterm and full-term patients with HIE on MRI. Materials and Methods This retrospective descriptive study was conducted at a tertiary care center between April 2017 and May 2019 on 50 patients with a clinical diagnosis of HIE using a General Electric (GE) 1.5-Tesla MRI scanner. Various patterns of HIE were evaluated on MRI in preterm and full-term patients. Results This retrospective study evaluated MRI findings in 50 infants diagnosed with HIE. Eighteen (36%) were preterm and 32 (64%) were full-term patients. Thirty-five (70%) were male and 15 (30%) were female patients. In the current study, developmental delay was the most commonly associated clinical entity in both preterm and full-term patients. In preterm patients, periventricular leukomalacia was the most prevalent MRI finding, and in full-term patients, subcortical and periventricular white matter hyperintensities on T2-weighted and fluid-attenuated inversion recovery (FLAIR) sequences were most commonly encountered. Conclusion MRI is the primary imaging modality of choice in preterm and full-term patients with HIE, as it helps determine the severity of hypoxic–ischemic injury by understanding the pattern of brain involvement. In the current study, distinguishable patterns of MRI findings secondary to birth asphyxia and ischemic insult were elucidated in both preterm and full-term patients who are highly dependent on the level of brain maturity at the time of imaging. Regular MRI follow-up has a prognostic significance in HIE with accurate prediction of neurodevelopmental outcome on follow-up studies.

Traumatic brain injury (TBI) is a significant public health problem in the United States, especially for children and adolescents. Current epidemiological data estimate over 600,000 patients younger than 20 years are treated for TBI in emergency rooms annually. While many patients experience a full recovery, for others there can be long-lasting cognitive, neurological, psychological, and behavioral disruptions. TBI in youth can disrupt ongoing brain development and create added family stress during a formative period. The neuroimaging methods used to assess brain injury improve each year, providing researchers a more detailed characterization of the injury and recovery process. In this review, we cover current imaging methods used to quantify brain disruption post-injury, including structural magnetic resonance imaging (MRI), diffusion MRI, functional MRI, resting state fMRI, and magnetic resonance spectroscopy (MRS), with brief coverage of other methods, including electroencephalography (EEG), single-photon emission computed tomography (SPECT), and positron emission tomography (PET). We include studies focusing on pediatric moderate-severe TBI from 2 months post-injury and beyond. While the morbidity of pediatric TBI is considerable, continuing advances in imaging methods have the potential to identify new treatment targets that can lead to significant improvements in outcome.

This tutorial/review covers functional brain-imaging methods and results used to study language and reading disabilities. Although the main focus is on functional MRI and functional MR spectroscopy, other imaging techniques are discussed briefly such as positron emission tomography (PET), electroencephalography (EEG), magnetoencepholography (MEG), and MR diffusion imaging. These functional brain-imaging studies have demonstrated that dyslexia is a brain-based disorder and that serial imaging studies can be used to study the effect of treatment on functional brain activity.

The possibility to perform virtual, non-invasive, quantitative, in vivo histological assessments might revolutionize entire fields, among which clinical and cognitive neurosciences. Magnetic Resonance Imaging (MRI) is an ideal non-invasive imaging technique to achieve these goals. Tremendous advancements in the last decades have favored the transition of MRI scanners from “imaging devices” to “measurement devices” (Novikov, 2021), thus capable to yield measurements in physical units, which might be further combined to provide quantities describing histological properties of substrates. A central role in this community endeavor has been played by diffusion-weighted MRI (dMRI), which by measuring the dynamics of spin diffusion, allows inferences on geometrical properties of tissues. Yet, conventional dMRI methodologies suffer from poor specificity. In this thesis, techniques aiming at improving the specificity of microstructural descriptions have been explored in dMRI datasets supporting an increasing level of complexity of the dMRI signal representations. Applications in individuals with different age range, in different populations, and for different MRI scanner fields, have been considered. Firstly, tractography has been combined with Diffusion Tensor Imaging (DTI), an along-tract framework, and morphometry, in the study of the microstructure of the optic radiations in different groups of blind individuals. Secondly, DTI has been combined with Free-Water Imaging (FWI) to monitor the effect of proton-irradiation in a pediatric brain tumor case study. Thirdly, FWI and Diffusion Kurtosis Imaging (DKI) have been combined with an advanced thalamic segmentation framework to study the associations between motor performance and thalamic microstructure in a cohort of individuals affected by Parkinson’s disease. Finally, the largest contribution of this thesis is represented by the adaptation of the Correlation Tensor Imaging - a technique increasing the specificity of DKI harnessing Double Diffusion Encoding previously applied only in preclinical settings - for a clinical 3 T scanner. The ensuing investigation revealed new important insights on the sources of diffusional kurtosis, in particular of the microscopic kurtosis (μK), a component so far neglected by contemporary neuroimaging techniques, which might carry an important clinical role (Alves et al., 2022), and can now be accessed by clinical scanners. In conclusion, strategies to increase the specificity of microstructural descriptions in the brain are presented for different datasets, and their strength and limitations are discussed.

This dissertation describes the development and implementation of advanced slice-accelerated (SMS) MRI methods for imaging blood perfusion and water diffusion in the human brain. Since its introduction in 1977, Echo-Planar Imaging (EPI) paved the way toward a detailed assessment of the structural and functional properties of the human brain. Currently, EPI is one of the most important MRI techniques for neuroscientific studies and clinical applications. Despite its high prevalence in modern medical imaging, EPI still suffers from sub-optimal time efficiency - especially when high isotropic resolutions are required to adequately resolve sophisticated structures as the human brain. The utilization of novel slice-acceleration methods can help to overcome issues related to low temporal efficiency of EPI acquisitions. The aim of the four studies outlining this thesis is to overcome current limitations of EPI by developing methods for slice-accelerated MRI. The first experimental work of this thesis describes the development of a slice-accelerated MRI sequence for dynamic susceptibility contrast imaging. This method for assessing blood perfusion is commonly employed for brain tumor classifications in clinical practice. Following up, the second project of this thesis aims to extend SMS imaging to diffusion MRI at 7 Tesla. Here, a specialized acquisition method was developed employing various methods to overcome problems related to increased energy deposition and strong image distortion. The increased energy depositions for slice-accelerated diffusion MRI are due to specific radiofrequency (RF) excitation pulses. High energy depositions can limit the acquisition speed of SMS imaging, if high slice-acceleration factors are employed. Therefore, the third project of this thesis aimed at developing a specialized RF pulse to reduce the amount of energy deposition. The increased temporal efficiency of SMS imaging can be employed to acquire higher amounts of imaging data for signal averaging and more stable model fits. This is especially true for diffusion MRI measurements, which suffer from intrinsically low signal-to-noise ratios. However, the typically acquired magnitude MRI data introduce a noise bias in diffusion images with low signal-to-noise ratio. Therefore, the last project of this thesis aimed to resolve the pressing issue of noise bias in diffusion MRI. This was achieved by transforming the diffusion magnitude data into a real-valued data representation without noise bias. In combination, the developed methods enable rapid MRI measurements with high temporal efficiency. The diminished noise bias widens the scope of applications of slice- accelerated MRI with high temporal efficiency by enabling true signal averaging and unbiased model fits. Slice-accelerated imaging for the assessment of water diffusion and blood perfusion represents a major step in the field of neuroimaging. It demonstrates that cur- rent limitations regarding temporal efficiency of EPI can be overcome by utilizing modern data acquisition and reconstruction strategies.

Diffusion-weighted (DW) magnetic resonance imaging is an important neuroimaging technique that has successful applications in diagnosis of ischemic stroke and methods based on diffusion tensor imaging (DTI). Tensor measures have been used for detecting changes in tissue microstructure and for non-invasively tracing white matter connections in vivo. The most common image acquistion strategy is to use a DW single-shot echo-planar imaging (ss-EPI) pulse sequence, which is attractive due to its robustness to motion artefacts and high imaging speed. However, this sequence has limited achievable spatial resolution and suffers from geometric distortion and blurring artefacts. Readout-segmented echo-planar imaging (rs-EPI) is a DW sequence that is capable of acquiring high-resolution images by segmenting the acquisition of k- space into multiple shots. The fast, short readouts reduce distortion and blurring and the problem of artefacts due to motion-induced phase changes between shots can be overcome with navigator techniques. The rs-EPI sequence has two main shortcomings. (i) The method is slow to produce image volumes, which is limiting for clinical scans due to patient welfare and prevents us from acquiring very many directions in DTI. (ii) The sequence (like other diffusion techniques) is far from the optimum repetition time (TR) for acquiring data with the highest possible signal-to-noise ratio (SNR) in a given time. The work in this thesis seeks to address both of these important issues using a range of approaches. In Chapter 4 a partial Fourier extension is presented, which addresses point (i) by reducing the number of readout segments acquired and estimating the missing data. This allows reductions in scan time by approximately 40% and the reliability of the images is demonstrated in comparisons with the original images. The application of a simultaneous multi-slice scheme to rs-EPI, to address points (i) and (ii), is described in Chapter 5. Using the slice-accelerated rs-EPI sequence, tractography data were compared to ss-EPI data and high-resolution trace-weighted data were acquired in clinically relevant scan times. Finally, a 3D multi-slab extension that addresses point (i) is presented in Chapter 6. A 3D sequence could also allow higher resolution in the slice direction than 2D multi-slice methods, which are limited by the difficulties in exciting thin, accurate slices. A 3D version of rs-EPI was simulated and implemented and a k-space acquisition synchronised to the cardiac cycle showed substantial improvements in image artefacts compared to a conventional k-space acquisition.

Diffusion-weighted magnetic resonance imaging (MRI) has allowed unprecedented non-invasive mapping of brain neural connectivity in vivo by means of fiber tractography applications. Fiber tractography has emerged as a useful tool for mapping brain white matter connectivity prior to surgery or in an intraoperative setting. The advent of high angular resolution diffusion-weighted imaging (HARDI) techniques in MRI for fiber tractography has allowed mapping of fiber tracts in areas of complex white matter fiber crossings. Raw HARDI images, as a result of elevated diffusion-weighting, suffer from depressed signal-to-noise ratio (SNR) levels. The accuracy of fiber tractography is dependent on the performance of the various methods extracting dominant fiber orientations from the HARDI-measured noisy diffusivity profiles. These methods will be sensitive to and directly affected by the noise. In the first part of the thesis this issue is addressed by applying an objective and adaptive smoothing to the noisy HARDI data via generalized cross-validation (GCV) by means of the smoothing splines on the sphere method for estimating the smooth diffusivity profiles in three dimensional diffusion space. Subsequently, fiber orientation distribution functions (ODFs) that reveal dominant fiber orientations in fiber crossings are then reconstructed from the smoothed diffusivity profiles using the Funk-Radon transform. Previous ODF smoothing techniques have been subjective and non-adaptive to data SNR. The GCV-smoothed ODFs from our method are accurate and are smoothed without external intervention facilitating more precise fiber tractography. Diffusion-weighted MRI studies in amyotrophic lateral sclerosis (ALS) have revealed significant changes in diffusion parameters in ALS patient brains. With the need for early detection of possibly discrete upper motor neuron (UMN) degeneration signs in patients with early ALS, a HARDI study is applied in order to investigate diffusion-sensitive changes reflected in the diffusion tensor imaging (DTI) measures axial and radial diffusivity as well as the more commonly used measures fractional anisotropy (FA) and mean diffusivity (MD). The hypothesis is that there would be added utility in considering axial and radial diffusivities which directly reflect changes in the diffusion tensors in addition to FA and MD to aid in revealing neurodegenerative changes in ALS. In addition, applying adaptive smoothing via GCV to the HARDI data further facilitates the application of fiber tractography by automatically eliminating spurious noisy peaks in reconstructed ODFs that would mislead fiber tracking.

This work explores if combining information from multiple Magnetic Resonance Imaging (MRI) modalities provides improved interpretation of brain biological architecture as each MR modality can reveal different characteristics of underlying anatomical structures. Structural MRI provides a means for high-resolution quantitative study of brain morphometry. Diffusion-weighted MR imaging (DWI) allows for low-resolution modeling of diffusivity properties of water molecules. Structural and diffusion-weighted MRI modalities are commonly used for monitoring the biological architecture of the brain in normal development or neurodegenerative disease processes. Structural MRI provides an overall map of brain tissue organization that is useful for identifying distinct anatomical boundaries that define gross organization of the brain. DWI models provide a reflection of the micro-structure of white matter (WM), thereby providing insightful information for measuring localized tissue properties or for generating maps of brain connectivity. Multispectral information from different structural MR modalities can lead to better delineation of anatomical boundaries, but careful considerations should be taken to deal with increased partial volume effects (PVE) when input modalities are provided in different spatial resolutions. Interpretation of diffusion-weighted MRI is strongly limited by its relatively low spatial resolution. PVE's are an inherent consequence of the limited spatial resolution in low-resolution images like DWI. This work develops novel methods to enhance tissue classification by addressing challenges of partial volume effects encountered from multi-modal data that are provided in different spatial resolutions. Additionally, this project addresses PVE in low-resolution DWI scans by introducing a novel super-resolution reconstruction approach that uses prior information from multi-modal structural MR images provided in higher spatial resolution. The major contributions of this work include: 1) Enhancing multi-modal tissue classification by addressing increased PVE when multispectral information come from different spatial resolutions. A novel method was introduced to find pure spatial samples that are not affected by partial volume composition. Once detecting pure samples, we can safely integrate multi-modal information in training/initialization of the classifier for an enhanced segmentation quality. Our method operates in physical spatial domain and is not limited by the constraints of voxel lattice spaces of different input modalities. 2) Enhancing the spatial resolution of DWI scans by introducing a novel method for super-resolution reconstruction of diffusion-weighted imaging data using high biological-resolution information provided by structural MRI data such that the voxel values at tissue boundaries of the reconstructed DWI image will be in agreement with the actual anatomical definitions of morphological data. We used 2D phantom data and 3D simulated multi-modal MR scans for quantitative evaluation of introduced tissue classification approach. The phantom study result demonstrates that the segmentation error rate is reduced when training samples were selected only from the pure samples. Quantitative results using Dice index from 3D simulated MR scans proves that the multi-modal segmentation quality with low-resolution second modality can approach the accuracy of high-resolution multi-modal segmentation when pure samples are incorporated in the training of classifier. We used high-resolution DWI from Human Connectome Project (HCP) as a gold standard for super-resolution reconstruction evaluation to measure the effectiveness of our method to recover high-resolution extrapolations from low-resolution DWI data using three evaluation approaches consisting of brain tractography, rotationally invariant scalars and tensor properties. Our validation demonstrates a significant improvement in the performance of developed approach in providing accurate assessment of brain connectivity and recovering the high-resolution rotationally invariant scalars (RIS) and tensor property measurements when our approach was compared with two common methods in the literature. The novel methods of this work provide important improvements in tools that assist with improving interpretation of brain biological architecture. We demonstrate an increased sensitivity for volumetric and diffusion measures commonly used in clinical trials to advance our understanding of both normal development and disease induced degeneration. The improved sensitivity may lead to a substantial decrease in the necessary sample size required to demonstrate statistical significance and thereby may reduce the cost of future studies or may allow more clinical and observational trials to be performed in parallel.

Dopamine is an important neurotransmitter that is involved in several human functions such as reward, cognition, emotions and movement. Abnormalities of the neurotransmitter itself, or the dopamine receptors through which it exerts its actions, contribute to a wide range of psychiatric and neurological disorders such as Parkinson’s disease and schizophrenia. Thus far, despite the great interest and extensive research, the exact role of dopamine and the causalities of dopamine related disorders are not fully understood. Here we have developed multimodal imaging methods, to investigate the release of dopamine and the distribution of the dopamine D2-like receptor family in-vivo in healthy humans. We use the [¹¹C]PHNO PET ligand, which enables exploration of dopamine-related parameters in striatal regions, and for the first time in extrastriatal regions, that are known to be associated with distinctive functions and disorders. Our methods involve robust approaches for the manual and automated delineation of these brain regions, in terms of structural and functional organisation, using information from structural and diffusion MRI images. These data have been combined with [¹¹C]PHNO PET data for quantitative dopamine imaging. Our investigation has revealed the distribution and the relative density of the D3R and D2R sites of the dopamine D2-like receptor family, in healthy humans. In addition, we have demonstrated that the release of dopamine has a functional rather than a structural specificity and that the relative densities of the D3R and D2R sites do not drive this specificity. We have also shown that the dopamine D3R receptor is primarily distributed in regions that have a central role in reward and addiction. A finding that supports theories that assigns a primarily limbic role to the D3R.

Tese de mestrado integrado em Engenharia Biomédica e Biofísica (Radiações em Diagnóstico e Terapia), apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2012
A neuroanatomia humana tem sido objecto de estudo científico desde que surgiu o interesse na organização do corpo humano e nas suas funções, quer como um todo quer através das partes que o constituem. Para atingir este fim, as autópsias foram a primeira forma de revelar algum conhecimento, o qual tem vindo a ser catalogado e sistematizado à medida que a medicina evolui. Passando por novas técnicas de conservação e tratamento de tecido humano, de que são exemplo as dissecções de Klinger, nas quais se fazem secções de material conservado criogenicamente, bem como por estudos histológicos através da utilização de corantes, conseguiu-se uma forma complementar de realizar estes estudos. Permanecia, no entanto, a impossibilidade de analisar in vivo a estrutura e função dos diferentes sistemas que constitutem o Homem. Com o surgimento das técnicas imagiológicas o diagnóstico e monitorização do corpo humano, bem como das patologias a ele associadas, melhoraram consideravelmente. Mais recentemente, com o aparecimento da ressonância magnética (MRI: do Inglês "Magnetic Resonance Imaging"), tornou-se possível estudar as propriedades magnéticas do tecido, reflectindo as suas características intrínsecas com base na aplicação de impulsos de radiofrequência. Através de ressonância magnética é possível estudar essas propriedades em vários núcleos atómicos, sendo mais comum o estudo do hidrogénio, pois somos maioritariamente consistituídos por água e gordura. Uma vez que só é possível medir variações do campo magnético, aplicam-se impulsos de radiofrequência para perturbar o equilíbrio dos spins e medir os seus mecanismos de relaxação, os quais, indirectamente, reflectem a estrutura do tecido. Contudo, o sinal medido é desprovido de qualquer informação espacial. De facto, para podermos proceder a essa quantificação, é necessária a utilização de gradientes de campo magnético, que permitem modificar localmente a frequência de precessão dos protões, através da alteração local do campo magnético, permitindo assim, adquirir o sinal de forma sequencial. A informação obtida constitui uma função variável no espaço e através da transformação de Fourier pode ser quantificada em frequências espaciais, sendo estes dados armazenados no espaço k. O preencimento deste espaço, caracterizado por frequências espaciais, bem como os gradientes de campo magnético que são aplicados, permitem determinar a resolução da imagem que podemos obter, aplicando uma transformação de Fourier inversa. O estudo da ressonância magnética não se restringe à análise da estrutura mas também ao estudo da função e difusão das moléculas de água. A difusão é um processo aleatório, que se traduz pelo movimento térmico das moléculas de água, e o seu estudo permite inferir sobre o estado do tecido e microestrutura associada, de uma forma não invasiva e in vivo. A técnica de imagiologia de ressonância magnética ponderada por difusão (DWI: do Inglês "Diffusion Weighted Imaging") permite o estudo da direccionalidade das moléculas de água e extracção de índices que reflectem directamente a integridade dos tecidos biológicos. De modo a sensibilizar as moléculas de água à difusão, é necessário aplicar sequências de ressonância magnética modificadas, nas quais se aplicam gradientes de campo magnético de difusão para quantificar o deslocamento das moléculas e a sua relação com o coeficiente de difusão das mesmas. Num ambiente livre e sem barreiras a difusão das moléculas de água é isotrópica, uma vez que se apresenta igual em todas as direcções. Todavia, tal não se verifica no corpo humano. A presença destas barreiras leva a que, na verdade, apenas possa ser medido um coeficiente de difusão aparente. Este, por sua vez, traduz a interacção entre as moléculas de água com a microestrutura e, como tal, uma anisotropia na sua difusão. Como caso particular de difusão anisotrópica a nível cerebral, tem-se a difusão das moléculas de água na matéria branca, uma vez que esta apresenta uma direccionalidade preferencial de acordo com a orientação dos axónios, visto estarem presentes menos restrições à sua propagação, ao contrário do que acontece com a direcção perpendicular (devido à membrana celular e às bainhas de mielina). Por oposição, a matéria cinzenta, constituída pelo aglomerado dos corpos celulares dos neurónios, e o líquido cefalorraquidiano apresentam uma difusão sem direcção preferencial (i.e. aproximadamente isotrópica). A informação obtida através da difusão das moléculas de água encontra-se limitada pelo número de direcções segundo o qual aplicamos os gradientes de difusão. Deste modo, surgiu a imagiologia por tensor de difusão (DTI: do Inglês "Diffusion Tensor Imaging"). Esta técnica permite extrair informação acerca da tridimensionalidade da distribuição da difusão de moléculas de água através da aplicação de seis gradientes de difusão não colineares entre si. A distribuição destas moléculas pode, então, ser vista como um elipsóide, no qual o principal vector próprio do tensor representa a contribuição da difusão das moléculas segundo a direcção do axónio (ou paralela), sendo os dois restantes componentes responsáveis pela contribuição transversal. Além da difusividade média (MD: do Inglês "Mean Diffusivity") e das contribuições da difusão paralela (MD//) e perpendicular (MD ) às fibras, é também possível extrair outros índices, como a anisotropia fraccional (FA: do Inglês "Fractional Anisotropy"), que fornece informação acerca da percentagem de difusão anisotrópica num determinado voxel. Para a matéria branca, tal como já foi referido, existe difusão preferencial e, portanto, a anisotropia fraccional será elevada. Por outro lado, para a matéria cinzenta e para o líquido cefalorraquidiano, verificar-se-á uma FA reduzida, devido à ausência de anisotropia. Todavia, regiões com reduzida anisotropia fraccional podem camuflar regiões de conformação de cruzamento de fibras, ou fibras muito anguladas, que a imagiologia por tensor de difusão não consegue resolver. A razão para esta limitação reside no número reduzido de diferentes direcções de difusão que são exploradas, assim como o pressuposto de que a distribuição das moléculas de água é Gaussiana em todo o cérebro, o que não é necessariamente verdade. A fim de se ultrapassar estas limitações, novas técnicas surgiram, nomeadamente as de elevada resolução angular (HARDI: do Inglês "High Angular Resolution Diffusion Imaging"). Estas fazem uso de uma aquisição em função de múltiplas direcções de gradiente e de uma diferente modelação dos dados obtidos, dividindo-se em dois tipos. As técnicas livres de modelos permitem extrair uma função de distribuição da orientação das fibras num determinado voxel directamente do sinal e/ou transformações da função densidade de probabilidade do deslocamento das moléculas de água. Contrariamente, as técnicas baseadas em modelos admitem existir determinados constrangimentos anatómicos e que o sinal proveniente de um determinado voxel é originado por um conjunto de sinais individuais de fibras, caracterizados por uma distribuição preferencial das direcções das fibras. Todos estes métodos têm como objectivo principal recuperar a direcção preferencial da difusão das moléculas de água e reconstruir um trajecto tridimensional que represente a organização das fibras neuronais, pelo que se designam métodos de tractografia. Esta representa a única ferramenta não invasiva de visualização in vivo da matéria branca cerebral e o seu estudo tem revelado uma grande expansão associada ao estabelecimento de marcador biológico para diversas patologias. Adicionalmente, esta técnica tem vindo a tornar-se uma modalidade clínica de rotina e de diversos protocolos de investigação, sendo inclusivamente utilizada para complementar o planeamento em cirurgia, devido à natureza dos dados que gera. Particularmente no caso de dissecções manuais, nas quais os dados de tractografia são manuseados por pessoal especializado, com vista a realizar a parcelização de diferentes tractos de interesse, o processo é moroso e dependente do utilizador, revelando-se necessária a automatização do mesmo. Na realidade, já existem técnicas automáticas que fazem uso de algoritmos de agregação1, nos quais fibras são analisadas e agrupadas segundo características semelhantes, assim como técnicas baseadas em regiões de interesse, em que se extraem apenas os tractos seleccionados entre as regiões escolhidas. O objectivo principal desta dissertação prende-se com a análise automática de dados de tractografia, bem como a parcelização personalizada de tractos de interesse, também esta automática. Em primeiro lugar, foi desenvolvido um algoritmo capaz de lidar automaticamente com funções básicas de carregamento dos ficheiros de tractografia, o seu armazenamento em variáveis fáceis de manusear e a sua filtragem básica de acordo com regiões de interesse de teste. Neste processo de filtragem é feita a avaliação das fibras que atravessam a região de interesse considerada. Assim, após a localização das fibras entre as regiões de interesse os tractos resultantes podem ser guardados de duas formas, as quais têm, necessariamente, que ser especificadas antes de utilizar o software: um ficheiro que contém todas as fibras resultantes da parcelização e outro que contém o mapa de densidade associado, isto é, o número de fibras que se encontra em cada voxel. Após esta fase inicial, a flexibilidade e complexidade do software foi aumentando, uma vez que foram implementados novos filtros e a possibilidade de utilizar regiões de interesse de diferentes espaços anatómicos padrão. Fazendo uma análise a esta última melhoria, pode referir-se que, através de um procedimento de registo não linear da imagem anatómica do espaço padrão ao espaço individual de cada sujeito, foi possível, de forma automática, guardar o campo de deformações que caracteriza a transformação e, assim, gerar regiões de interesse personalizadas ao espaço do sujeito. Estas regiões de interesse serviram depois para a parcelização básica e para seleccionar tractos, mas também para filtragens adicionais, como a exclusão de fibras artefactuosas2 e um filtro especial, no qual apenas os pontos que ligam directamente as diferentes regiões são mantidos. Além do que já foi referido, recorreu-se também à aplicação de planos de interesse que actuam como constrangimentos neuroanatómicos, o que não permite, por exemplo, no caso da radiação óptica, que as fibras se propaguem para o lobo frontal. Esta ferramenta foi utilizada com sucesso para a parcelização automática do Fascículo Arcuado, Corpo Caloso e Radiação Óptica, tendo sido feita a comparação com a dissecção manual, em todos os casos. O estudo do Fasciculo Arcuado demonstrou ser o teste ideal para a ferramenta desenvolvida na medida que permitiu identificar o segmento longo, assim como descrito na literatura. O método automático de duas regiões de interesse deu a origem aos mesmos resultados obtidos manualmente e permitiu confirmar a necessidade de estudos mais aprofundados. Aumentando a complexidade do estudo, realizou-se a parcelização do Corpo Caloso de acordo com conectividade estrutural, isto é, com diferentes regiões envolvidas em funções distintas. Procedeu-se deste modo, e não com base em informação acerca de divisões geométricas, uma vez que estas já demonstraram incongruências quando correlacionadas com subdivisões funcionais. O uso adicional de regiões de interesse para a exclusão de fibras demonstrou-se benéfico na obtenção dos mapas finais. Finalmente, incluiu-se a utilização de um novo filtro para realizar a parcelização da Radiação Óptica, comparando os resultados para DTI e SD(do Inglês "Spherical Deconvolution"). Foi possível determinar limitações na primeira técnica que foram, no entanto, ultrapassadas pela utilização de SD. O atlas final gerado apresenta-se como uma mais-valia para o planeamento cirúrgico num ambiente clínico. O desenvolvimento desta ferramenta resultou em duas apresentações orais em conferências internacionais e encontra-se, de momento, a ser melhorada, a fim de se submeter um artigo de investigação original. Embora se tenha chegado a um resultado final positivo, tendo em conta a meta previamente estabelecida, está aberto o caminho para o seu aperfeiçoamento. Como exemplo disso, poder-se-á recorrer ao uso combinado das duas abordagens de parcelização automática e à utilização de índices específicos dos tractos, o que poderá trazer uma nova força à delineação dos tractos de interesse. Adicionalmente, é também possível melhorar os algoritmos de registo de imagem, tendo em conta a elevada variabilidade anatómica que alguns sujeitos apresentam. Como nota final, gostaria apenas de salientar que a imagiologia por difusão e, em particular, a tractografia, têm ainda muito espaço para progredir. A veracidade desta afirmação traduz-se pela existência de uma grande variedade de modelos e algoritmos implementados, sem que, no entanto, exista consenso na comunidade científica acerca da melhor abordagem a seguir.
Diffusion weighted imaging (DWI) has provided us a non-invasive technique to determine physiological information and infer about tissue microstructure. The human body is filled with barriers affecting the mobility of molecules and preventing it from being constant in different directions (anisotropic diffusion). In the brain, the sources for this anisotropy arise from dense packing axons and from the myelin sheath that surrounds them. Only with Diffusion Tensor Imaging (DTI) it was possible to fully characterize anisotropy by offering estimations for average diffusivities in each voxel. However, these methods were limited, not being able to reflect the index of anisotropic diffusion in regions with complex fibre conformations. It was possible to reduce those problems through the acquisition of many gradient directions with High Angular Resolution Diffusion Imaging (HARDI). There are model-free approaches such as Diffusion Spectrum Imaging (DSI) and Q-ball Imaging (QBI) which retrieve an orientation distribution function (ODF) directly from the water molecular displacement. Another method is Spherical Deconvolution, which is a model-based approach based on the computation of a fibre orientation distribution (FOD) from the deconvolution of the diffusion signal and a chosen fibre response function. Reconstructing the fibre orientations from the diffusion profile, generates a three-dimensional reconstruction of neuronal fibres (Tractography) whether in a deterministic, probabilistic or global way. Tractography has two main purposes: non-invasive and in vivo mapping of human white matter and neurosurgical planning. In order to achieve those purposes it is common to apply parcellation techniques which can be subdivided into ROI-based or Clustering base. The aim of this project is to develop an automated method of tract-based parcellation of different brain regions. This tool is essential to retrieve information about the architecture and connectivity of the brain, overcoming time consuming and expertise related issues derived from manual dissections. Firstly we investigated basic functions to handle diffusion and tractography data. In particular, we focused on how to load track files, filter them according to regions of interest and save the output in different formats. Results were always compared with manual dissection. The developed tool increased complexity by introduction a new filtering and the use of regions of interest from different standard spaces, created trough non-linear registrations. Three major tracts of interest were analysed: Arcuate Fasciculus, Corpus Callosum and Optic Radiation.

AbstractDiffusion-weighted magnetic resonance imaging (MRI) is sensitive to ensemble-averaged molecular displacements, which provide valuable information on e.g. structural anisotropy in brain tissue. However, a concrete interpretation of diffusion-weighted MRI data in terms of physiological or structural parameters turns out to be extremely challenging. One of the main reasons for this is the multi-scale nature of the diffusion-weighted signal, as it is sensitive to the microscopic motion of particles averaged over macroscopic volumes. In order to analyze the geometrical patterns that occur in (diffusion-weighted measurements of) biological tissue and many other structures, we may invoke tools from the field of stochastic geometry. Stochastic geometry describes statistical methods and models that apply to random geometrical patterns of which we may only know the distribution. Despite its many uses in geology, astronomy, telecommunications, etc., its application in diffusion-weighted MRI has so far remained limited. In this work we review some fundamental results in the field of diffusion-weighted MRI from a stochastic geometrical perspective, and discuss briefly for which other questions stochastic geometry may prove useful. The observations presented in this paper are partly inspired by the Workshop on Diffusion MRI and Stochastic Geometry held at Sandbjerg Estate (Denmark) in 2019, which aimed to foster communication and collaboration between the two fields of research.

While the neuroscience of sleep has traditionally been studied using electroencephalography (EEG), newer technologies have allowed for an enriched understanding of the brain’s ongoing activity during transitions into sleep, as well as during the distinct stages of sleep observed in humans. Neuroimaging techniques such as magnetic resonance imaging (MRI), functional MRI (fMRI), voxel-based morphometry (VBM), diffusion tensor imaging (DTI), magnetic resonance spectroscopy (MRS), positron emission tomography (PET), and single-photon emission computed tomography (SPECT) allow researchers a window into the brain during both waking and sleep. As an extension, deviations from brain activity patterns observed in healthy good sleepers give clues to the specific brain abnormalities associated with disorders of sleep such as insomnia. This chapter will provide a selected overview of neuroimaging studies in sleep and sleep disorders.

Diffusion Tensor Imaging (DTI) is a magnetic resonance imaging (MRI) modality which can significantly improve our understanding of the brain structures and neural connectivity. DTI measures are thought to be representative of brain tissue microstructure and are particularly useful for examining organized brain regions, such as white matter tract areas. DTI measures the water diffusion tensor using diffusion weighted pulse sequences which are sensitive to microscopic random water motion. The resulting diffusion weighted images (DWI) display and allow quantification of how water diffuses along axes or diffusion encoding directions. This can help to measure and quantify the tissue’s orientation and structure, making it an ideal tool for examining cerebral white matter and neural fiber tracts. In this chapter the authors discuss the theoretical aspects of DTI, the information that can be extracted from DTI data, and the use of the extracted information for the reconstruction of fiber tracts and the diagnosis of a disease. In addition, a review of known fiber tracking algorithms is presented.

Brain imaging is essential for the diagnosis of acute stroke and vascular aphasia. Magnetic resonance imaging (MRI) is the modality of choice for the etiological diagnosis of aphasia, the assessment of its severity, and the prediction of recovery. Diffusion weighted imaging is used to detect, localize, and quantify the extension of the irreversibly injured brain tissue called ischemic core. Perfusion weighted imaging (from MRI or CT) is useful to assess the extension of hypoperfused but salvageable tissue called penumbra. Functional imaging (positron emission tomography (PET), functional MRI (fMRI)) may help predicting recovery and is useful for the understanding of language networks and individual variability. This chapter is meant to review the state of the art of morphological and functional imaging of vascular aphasia and to illustrate the MRI profiles of different aphasic syndromes.

Neuroimaging plays a key role in management of critically ill neonates with neurological problems. Magnetic Resonance Imaging (MRI) is the most commonly used neuroimaging modality in evaluation of neonatal encephalopathy, because MRI provides better image quality and accurate delineation of the lesion. Newer modalities of MRI like Diffusion Weighted Imaging (DWI), Diffusion Tensor Imaging (DTI) are useful in identifying the brain lesion and also in predicting the neurodevelopmental outcome. Magnetic Resonance Angiography (MRA) and Magnetic Resonance Venography (MRV) are used to assess the cerebral arteries and veins with or without the use of contrast material. Arterial Spin Labelling (ASL) MRI and Phase Contrast (PC) MRI are newer modalities of MRI used to assess the cerebral perfusion without the use of contrast material. Magnetic Resonance Spectroscopy (MRS) is a functional MRI modality used to assess the level of brain metabolites which help us in diagnosing neuro metabolic disorders, peroxisomal disorders and mitochondrial disorders. Several predictive scores are available based on the size and location of lesions in MRI, and these scores are used to predict the neurodevelopmental outcome in term neonates with encephalopathy. MRI at term equivalent age in preterm neonates used to predict neurodevelopmental outcome in later life.

Historically, the success of DBS depends on the accuracy of electrode localization in neuroanatomical structures. With time, diffusion-weighted magnetic resonance imaging (MRI) and functional MRI have been introduced to study the structural connectivity and functional connectivity in patients with neurodegenerative disorders such as PD. Unlike the traditional lesion-based stimulation theory, this new network stimulation theory suggested that stimulation of specific brain circuits can modulate the pathological network and restore it to its physiological state, hence causing normalization of human brain connectome in PD patients. In this review, we discuss the feasibility of network-based stimulation and the use of connectomic DBS in PD.

Abstract Finite element analysis is used to study brain axonal injury and develop Brain White Matter (BWM) models while accounting for both the strain magnitude and the strain rate. These models are becoming more sophisticated and complicated due to the complex nature of the BMW composite structure with different material properties for each constituent phase. State-of-the-art studies, focus on employing techniques that combine information about the local axonal directionality in different areas of the brain with diagnostic tools such as Diffusion-Weighted Magnetic Resonance Imaging (Diffusion-MRI). The diffusion-MRI data offers localization and orientation information of axonal tracks which are analyzed in finite element models to simulate virtual loading scenarios. Here, a BMW biphasic material model comprised of axons and neuroglia is considered. The model’s architectural anisotropy represented by a multitude of axonal orientations, that depend on specific brain regions, adds to its complexity. During this effort, we develop a finite element method to merge micro-scale Representative Volume Elements (RVEs) with orthotropic frequency domain viscoelasticity to an integrated macro-scale BWM finite element model, which incorporates local axonal orientation. Previous studies of this group focused on building RVEs that combined different volume fractions of axons and neuroglia and simulating their anisotropic viscoelastic properties. Via the proposed model, we can assign material properties and local architecture on each element based on the information from the orientation of the axonal traces. Consecutively, a BWM finite element model is derived with fully defined both material properties and material orientation. The frequency-domain dynamic response of the BMW model is analyzed to simulate larger scale diagnostic modalities such as MRI and MRE.

Mild traumatic brain injury (TBI) is a very common injury to service members in recent conflicts. Computational models can offer insights in understanding the underlying mechanism of brain injury, which can aid in the development of effective personal protective equipment. This paper attempts to correlate simulation results with clinical data from advanced techniques such as magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), functional MRI (fMRI), MR spectroscopy and susceptibility weighted imaging (SWI), to identify TBI related subtle alterations in brain morphology, function and metabolism. High-resolution image data were obtained from the MRI scan of a young adult male, from a concussive head injury caused by a road traffic accident. The falling accident of human was modeled by combing high-resolution human head model with an articulated human body model. This mixed, multi-fidelity computational modeling approach can efficiently investigate such accident-related TBI. A high-fidelity computational head model was used to accurately reproduce the complex structures of the head. For most soft materials, the hyper-viscoelastic model was used to captures the strain rate dependence and finite strain nonlinearity. Stiffer materials, such as bony structure were simulated using an elasto-plastic material model to capture the permanent deformation. We used the enhanced linear tetrahedral elements to remove the parasitic locking problem in modeling such incompressible biological tissues. The bio-fidelity of human head model was validated from human cadaver tests. The accidental fall was reconstructed using such multi-fidelity models. The localized large deformation in the head was simulated and compared with the MRI images. The shear stress and shear strain were used to correlate with the post-accident medical images with respect to the injury location and severity in the brain. The correspondence between model results and MRI findings further validates the human head models and enhances our understanding of the mechanism, extent and impact of TBI.