Co-registration of paired histological sections and MRI scans of the rabbit larynx

Co-registering images of different modalities, termed intermodal image registration, is an important tool in improving our understanding of how certain features detectable in one modality might manifest in the other. However, structural changes – usually the result of tissue processing or noise in image acquisition – can make matching difficult. In this thesis, I outline a pre-processing protocol for co-registration of paired histological sections and MRI scans as well as discuss different co-registration strategies using the rabbit larynx as a model system

Fitting a biomechanical model of the folds to high-speed video data through bayesian estimation

High-speed video recording of the vocal folds during sustained phonation has become a widespread diagnostic tool, and the development of imaging techniques able to perform automated tracking and analysis of relevant glottal cues, such as folds edge position or glottal area, is an active research field. In this paper, a vocal folds vibration analysis method based on the processing of visual data through a biomechanical model of the layngeal dynamics is proposed. The procedure relies on a Bayesian non-stationary estimation of the biomechanical model parameters and state, to fit the folds edge position extracted from the high-speed video endoscopic data. This finely tuned dynamical model is then used as a state transition model in a Bayesian setting, and it allows to obtain a physiologically motivated estimation of upper and lower vocal folds edge position. Based on model prediction, an hypothesis on the lower fold position can be made even in complete fold occlusion conditions occurring during the end of the closed phase and the beginning of the open phase of the glottal cycle. To demonstrate the suitability of the procedure, the method is assessed on a set of audiovisual recordings featuring high-speed video endoscopic data from healthy subjects producing sustained voiced phonation with different laryngeal settings

Models and analysis of vocal emissions for biomedical applications: 5th International Workshop: December 13-15, 2007, Firenze, Italy

The MAVEBA Workshop proceedings, held on a biannual basis, collect the scientific papers presented both as oral and poster contributions, during the conference. The main subjects are: development of theoretical and mechanical models as an aid to the study of main phonatory dysfunctions, as well as the biomedical engineering methods for the analysis of voice signals and images, as a support to clinical diagnosis and classification of vocal pathologies. The Workshop has the sponsorship of: Ente Cassa Risparmio di Firenze, COST Action 2103, Biomedical Signal Processing and Control Journal (Elsevier Eds.), IEEE Biomedical Engineering Soc. Special Issues of International Journals have been, and will be, published, collecting selected papers from the conference

운율 정보를 이용한 마비말장애 음성 자동 검출 및 평가

학위논문 (석사) -- 서울대학교 대학원 : 인문대학 언어학과, 2020. 8. Minhwa Chung.말장애는 신경계 또는 퇴행성 질환에서 가장 빨리 나타나는 증 상 중 하나이다. 마비말장애는 파킨슨병, 뇌성 마비, 근위축성 측삭 경화증, 다발성 경화증 환자 등 다양한 환자군에서 나타난다. 마비말장애는 조음기관 신경의 손상으로 부정확한 조음을 주요 특징으로 가지고, 운율에도 영향을 미치는 것으로 보고된다. 선행 연구에서는 운율 기반 측정치를 비장애 발화와 마비말장애 발화를 구별하는 것에 사용했다. 임상 현장에서는 마비말장애에 대한 운율 기반 분석이 마비말장애를 진단하거나 장애 양상에 따른 알맞은 치료법을 준비하는 것에 도움이 될 것이다. 따라서 마비말장애가 운율에 영향을 미치는 양상뿐만 아니라 마비말장애의 운율 특징을 긴밀하게 살펴보는 것이 필요하다. 구체 적으로, 운율이 어떤 측면에서 마비말장애에 영향을 받는지, 그리고 운율 애가 장애 정도에 따라 어떻게 다르게 나타나는지에 대한 분석이 필요하다. 본 논문은 음높이, 음질, 말속도, 리듬 등 운율을 다양한 측면에 서 살펴보고, 마비말장애 검출 및 평가에 사용하였다. 추출된 운율 특징들은 몇 가지 특징 선택 알고리즘을 통해 최적화되어 머신러닝 기반 분류기의 입력값으로 사용되었다. 분류기의 성능은 정확도, 정밀도, 재현율, F1-점수로 평가되었다. 또한, 본 논문은 장애 중증도(경도, 중등도, 심도)에 따라 운율 정보 사용의 유용성을 분석하였다. 마지막으로, 장애 발화 수집이 어려운 만큼, 본 연구는 교차 언어 분류기를 사용하였다. 한국어와 영어 장애 발화가 훈련 셋으로 사용되었으며, 테스트셋으로는 각 목표 언어만이 사용되었다. 실험 결과는 다음과 같이 세 가지를 시사한다. 첫째, 운율 정보 를 사용하는 것은 마비말장애 검출 및 평가에 도움이 된다. MFCC 만을 사용했을 때와 비교했을 때, 운율 정보를 함께 사용하는 것이 한국어와 영어 데이터셋 모두에서 도움이 되었다. 둘째, 운율 정보는 평가에 특히 유용하다. 영어의 경우 검출과 평가에서 각각 1.82%와 20.6%의 상대적 정확도 향상을 보였다. 한국어의 경우 검출에서는 향상을 보이지 않았지만, 평가에서는 13.6%의 상대적 향상이 나타났다. 셋째, 교차 언어 분류기는 단일 언어 분류기보다 향상된 결과를 보인다. 실험 결과 교차언어 분류기는 단일 언어 분류기와 비교했을 때 상대적으로 4.12% 높은 정확도를 보였다. 이것은 특정 운율 장애는 범언어적 특징을 가지며, 다른 언어 데이터를 포함시켜 데이터가 부족한 훈련 셋을 보완할 수 있 음을 시사한다.One of the earliest cues for neurological or degenerative disorders are speech impairments. Individuals with Parkinsons Disease, Cerebral Palsy, Amyotrophic lateral Sclerosis, Multiple Sclerosis among others are often diagnosed with dysarthria. Dysarthria is a group of speech disorders mainly affecting the articulatory muscles which eventually leads to severe misarticulation. However, impairments in the suprasegmental domain are also present and previous studies have shown that the prosodic patterns of speakers with dysarthria differ from the prosody of healthy speakers. In a clinical setting, a prosodic-based analysis of dysarthric speech can be helpful for diagnosing the presence of dysarthria. Therefore, there is a need to not only determine how the prosody of speech is affected by dysarthria, but also what aspects of prosody are more affected and how prosodic impairments change by the severity of dysarthria. In the current study, several prosodic features related to pitch, voice quality, rhythm and speech rate are used as features for detecting dysarthria in a given speech signal. A variety of feature selection methods are utilized to determine which set of features are optimal for accurate detection. After selecting an optimal set of prosodic features we use them as input to machine learning-based classifiers and assess the performance using the evaluation metrics: accuracy, precision, recall and F1-score. Furthermore, we examine the usefulness of prosodic measures for assessing different levels of severity (e.g. mild, moderate, severe). Finally, as collecting impaired speech data can be difficult, we also implement cross-language classifiers where both Korean and English data are used for training but only one language used for testing. Results suggest that in comparison to solely using Mel-frequency cepstral coefficients, including prosodic measurements can improve the accuracy of classifiers for both Korean and English datasets. In particular, large improvements were seen when assessing different severity levels. For English a relative accuracy improvement of 1.82% for detection and 20.6% for assessment was seen. The Korean dataset saw no improvements for detection but a relative improvement of 13.6% for assessment. The results from cross-language experiments showed a relative improvement of up to 4.12% in comparison to only using a single language during training. It was found that certain prosodic impairments such as pitch and duration may be language independent. Therefore, when training sets of individual languages are limited, they may be supplemented by including data from other languages.1. Introduction 1 1.1. Dysarthria 1 1.2. Impaired Speech Detection 3 1.3. Research Goals & Outline 6 2. Background Research 8 2.1. Prosodic Impairments 8 2.1.1. English 8 2.1.2. Korean 10 2.2. Machine Learning Approaches 12 3. Database 18 3.1. English-TORGO 20 3.2. Korean-QoLT 21 4. Methods 23 4.1. Prosodic Features 23 4.1.1. Pitch 23 4.1.2. Voice Quality 26 4.1.3. Speech Rate 29 4.1.3. Rhythm 30 4.2. Feature Selection 34 4.3. Classification Models 38 4.3.1. Random Forest 38 4.3.1. Support Vector Machine 40 4.3.1 Feed-Forward Neural Network 42 4.4. Mel-Frequency Cepstral Coefficients 43 5. Experiment 46 5.1. Model Parameters 47 5.2. Training Procedure 48 5.2.1. Dysarthria Detection 48 5.2.2. Severity Assessment 50 5.2.3. Cross-Language 51 6. Results 52 6.1. TORGO 52 6.1.1. Dysarthria Detection 52 6.1.2. Severity Assessment 56 6.2. QoLT 57 6.2.1. Dysarthria Detection 57 6.2.2. Severity Assessment 58 6.1. Cross-Language 59 7. Discussion 62 7.1. Linguistic Implications 62 7.2. Clinical Applications 65 8. Conclusion 67 References 69 Appendix 76 Abstract in Korean 79Maste

Models and analysis of vocal emissions for biomedical applications

This book of Proceedings collects the papers presented at the 3rd International Workshop on Models and Analysis of Vocal Emissions for Biomedical Applications, MAVEBA 2003, held 10-12 December 2003, Firenze, Italy. The workshop is organised every two years, and aims to stimulate contacts between specialists active in research and industrial developments, in the area of voice analysis for biomedical applications. The scope of the Workshop includes all aspects of voice modelling and analysis, ranging from fundamental research to all kinds of biomedical applications and related established and advanced technologies

Combined brain language connectivity and intraoperative neurophysiologic techniques in awake craniotomy for eloquent-area brain tumor resection

Speech processing can be disturbed by primary brain tumors (PBT). Improvement of presurgical planning techniques decrease neurological morbidity associated to tumor resection during awake craniotomy. The aims of this work were: 1. To perform Diffusion Kurtosis Imaging based tractography (DKI-tract) in the detection of brain tracts involved in language; 2. To investigate which factors contribute to functional magnetic resonance imaging (fMRI) maps in predicting eloquent language regional reorganization; 3. To determine the technical aspects of accelerometric (ACC) recording of speech during surgery. DKI-tracts were streamlined using a 1.5T magnetic resonance scanner. Number of tracts and fiber pathways were compared between DKI and standard Diffusion Tensor Imaging (DTI) in healthy subjects (HS) and PBT patients. fMRI data were acquired using task-specific and resting-state paradigms during language and motor tasks. After testing intraoperative fMRI’s influence on direct cortical stimulation (DCS) number of stimuli, graph-theory measures were extracted and analyzed. Regarding speech recording, ACC signals were recorded after evaluating neck positions and filter bandwidths. To test this method, language disturbances were recorded in patients with dysphonia and after applying DCS in the inferior frontal gyrus. In contrast, HS reaction time was recorded during speech execution. DKI-tract showed increased number of arcuate fascicle tracts in PBT patients. Lower spurious tracts were identified with DKI-tract. Intraoperative fMRI and DCS showed similar stimuli in comparison with DCS alone. Increased local centrality accompanied language ipsilateral and contralateral reorganization. ACC recordings showed minor artifact contamination when placed at the suprasternal notch using a 20-200 Hz filter bandwidth. Patients with dysphonia showed decreased amplitude and frequency in comparison with HS. ACC detected an additional 11% disturbances after DCS, and a shortening of latency within the presence of a loud stimuli during speech execution. This work improved current knowledge on presurgical planning techniques based on brain structural and functional neuroimaging connectivity, and speech recordingA função linguística do ser humano pode ser afetada pela presença de tumores cerebrais (TC) A melhoria de técnicas de planeamento pré-cirurgico diminui a morbilidade neurológica iatrogénica associada ao seu tratamento cirúrgico. O objetivo deste trabalho é: 1. Testar a fiabilidade da tractografia estimada por difusor de kurtose (tract-DKI), dos feixes cerebrais envolvidos na linguagem 2. Identificar os fatores que contribuem para o mapeamento linguagem por ressonância magnética funcional (RMf) na predição da neuroplasticidade. 3. Identificar aspetos técnicos do registo da linguagem por accelerometria (ACC). A DKI-tract foi estimada após realização de RM cerebral com 1.5T. O número e percurso das fibras foi avaliado. A RMf foi adquirida durante realização de tarefas linguísticas, motoras, e em repouso. Foi testada influência dos mapas de ativação calculados por RMf, no número de estímulos realizados durante a estimulação direta cortical (EDC) intraoperatória. Medidas de conectividade foram extraídas de regiões cerebrais. A posição e filtragem de sinal ACC foram estudadas após vocalização de palavras. O sinal ACC obtido em voluntários foi comparado com doentes disfónicos, após estimulação do giro inferior frontal, e após a adição de um estímulo sonoro perturbador durante vocalização. A tract-DKI estimou um elevado número de fascículos do feixe arcuato com menos falsos negativos. Os mapas linguísticos de RMf intraoperatória, não influenciou a EDC. Medidas de centralidade aumentaram após neuroplasticidade ipsilateral e contralateral. A posição supraesternal e a filtragem de sinal ACC entre 20-200Hz demonstrou menor ruido de contaminação. Este método identificou diminuição de frequência e amplitude em doentes com disfonia, 11% de erros linguísticos adicionais após estimulação e diminuição do tempo de latência quando presente o sinal sonoro perturbador. Este trabalho promoveu a utilização de novas técnicas no planeamento pré-cirúrgico do doente com tumor cerebral e alterações da linguagem através do estudo de conectividade estrutural, funcional e registo da linguagem

Advanced analyses of physiological signals and their role in Neonatal Intensive Care

Preterm infants admitted to the neonatal intensive care unit (NICU) face an array of life-threatening diseases requiring procedures such as resuscitation and invasive monitoring, and other risks related to exposure to the hospital environment, all of which may have lifelong implications. This thesis examined a range of applications for advanced signal analyses in the NICU, from identifying of physiological patterns associated with neonatal outcomes, to evaluating the impact of certain treatments on physiological variability. Firstly, the thesis examined the potential to identify infants at risk of developing intraventricular haemorrhage, often interrelated with factors leading to preterm birth, mechanical ventilation, hypoxia and prolonged apnoeas. This thesis then characterised the cardiovascular impact of caffeine therapy which is often administered to prevent and treat apnoea of prematurity, finding greater pulse pressure variability and enhanced responsiveness of the autonomic nervous system. Cerebral autoregulation maintains cerebral blood flow despite fluctuations in arterial blood pressure and is an important consideration for preterm infants who are especially vulnerable to brain injury. Using various time and frequency domain correlation techniques, the thesis found acute changes in cerebral autoregulation of preterm infants following caffeine therapy. Nutrition in early life may also affect neurodevelopment and morbidity in later life. This thesis developed models for identifying malnutrition risk using anthropometry and near-infrared interactance features. This thesis has presented a range of ways in which advanced analyses including time series analysis, feature selection and model development can be applied to neonatal intensive care. There is a clear role for such analyses in early detection of clinical outcomes, characterising the effects of relevant treatments or pathologies and identifying infants at risk of later morbidity

The Effectiveness of Transfer Learning Systems on Medical Images

Deep neural networks have revolutionized the performances of many machine learning tasks such as medical image classification and segmentation. Current deep learning (DL) algorithms, specifically convolutional neural networks are increasingly becoming the methodological choice for most medical image analysis. However, training these deep neural networks requires high computational resources and very large amounts of labeled data which is often expensive and laborious. Meanwhile, recent studies have shown the transfer learning (TL) paradigm as an attractive choice in providing promising solutions to challenges of shortage in the availability of labeled medical images. Accordingly, TL enables us to leverage the knowledge learned from related data to solve a new problem. The objective of this dissertation is to examine the effectiveness of TL systems on medical images. First, a comprehensive systematic literature review was performed to provide an up-to-date status of TL systems on medical images. Specifically, we proposed a novel conceptual framework to organize the review. Second, a novel DL network was pretrained on natural images and utilized to evaluate the effectiveness of TL on a very large medical image dataset, specifically Chest X-rays images. Lastly, domain adaptation using an autoencoder was evaluated on the medical image dataset and the results confirmed the effectiveness of TL through fine-tuning strategies. We make several contributions to TL systems on medical image analysis: Firstly, we present a novel survey of TL on medical images and propose a new conceptual framework to organize the findings. Secondly, we propose a novel DL architecture to improve learned representations of medical images while mitigating the problem of vanishing gradients. Additionally, we identified the optimal cut-off layer (OCL) that provided the best model performance. We found that the higher layers in the proposed deep model give a better feature representation of our medical image task. Finally, we analyzed the effect of domain adaptation by fine-tuning an autoencoder on our medical images and provide theoretical contributions on the application of the transductive TL approach. The contributions herein reveal several research gaps to motivate future research and contribute to the body of literature in this active research area of TL systems on medical image analysis

Multiparametric Magnetic Resonance Imaging Artificial Intelligence Pipeline for Oropharyngeal Cancer Radiotherapy Treatment Guidance

Oropharyngeal cancer (OPC) is a widespread disease and one of the few domestic cancers that is rising in incidence. Radiographic images are crucial for assessment of OPC and aid in radiotherapy (RT) treatment. However, RT planning with conventional imaging approaches requires operator-dependent tumor segmentation, which is the primary source of treatment error. Further, OPC expresses differential tumor/node mid-RT response (rapid response) rates, resulting in significant differences between planned and delivered RT dose. Finally, clinical outcomes for OPC patients can also be variable, which warrants the investigation of prognostic models. Multiparametric MRI (mpMRI) techniques that incorporate simultaneous anatomical and functional information coupled to artificial intelligence (AI) approaches could improve clinical decision support for OPC by providing immediately actionable clinical rationale for adaptive RT planning. If tumors could be reproducibly segmented, rapid response could be classified, and prognosis could be reliably determined, overall patient outcomes would be optimized to improve the therapeutic index as a function of more risk-adapted RT volumes. Consequently, there is an unmet need for automated and reproducible imaging which can simultaneously segment tumors and provide predictive value for actionable RT adaptation. This dissertation primarily seeks to explore and optimize image processing, tumor segmentation, and patient outcomes in OPC through a combination of advanced imaging techniques and AI algorithms. In the first specific aim of this dissertation, we develop and evaluate mpMRI pre-processing techniques for use in downstream segmentation, response prediction, and outcome prediction pipelines. Various MRI intensity standardization and registration approaches were systematically compared and benchmarked. Moreover, synthetic image algorithms were developed to decrease MRI scan time in an effort to optimize our AI pipelines. We demonstrated that proper intensity standardization and image registration can improve mpMRI quality for use in AI algorithms, and developed a novel method to decrease mpMRI acquisition time. Subsequently, in the second specific aim of this dissertation, we investigated underlying questions regarding the implementation of RT-related auto-segmentation. Firstly, we quantified interobserver variability for an unprecedented large number of observers for various radiotherapy structures in several disease sites (with a particular emphasis on OPC) using a novel crowdsourcing platform. We then trained an AI algorithm on a series of extant matched mpMRI datasets to segment OPC primary tumors. Moreover, we validated and compared our best model\u27s performance to clinical expert observers. We demonstrated that AI-based mpMRI OPC tumor auto-segmentation offers decreased variability and comparable accuracy to clinical experts, and certain mpMRI input channel combinations could further improve performance. Finally, in the third specific aim of this dissertation, we predicted OPC primary tumor mid-therapy (rapid) treatment response and prognostic outcomes. Using co-registered pre-therapy and mid-therapy primary tumor manual segmentations of OPC patients, we generated and characterized treatment sensitive and treatment resistant pre-RT sub-volumes. These sub-volumes were used to train an AI algorithm to predict individual voxel-wise treatment resistance. Additionally, we developed an AI algorithm to predict OPC patient progression free survival using pre-therapy imaging from an international data science competition (ranking 1st place), and then translated these approaches to mpMRI data. We demonstrated AI models could be used to predict rapid response and prognostic outcomes using pre-therapy imaging, which could help guide treatment adaptation, though further work is needed. In summary, the completion of these aims facilitates the development of an image-guided fully automated OPC clinical decision support tool. The resultant deliverables from this project will positively impact patients by enabling optimized therapeutic interventions in OPC. Future work should consider investigating additional imaging timepoints, imaging modalities, uncertainty quantification, perceptual and ethical considerations, and prospective studies for eventual clinical implementation. A dynamic version of this dissertation is publicly available and assigned a digital object identifier through Figshare (doi: 10.6084/m9.figshare.22141871)