Texture analysis of cardiac cine magnetic resonance imaging to detect nonviable segments in patients with chronic myocardial infarction

[EN] Purpose: To investigate the ability of texture analysis to differentiate between infarcted nonviable, viable, and remote segments on cardiac cine magnetic resonance imaging (MRI). Methods: This retrospective study included 50 patients suffering chronic myocardial infarction. The data were randomly split into training (30 patients) and testing (20 patients) sets. The left ventricular myocardium was segmented according to the 17-segment model in both cine and late gadolinium enhancement (LGE) MRI. Infarcted myocardium regions were identified on LGE in short-axis views. Nonviable segments were identified as those showing LGE 50%, and viable segments those showing 0 < LGE < 50% transmural extension. Features derived from five texture analysis methods were extracted from the segments on cine images. A support vector machine (SVM) classifier was trained with different combination of texture features to obtain a model that provided optimal classification performance. Results: The best classification on testing set was achieved with local binary patterns features using a 2D + t approach, in which the features are computed by including information of the time dimension available in cine sequences. The best overall area under the receiver operating characteristic curve (AUC) were: 0.849, sensitivity of 92% to detect nonviable segments, 72% to detect viable segments, and 85% to detect remote segments. Conclusion: Nonviable segments can be detected on cine MRI using texture analysis and this may be used as hypothesis for future research aiming to detect the infarcted myocardium by means of a gadolinium-free approach.This work was supported in part by the Spanish Ministerio de Economia y Competitividad (MINECO) and FEDER funds under grant BFU2015-64380-C2-2-R, by Instituto de Salud Carlos III and FEDER funds under grants FIS PI14/00271 and PIE15/00013 and by the Generalitat Valenciana under grant PROMETEO/2013/007. The first author, Andres Larroza, was supported by grant FPU12/01140 from the Spanish Ministerio de Educacion, Cultura y Deporte (MECD).Larroza, A.; López-Lereu, M.; Monmeneu, J.; Gavara-Doñate, J.; Chorro, F.; Bodi, V.; Moratal, D. (2018). Texture analysis of cardiac cine magnetic resonance imaging to detect nonviable segments in patients with chronic myocardial infarction. Medical Physics. 45(4):1471-1480. https://doi.org/10.1002/mp.12783S14711480454Castellano, G., Bonilha, L., Li, L. M., & Cendes, F. (2004). Texture analysis of medical images. Clinical Radiology, 59(12), 1061-1069. doi:10.1016/j.crad.2004.07.008Hodgdon, T., McInnes, M. D. F., Schieda, N., Flood, T. A., Lamb, L., & Thornhill, R. E. (2015). Can Quantitative CT Texture Analysis be Used to Differentiate Fat-poor Renal Angiomyolipoma from Renal Cell Carcinoma on Unenhanced CT Images? Radiology, 276(3), 787-796. doi:10.1148/radiol.2015142215Larroza, A., Moratal, D., Paredes-Sánchez, A., Soria-Olivas, E., Chust, M. 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Rapid Segmentation Techniques for Cardiac and Neuroimage Analysis

Recent technological advances in medical imaging have allowed for the quick acquisition of highly resolved data to aid in diagnosis and characterization of diseases or to guide interventions. In order to to be integrated into a clinical work flow, accurate and robust methods of analysis must be developed which manage this increase in data. Recent improvements in in- expensive commercially available graphics hardware and General-Purpose Programming on Graphics Processing Units (GPGPU) have allowed for many large scale data analysis problems to be addressed in meaningful time and will continue to as parallel computing technology improves. In this thesis we propose methods to tackle two clinically relevant image segmentation problems: a user-guided segmentation of myocardial scar from Late-Enhancement Magnetic Resonance Images (LE-MRI) and a multi-atlas segmentation pipeline to automatically segment and partition brain tissue from multi-channel MRI. Both methods are based on recent advances in computer vision, in particular max-flow optimization that aims at solving the segmentation problem in continuous space. This allows for (approximately) globally optimal solvers to be employed in multi-region segmentation problems, without the particular drawbacks of their discrete counterparts, graph cuts, which typically present with metrication artefacts. Max-flow solvers are generally able to produce robust results, but are known for being computationally expensive, especially with large datasets, such as volume images. Additionally, we propose two new deformable registration methods based on Gauss-Newton optimization and smooth the resulting deformation fields via total-variation regularization to guarantee the problem is mathematically well-posed. We compare the performance of these two methods against four highly ranked and well-known deformable registration methods on four publicly available databases and are able to demonstrate a highly accurate performance with low run times. The best performing variant is subsequently used in a multi-atlas segmentation pipeline for the segmentation of brain tissue and facilitates fast run times for this computationally expensive approach. All proposed methods are implemented using GPGPU for a substantial increase in computational performance and so facilitate deployment into clinical work flows. We evaluate all proposed algorithms in terms of run times, accuracy, repeatability and errors arising from user interactions and we demonstrate that these methods are able to outperform established methods. The presented approaches demonstrate high performance in comparison with established methods in terms of accuracy and repeatability while largely reducing run times due to the employment of GPU hardware

Diagnosis and prognosis of cardiovascular diseases by means of texture analysis in magnetic resonance imaging

Cardiovascular diseases constitute the leading global cause of morbidity and mortality. Magnetic resonance imaging (MRI) has become the gold standard technique for the assessment of patients with myocardial infarction. However, limitations still exist thus new alternatives are open to investigation. Texture analysis is a technique that aims to quantify the texture of the images that are not always perceptible by the human eye. It has been successfully applied in medical imaging but applications to cardiac MRI (CMR) are still scarce. Therefore, the purpose of this thesis was to apply texture analysis in conventional CMR images for the assessment of patients with myocardial infarction, as an alternative to current methods. Three applications of texture analysis and machine learning techniques were studied: i) Detection of infarcted myocardium in late gadolinium enhancement (LGE) CMR. Segmentation of the infarcted myocardium is routinely performed using image intensity thresholds. The inclusion of texture features to aid the segmentation was analyzed obtaining overall good results. The method was developed using 10 LGE CMR datasets and tested on a separate dataset comprising 5 cases that were acquired with a completely different scanner than that used for training. Therefore, this preliminary study showed the transferability of texture analysis which is important for clinical applicability. ii) Differentiation of acute and chronic myocardial infarction using LGE CMR and standard pre-contrast cine CMR. In this study, two different feature selection techniques and six different machine learning classifiers were studied and compared. The best classification was achieved using a polynomial SVM obtaining an overall AUC of 0.87 ± 0.06 in LGE CMR. Interestingly, results on cine CMR in which infarctions are visually imperceptible in most cases were also good (AUC = 0.83 ± 0.08). iii) Detection of infarcted non-viable segments in cine CMR. This study was motivated by the findings of the previous one. It demonstrated that texture analysis can be used to distinguish non-viable, viable and remote segments using standard pre-contrast cine CMR solely. This was the most relevant contribution of this thesis as it can be used as hypothesis for future work aiming to accurately delineate the infarcted myocardium as a gadolinium-free alternative that will have potential advantages. The three proposed applications were successfully performed obtaining promising results. In conclusion, texture analysis can be successfully applied to conventional CMR images and provides a potential quantitative alternative to existing methods

Integration of cardiovascular risk assessment with COVID-19 using artificial intelligence

Artificial Intelligence (AI), in general, refers to the machines (or computers) that mimic "cognitive" functions that we associate with our mind, such as "learning" and "solving problem". New biomarkers derived from medical imaging are being discovered and are then fused with non-imaging biomarkers (such as office, laboratory, physiological, genetic, epidemiological, and clinical-based biomarkers) in a big data framework, to develop AI systems. These systems can support risk prediction and monitoring. This perspective narrative shows the powerful methods of AI for tracking cardiovascular risks. We conclude that AI could potentially become an integral part of the COVID-19 disease management system. Countries, large and small, should join hands with the WHO in building biobanks for scientists around the world to build AI-based platforms for tracking the cardiovascular risk assessment during COVID-19 times and long-term follow-up of the survivors

Image Quality Assessment for Population Cardiac MRI: From Detection to Synthesis

Cardiac magnetic resonance (CMR) images play a growing role in diagnostic imaging of cardiovascular diseases. Left Ventricular (LV) cardiac anatomy and function are widely used for diagnosis and monitoring disease progression in cardiology and to assess the patient's response to cardiac surgery and interventional procedures. For population imaging studies, CMR is arguably the most comprehensive imaging modality for non-invasive and non-ionising imaging of the heart and great vessels and, hence, most suited for population imaging cohorts. Due to insufficient radiographer's experience in planning a scan, natural cardiac muscle contraction, breathing motion, and imperfect triggering, CMR can display incomplete LV coverage, which hampers quantitative LV characterization and diagnostic accuracy. To tackle this limitation and enhance the accuracy and robustness of the automated cardiac volume and functional assessment, this thesis focuses on the development and application of state-of-the-art deep learning (DL) techniques in cardiac imaging. Specifically, we propose new image feature representation types that are learnt with DL models and aimed at highlighting the CMR image quality cross-dataset. These representations are also intended to estimate the CMR image quality for better interpretation and analysis. Moreover, we investigate how quantitative analysis can benefit when these learnt image representations are used in image synthesis. Specifically, a 3D fisher discriminative representation is introduced to identify CMR image quality in the UK Biobank cardiac data. Additionally, a novel adversarial learning (AL) framework is introduced for the cross-dataset CMR image quality assessment and we show that the common representations learnt by AL can be useful and informative for cross-dataset CMR image analysis. Moreover, we utilize the dataset invariance (DI) representations for CMR volumes interpolation by introducing a novel generative adversarial nets (GANs) based image synthesis framework, which enhance the CMR image quality cross-dataset

Post-revascularization Ejection Fraction Prediction for Patients Undergoing Percutaneous Coronary Intervention Based on Myocardial Perfusion SPECT Imaging Radiomics:a Preliminary Machine Learning Study

In this study, the ability of radiomics features extracted from myocardial perfusion imaging with SPECT (MPI-SPECT) was investigated for the prediction of ejection fraction (EF) post-percutaneous coronary intervention (PCI) treatment. A total of 52 patients who had undergone pre-PCI MPI-SPECT were enrolled in this study. After normalization of the images, features were extracted from the left ventricle, initially automatically segmented by k-means and active contour methods, and finally edited and approved by an expert radiologist. More than 1700 2D and 3D radiomics features were extracted from each patient’s scan. A cross-combination of three feature selections and seven classifier methods was implemented. Three classes of no or dis-improvement (class 1), improved EF from 0 to 5% (class 2), and improved EF over 5% (class 3) were predicted by using tenfold cross-validation. Lastly, the models were evaluated based on accuracy, AUC, sensitivity, specificity, precision, and F-score. Neighborhood component analysis (NCA) selected the most predictive feature signatures, including Gabor, first-order, and NGTDM features. Among the classifiers, the best performance was achieved by the fine KNN classifier, which yielded mean accuracy, AUC, sensitivity, specificity, precision, and F-score of 0.84, 0.83, 0.75, 0.87, 0.78, and 0.76, respectively, in 100 iterations of classification, within the 52 patients with 10-fold cross-validation. The MPI-SPECT-based radiomic features are well suited for predicting post-revascularization EF and therefore provide a helpful approach for deciding on the most appropriate treatment.</p

Deep learning assisted MRI guided attenuation correction in PET

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University LondonPositron emission tomography (PET) is a unique imaging modality that provides physiological and functional details of the tissue at the molecular level. However, the acquired PET images have some limitations such as the attenuation. PET attenuation correction is an essential step to obtain the full potential of PET quantification. With the wide use of hybrid PET/MR scanners, magnetic resonance (MR) images are used to address the problem of PET attenuation correction. The MR images segmentation is one simple and robust approach to create pseudo computed tomography (CT) images, which are used to generate attenuation coefficient maps to correct the PET attenuation. Recently, deep learning has been proposed and used as a promising technique to efficiently perform MR and various medical images segmentation. In this research work, deep learning guided segmentation approaches have been proposed to enhance the bone class segmentation of MR brain images in order to generate accurate pseudo-CT images. The first approach has introduced the combination of handcrafted features with deep learning features to enrich the set of features. Multiresolution analysis techniques, which generate multiscale and multidirectional coefficients of an image such as contourlet and shearlet transforms, are applied and combined with deep convolutional neural network (CNN) features. Different experiments have been conducted to investigate the number of selected coefficients and the insertion location of the handcrafted features. The second approach aims at reducing the segmentation algorithm’s complexity while maintaining the segmentation performance. An attention based convolutional encode-decoder network has been proposed to adaptively recalibrate the deep network features. This attention based network consists of two different squeeze and excitation blocks that excite the features spatially and channel wise. The two blocks are combined sequentially to decrease the number of network’s parameters and reduces the model complexity. The third approach has been focuses on the application of transfer learning from different MR sequences such as T1 weighted (T1-w) and T2 weighted (T2-w) images. A pretrained model with T1-w MR sequences is fine tuned to perform the segmentation of T2-w images. Multiple fine tuning approaches and experiments have been conducted to study the best fine tuning mechanism that is able to build an efficient segmentation model for both T1-w and T2-w segmentation. Clinical datasets of fifty patients with different conditions and diagnosis have been used to carry an objective evaluation to measure the segmentation performance of the results obtained by the three proposed methods. The first and second approaches have been validated with other studies in the literature that applied deep network based segmentation technique to perform MR based attenuation correction for PET images. The proposed methods have shown an enhancement in the bone segmentation with an increase of dice similarity coefficient (DSC) from 0.6179 to 0.6567 using an ensemble of CNNs with an improvement percentage of 6.3%. The proposed excitation-based CNN has decreased the model complexity by decreasing the number of trainable parameters by more than 46% where less computing resources are required to train the model. The proposed hybrid transfer learning method has shown its superiority to build a multi-sequences (T1-w and T2-w) segmentation approach compared to other applied transfer learning methods especially with the bone class where the DSC is increased from 0.3841 to 0.5393. Moreover, the hybrid transfer learning approach requires less computing time than transfer learning using open and conservative fine tuning

Contribuciones de las técnicas machine learning a la cardiología. Predicción de reestenosis tras implante de stent coronario

[ES]Antecedentes: Existen pocos temas de actualidad equiparables a la posibilidad de la tecnología actual para desarrollar las mismas capacidades que el ser humano, incluso en medicina. Esta capacidad de simular los procesos de inteligencia humana por parte de máquinas o sistemas informáticos es lo que conocemos hoy en día como inteligencia artificial. Uno de los campos de la inteligencia artificial con mayor aplicación a día de hoy en medicina es el de la predicción, recomendación o diagnóstico, donde se aplican las técnicas machine learning. Asimismo, existe un creciente interés en las técnicas de medicina de precisión, donde las técnicas machine learning pueden ofrecer atención médica individualizada a cada paciente. El intervencionismo coronario percutáneo (ICP) con stent se ha convertido en una práctica habitual en la revascularización de los vasos coronarios con enfermedad aterosclerótica obstructiva significativa. El ICP es asimismo patrón oro de tratamiento en pacientes con infarto agudo de miocardio; reduciendo las tasas de muerte e isquemia recurrente en comparación con el tratamiento médico. El éxito a largo plazo del procedimiento está limitado por la reestenosis del stent, un proceso patológico que provoca un estrechamiento arterial recurrente en el sitio de la ICP. Identificar qué pacientes harán reestenosis es un desafío clínico importante; ya que puede manifestarse como un nuevo infarto agudo de miocardio o forzar una nueva resvascularización del vaso afectado, y que en casos de reestenosis recurrente representa un reto terapéutico. Objetivos: Después de realizar una revisión de las técnicas de inteligencia artificial aplicadas a la medicina y con mayor profundidad, de las técnicas machine learning aplicadas a la cardiología, el objetivo principal de esta tesis doctoral ha sido desarrollar un modelo machine learning para predecir la aparición de reestenosis en pacientes con infarto agudo de miocardio sometidos a ICP con implante de un stent. Asimismo, han sido objetivos secundarios comparar el modelo desarrollado con machine learning con los scores clásicos de riesgo de reestenosis utilizados hasta la fecha; y desarrollar un software que permita trasladar esta contribución a la práctica clínica diaria de forma sencilla. Para desarrollar un modelo fácilmente aplicable, realizamos nuestras predicciones sin variables adicionales a las obtenidas en la práctica rutinaria. Material: El conjunto de datos, obtenido del ensayo GRACIA-3, consistió en 263 pacientes con características demográficas, clínicas y angiográficas; 23 de ellos presentaron reestenosis a los 12 meses después de la implantación del stent. Todos los desarrollos llevados a cabo se han hecho en Python y se ha utilizado computación en la nube, en concreto AWS (Amazon Web Services). Metodología: Se ha utilizado una metodología para trabajar con conjuntos de datos pequeños y no balanceados, siendo importante el esquema de validación cruzada anidada utilizado, así como la utilización de las curvas PR (precision-recall, exhaustividad-sensibilidad), además de las curvas ROC, para la interpretación de los modelos. Se han entrenado los algoritmos más habituales en la literatura para elegir el que mejor comportamiento ha presentado. Resultados: El modelo con mejores resultados ha sido el desarrollado con un clasificador extremely randomized trees; que superó significativamente (0,77; área bajo la curva ROC a los tres scores clínicos clásicos; PRESTO-1 (0,58), PRESTO-2 (0,58) y TLR (0,62). Las curvas exhaustividad sensibilidad ofrecieron una imagen más precisa del rendimiento del modelo extremely randomized trees que muestra un algoritmo eficiente (0,96) para no reestenosis, con alta exhaustividad y alta sensibilidad. Para un umbral considerado óptimo, de 1,000 pacientes sometidos a implante de stent, nuestro modelo machine learning predeciría correctamente 181 (18%) más casos en comparación con el mejor score de riesgo clásico (TLR). Las variables más importantes clasificadas según su contribución a las predicciones fueron diabetes, enfermedad coronaria en 2 ó más vasos, flujo TIMI post-ICP, plaquetas anormales, trombo post-ICP y colesterol anormal. Finalmente, se ha desarrollado una calculadora para trasladar el modelo a la práctica clínica. La calculadora permite estimar el riesgo individual de cada paciente y situarlo en una zona de riesgo, facilitando la toma de decisión al médico en cuanto al seguimiento adecuado para el mismo. Conclusiones: Aplicado inmediatamente después de la implantación del stent, un modelo machine learning diferencia mejor a aquellos pacientes que presentarán o no reestenosis respecto a los discriminadores clásicos actuales