OncoSpineSeg: A Software Tool for a Manual Segmentation of Computed Tomography of the Spine on Cancer Patients

The organ most commonly affected by metastatic cancer is the skeleton, and spine is the site where it causes the highest morbidity. Computer-aided diagnosis (CAD) for detecting and assessing metastatic disease in bone or other spine disorders can assist physicians to perform their decision-making tasks. A precise segmentation of the spine is important as a first stage in any automatic diagnosis task. However, it is a challenging problem to segment correctly an affected spine, and it is a crucial step to assess quantitatively the results of segmentation by comparing them with the results of a manual segmentation, reviewed by one experienced radiologist. This chapter presents the design of a MATLAB-based software for the manual segmentation of the spine. The software tool has a simple and easy to use interface, and it works with either computed tomography or magnetic resonance imaging (MRI). A typical workflow includes loading the image volume, creating multi-planar reconstructions, manually contouring the vertebrae, spinal lesions, intervertebral discs and spinal canal with availability of different segmentation tools, classification of the bone into healthy bone, osteolytic metastases, osteoblastic metastases or mixed lesions, being also possible to classify an object as a false-positive and a 3D reconstruction of the segmented objects

CARACTERIZACIÓN CUANTITATIVA DE LA PATOLOGÍA DISCAL Y LUMBAR DEGENERATIVA MEDIANTE ANÁLISIS DE IMAGEN POR RESONANCIA MAGNÉTICA Y DETECCIÓN Y SEGMENTACIÓN DE LA COLUMNA VERTEBRAL EN PACIENTES ONCOLÓGICOS A PARTIR DEL ANÁLISIS DE IMAGEN EN TOMOGRAFÍA COMPUTARIZADA

[EN] Over the last 20 years health system has been revolutionized by imaging technology so diagnostic imaging has become the mainstay of the management of patients. Nowadays, degeneration of the intervertebral discs, herniation and spinal stenosis are very common entities that affect millions of people and cause back pain. The development of computer-aided diagnosis (CAD) methods for classifying and quantifying these pathologies has increased in the past decade as a way to assist radiologists in the diagnosis task. So, the main objective of the first part of this Doctoral Thesis is the development of a CAD software for the classification and quantification of spine disease by means of Magnetic Resonance image analysis. To this end, two different groups of patients have been used, one as training group (14 patients) and the other as testing group (53 patients). To classify disc degeneration according to the gold standard, Pfirrmann classification, a method mainly based on the measurement of disc signal intensity and structure has been developed. The method developed to detect disc herniations has been focused on disc segmentation and its approximation by an ellipse, in this way it is possible to extract disc shape features for detecting contour abnormalities. The method developed to detect spinal stenosis, based on signal intensity, has been developed to extract the spinal canal and, by applying different techniques, to detect spinal stenosis at every intervertebral disc level and quantify the severity of the pathology. The results have shown a segmentation inaccuracy below 1%. Regarding reproducibility, it has been obtained an almost perfect agreement (measured by the k and ICC statistics) for all the analysed pathologies. The results have shown that the developed methods can assist radiologists to perform their decision-making tasks, providing support for enhanced reproducibility of MRI reports and achieving greater objectivity. However, not only the intervertebral discs are susceptible to suffer several pathologies. The vertebral bodies are also subject to a wide variety of diseases because of different circumstances. So, prior to any diagnosis task, an accurate detection and segmentation of the vertebral bodies are the first crucial steps. Therefore, the main objective of the second part of this Doctoral Thesis is the development of an automatic method for the detection and segmentation of the spine in Computed Tomography imaging. Performing an automatic and robust segmentation is a very challenging task due to the difficulty discriminating between the ribs and the vertebral bodies. To overcome this problem, two different segmentation methods have been combined: the first method uses a Level-Set method to perform an initial segmentation; the second method uses a probabilistic atlas to refine the initial segmentation with a special focus on ribs suppression. So a 3D volume indicating the probability of each voxel of belonging to the spine has been developed, by means of a set of images, corresponding to 14 patients (training group), manually segmented by an expert. The generated probability map has been deformed and adapted to each testing case. To evaluate the segmentation results and the improvement obtained after applying the atlas to the initial segmentation, the Dice similarity coefficient (DSC) and the Hausdorff distance (HD) have been used. The results have shown up an average of 11 mm of improvement in segmentation accuracy in terms of HD, obtaining an overall final average of 14,98 ± 1,32 mm. A refinement of 1,3 % has been obtained in terms of DSC, with a global value of 91,75 ± 1,20 %. The study has demonstrated that the atlas is able to detect and appropriately eliminate the ribs while improving the segmentation accuracy.[ES] En los últimos 20 años el sistema sanitario se ha visto revolucionado por la tecnología de la imagen, por lo que el diagnóstico por imagen se ha convertido en un pilar fundamental en el manejo de los pacientes. Hoy en día la degeneración de los discos intervertebrales, la hernia discal y la estenosis del canal vertebral, son tres patologías que afectan a millones de personas y causan dolor de espalda. El desarrollo de sistemas CAD para clasificar y cuantificar estas patologías se ha incrementado en la última década como una forma de ayuda al radiólogo en el diagnóstico. Por tanto, la primera parte de esta Tesis Doctoral tiene como objetivo el desarrollo de un sistema CAD para la clasificación y cuantificación de la patología discal por medio del análisis de Imagen por Resonancia Magnética. Con este fin se han utilizado dos grupos de pacientes, uno como grupo de entrenamiento (14 pacientes) y el otro como grupo de prueba (53 pacientes). Para la clasificación de la degeneración discal se ha desarrollado un método basado en el cálculo de la estructura del disco y de su señal de intensidad. El método de detección de herniaciones se ha centrado en la segmentación del disco y su aproximación por una elipse, para extraer así información sobre la forma del disco. El método de detección de estenosis, basado en la señal de intensidad, ha sido desarrollado para extraer el canal vertebral y, con la aplicación de diferentes técnicas, detectar estrechamientos a la altura de los discos y cuantificar la gravedad de los mismos. Los resultados han demostrado una alta precisión en la segmentación, con un error inferior al 1 %. En cuanto a la reproducibilidad, se ha obtenido un acuerdo casi perfecto (medido con los coeficientes CCI y k) para todas las patologías analizadas. Los resultados obtenidos demuestran que los métodos desarrollados pueden servir de ayuda al radiólogo en el diagnóstico, mejorando la reproducibilidad y logrando una mayor objetividad. Sin embargo, no sólo los discos intervertebrales son susceptibles de sufrir alguna patología. Los cuerpos vertebrales también pueden sufrir lesiones por diversas circunstancias. No obstante, antes de realizar cualquier tarea de diagnóstico, llevar a cabo una detección y segmentación precisa de los cuerpos vertebrales es un primer paso crucial. Así pues, la segunda parte de esta Tesis Doctoral tiene como objetivo el desarrollo de un método automático para la detección y segmentación de la columna vertebral por medio del análisis de Tomografía Computarizada. Llevar a cabo una segmentación automática y precisa es una tarea complicada debido principalmente a la gran dificultad para distinguir entre los cuerpos vertebrales y las costillas. Para solucionar este problema se han combinado dos métodos de segmentación diferentes: el primero utiliza un método Level-Set para llevar a cabo una segmentación inicial; el segundo utiliza un atlas probabilístico, para refinar la segmentación inicial, con un enfoque especial en la supresión de las costillas. Por tanto, se ha obtenido un volumen 3D indicando la probabilidad de cada voxel de pertenecer o no a la columna vertebral, por medio de un conjunto de imágenes correspondientes a 14 pacientes segmentadas manualmente por un experto. El mapa de probabilidad generado ha sido deformado y adaptado a cada uno de los 7 pacientes del grupo de prueba. Para evaluar los resultados de la segmentación y la mejora obtenida después de aplicar el atlas a la segmentación inicial, se ha utilizado el coeficiente Dice (DSC) y la distancia Hausdorff (HD). Los resultados han demostrado una mejora en la precisión de la segmentación de 11 mm de media en términos de HD, con una media global de 14,98 ± 1,32 mm. En términos de DSC se ha obtenido una mejora de un 1,3 % , con una media global de 91,75 ± 1,20 %. El estudio ha demostrado que el atlas es capaz de detectar y eliminar apropiadamente las estructuras costales[CA] En els últims 20 anys el sistema sanitari s'ha vist revolucionat per la tecnologia de la imatge, per la qual cosa el diagnòstic per imatge s'ha convertit en un pilar fonamental en el maneig dels pacients. Hui en dia la degeneració dels discos intervertebrals, l'hèrnia discal i l'estenosi del canal vertebral, són tres patologies molt comunes que afecten milions de persones i causen dolor d'esquena. El desenvolupament de sistemes CAD per a classificar i quantificar estes patologies s'ha incrementat en l'última dècada com una forma d'ajuda al radiòleg en el diagnòstic. Per tant, la primera part d'aquesta Tesi Doctoral té com a objectiu el desenvolupament d'un sistema CAD per a la classificació i quantificació de la patologia discal per mitjà de l'anàlisi d'Imatge per Ressonància Magnètica. Amb aquest fi s'han utilitzat dos grups de pacients distints, un com a grup d'entrenament (14 pacients) i l'altre com a grup de prova (53 pacients). Per a la classificació de la degeneració discal, s'ha desenvolupat un mètode basat en el càlcul de l'estructura del disc i del seu senyal d'intensitat. El mètode de detecció d'herniacions s'ha centrat en la segmentació del disc i la seua aproximació per una el·lipse, per a extraure així informació sobre la forma del disc. El mètode de detecció d'estenosi, basat en el senyal d'intensitat, ha sigut desenvolupat per a extraure el canal vertebral i amb l'aplicació de diferents tècniques detectar estrenyiments a l'altura dels discos i quantificar la gravetat dels mateixos. Els resultats han demostrat una alta precisió en la segmentació, amb un error inferior a l'1 %. En quant a la reproduïbilitat, s'ha obtingut un acord quasi perfecte (mesurat amb els coeficients CCI i k) per a totes les patologies analitzades. Els resultats obtinguts demostren que els mètodes desenvolupats poden servir d'ajuda al radiòleg en el diagnòstic, millorant la reproduïbilitat i aconseguint una major objectivitat. No obstant això, no sols els discos intervertebrals són susceptibles de patir alguna patologia. Els cossos vertebrals també poden patir lesions per diverses circumstàncies. Per tant, abans de realitzar qualsevol tasca de diagnòstic, dur a terme una detecció i segmentació precisa dels cossos vertebrals és un primer pas crucial. Així, doncs, la segona part d'aquesta Tesi Doctoral té com a objectiu el desenvolupament d'un mètode automàtic per a la detecció i segmentació de la columna vertebral per mitjà de l'anàlisi de Tomografia Computada. Dur a terme una segmentació automàtica i precisa és una tasca complicada degut principalment a la gran dificultat per a distingir entre els cossos vertebrals i les costelles. Per a solucionar aquest problema s'han combinat dos mètodes de segmentació diferents: el primer utilitza un mètode Level-Set per a dur a terme una segmentació inicial; el segon utilitza un atles probabilístic, per a refinar la segmentació inicial amb un enfocament especial en la supressió de les costelles. Per tant, s'ha obtingut un volum 3D indicant la probabilitat de cada voxel de pertànyer o no a la columna vertebral, per mitjà d'un conjunt d'imatges corresponents a 14 pacients (grup d'entrenament) segmentades manualment per un expert. El mapa de probabilitat generat ha sigut deformat i adaptat a cadascun dels 7 pacients del grup de prova. Per a avaluar els resultats de la segmentació i la millora obtinguda després d'aplicar l'atles a la segmentació inicial, s'ha utilitzat el coeficient Dice (DSC) i la distància Hausdorff (HD). Els resultats han demostrat una millora en la precisió de la segmentació d'11 mm de mitja en termes de HD, amb una mitja global de 14,98 ± 1,32 mm. S'ha obtingut una millora d'un 1,3 % en termes de DSC, amb una mitja global de 91,75 ± 1,20 %. L'estudi ha demostrat que l'atles és capaç de detectar i eliminar apropiadament les estructures costals alhora que millora la precisió de la segmentació.Ruiz España, S. (2016). CARACTERIZACIÓN CUANTITATIVA DE LA PATOLOGÍA DISCAL Y LUMBAR DEGENERATIVA MEDIANTE ANÁLISIS DE IMAGEN POR RESONANCIA MAGNÉTICA Y DETECCIÓN Y SEGMENTACIÓN DE LA COLUMNA VERTEBRAL EN PACIENTES ONCOLÓGICOS A PARTIR DEL ANÁLISIS DE IMAGEN EN TOMOGRAFÍA COMPUTARIZADA [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/68485TESI

Assessment and risk prediction of frailty using texture-based muscle ultrasound image analysis and machine learning techniques

[EN] The purpose of this study was to evaluate texture-based muscle ultrasound image analysis for the assessment and risk prediction of frailty phenotype. This retrospective study of prospectively acquired data included 101 participants who underwent ultrasound scanning of the anterior thigh. Participants were subdivided according to frailty phenotype and were followed up for two years. Primary and secondary outcome measures were death and comorbidity, respectively. Forty-three texture features were computed from the rectus femoris and the vastus intermedius muscles using statistical methods. Model performance was evaluated by computing the area under the receiver operating characteristic curve (AUC) while outcome prediction was evaluated using regression analysis. Models developed achieved a moderate to good AUC (0.67 <= AUC <= 0.79) for categorizing frailty. The stepwise multiple logistic regression analysis demonstrated that they correctly classified 70-87% of the cases. The models were associated with increased comorbidity (0.01 <= p <= 0.18) and were predictive of death for pre-frail and frail participants (0.001 <= p <= 0.016). In conclusion, texture analysis can be useful to identify frailty and assess risk prediction (i.e. mortality) using texture features extracted from muscle ultrasound images in combination with a machine learning approach.This work was supported by the following grants: Grant PID2020-113839RB-I00 funded by MCIN/AEI/10.13039/501100011033 to C.B. DM acknowledges financial support from the Conselleria d ' Educacio, Investigacio, Cultura i Esport, Generalitat Valenciana (grants AEST/2018/021 and AEST/2019/037) .Mirón-Mombiela, R.; Ruiz-España, S.; Moratal, D.; Borrás, C. (2023). Assessment and risk prediction of frailty using texture-based muscle ultrasound image analysis and machine learning techniques. Mechanisms of Ageing and Development. 215. https://doi.org/10.1016/j.mad.2023.11186021

Classifying brain metastases by their primary site of origin using a radiomics approach based on texture analysis: a feasibility study

[EN] Objective To examine the capability of MRI texture analysis to differentiate the primary site of origin of brain metastases following a radiomics approach. Methods Sixty-seven untreated brain metastases (BM) were found in 3D T1-weighted MRI of 38 patients with cancer: 27 from lung cancer, 23 from melanoma and 17 from breast cancer. These lesions were segmented in 2D and 3D to compare the discriminative power of 2D and 3D texture features. The images were quantized using different number of gray-levels to test the influence of quantization. Forty-three rotation-invariant texture features were examined. Feature selection and random forest classification were implemented within a nested cross-validation structure. Classification was evaluated with the area under receiver operating characteristic curve (AUC) considering two strategies: multiclass and one-versus-one. Results In the multiclass approach, 3D texture features were more discriminative than 2D features. The best results were achieved for images quantized with 32 gray-levels (AUC = 0.873 +/- 0.064) using the top four features provided by the feature selection method based on the p-value. In the one-versus-one approach, high accuracy was obtained when differentiating lung cancer BM from breast cancer BM (four features, AUC = 0.963 +/- 0.054) and melanoma BM (eight features, AUC = 0.936 +/- 0.070) using the optimal dataset (3D features, 32 gray-levels). Classification of breast cancer and melanoma BM was unsatisfactory (AUC = 0.607 +/- 0.180). Conclusion Volumetric MRI texture features can be useful to differentiate brain metastases from different primary cancers after quantizing the images with the proper number of gray-levels.This work has been partially funded by the Spanish Ministerio de Economia y Competitividad (MINECO) and FEDER funds under Grant BFU2015-64380-C2-2-R. Rafael Ortiz-Ramon was supported by grant ACIF/2015/078 from the Conselleria d'Educacio, Investigacio, Cultura i Esport of the Valencian Community (Spain). Andres Larroza was supported by grant FPU12/01140 from the Spanish Ministerio de Educacion, Cultura y Deporte (MECD).Ortiz-Ramón, R.; Larroza-Santacruz, A.; Ruiz-España, S.; Arana Fernandez De Moya, E.; Moratal, D. (2018). Classifying brain metastases by their primary site of origin using a radiomics approach based on texture analysis: a feasibility study. European Radiology. 28(11):4514-4523. https://doi.org/10.1007/s00330-018-5463-6S451445232811Gavrilovic IT, Posner JB (2005) Brain metastases: epidemiology and pathophysiology. J Neurooncol 75:5–14Stelzer KJ (2013) Epidemiology and prognosis of brain metastases. Surg Neurol Int 4:S192–S202Soffietti R, Cornu P, Delattre JY et al (2006) EFNS Guidelines on diagnosis and treatment of brain metastases: report of an EFNS Task Force. Eur J Neurol 13:674–681Kaal ECA, Taphoorn MJB, Vecht CJ (2005) Symptomatic management and imaging of brain metastases. J Neurooncol 75:15–20Nayak L, Lee EQ, Wen PY (2012) Epidemiology of brain metastases. Curr Oncol Rep 14:48–54Bartelt S, Lutterbach J (2003) Brain metastases in patients with cancer of unknown primary. J Neurooncol 64:249–253Agazzi S, Pampallona S, Pica A et al (2004) The origin of brain metastases in patients with an undiagnosed primary tumor. Acta Neurochir (Wien) 146:153–157Pekmezci M, Perry A (2013) Neuropathology of brain metastases. Surg Neurol Int 4:245Zakaria R, Das K, Bhojak M et al (2014) The role of magnetic resonance imaging in the management of brain metastases: diagnosis to prognosis. Cancer Imaging 14:1–8Bekaert L, Emery E, Levallet G, Lechapt-Zalcman E (2017) Histopathologic diagnosis of brain metastases: current trends in management and future considerations. Brain Tumor Pathol 34:8–19Gillies RJ, Kinahan PE, Hricak H (2016) Radiomics: images are more than pictures, they are data. Radiology 278:563–577Lambin P, Rios-Velazquez E, Leijenaar R et al (2012) Radiomics: extracting more information from medical images using advanced feature analysis. Eur J Cancer 48:441–446Yip SSF, Aerts HJWL (2016) Applications and limitations of radiomics. Phys Med Biol 61:R150–R166Kumar V, Gu Y, Basu S et al (2012) Radiomics: the process and the challenges. Magn Reson Imaging 30:1234–1248Castellano G, Bonilha L, Li LM, Cendes F (2004) Texture analysis of medical images. Clin Radiol 59:1061–1069Kassner A, Thornhill RE (2010) Texture analysis: a review of neurologic MR imaging applications. AJNR Am J Neuroradiol 31:809–816Mahmoud-Ghoneim D, Toussaint G, Constans JM, De Certaines JD (2003) Three dimensional texture analysis in MRI: a preliminary evaluation in gliomas. Magn Reson Imaging 21:983–987Fetit AE, Novak J, Peet AC, Arvanitis TN (2015) Three-dimensional textural features of conventional MRI improve diagnostic classification of childhood brain tumors. NMR Biomed 28:1174–1184Zacharaki EI, Wang S, Chawla S et al (2009) Classification of brain tumor type and grade using MRI texture and shape in a machine learning scheme. Magn Reson Med 62:1609–1618Georgiadis P, Cavouras D, Kalatzis I et al (2009) Enhancing the discrimination accuracy between metastases, gliomas and meningiomas on brain MRI by volumetric textural features and ensemble pattern recognition methods. Magn Reson Imaging 27:120–130Larroza A, Moratal D, Paredes-Sánchez A et al (2015) Support vector machine classification of brain metastasis and radiation necrosis based on texture analysis in MRI. J Magn Reson Imaging 42:1362–1368Li Z, Mao Y, Li H et al (2016) Differentiating brain metastases from different pathological types of lung cancers using texture analysis of T1 postcontrast MR. Magn Reson Med 76:1410–1419Fink KR, Fink JR (2013) Imaging of brain metastases. Surg Neurol Int 4:S209–S219Larroza A, Bodí V, Moratal D (2016) Texture analysis in magnetic resonance imaging: review and considerations for future applications. In: Assessment of cellular and organ function and dysfunction using direct and derived MRI methodologies. InTech, Rijeka, Croatia, pp 75–106Leite M, Rittner L, Appenzeller S et al (2015) Etiology-based classification of brain white matter hyperintensity on magnetic resonance imaging. J Med Imaging 2:14002Mahmoud-Ghoneim D, Alkaabi MK, De Certaines JD, Goettsche F-M (2008) The impact of image dynamic range on texture classification of brain white matter. BMC Med Imaging 8:1–8Depeursinge A, Foncubierta-Rodriguez A, Van De Ville D, Müller H (2014) Three-dimensional solid texture analysis in biomedical imaging: review and opportunities. Med Image Anal 18:176–196Ellingson BM, Bendszus M, Boxerman J et al (2015) Consensus recommendations for a standardized Brain Tumor Imaging Protocol in clinical trials. Neuro Oncol 17:1188–1198Mayerhoefer ME, Breitenseher MJ, Kramer J et al (2005) Texture analysis for tissue discrimination on T1-weighted MR images of the knee joint in a multicenter study: Transferability of texture features and comparison of feature selection methods and classifiers. J Magn Reson Imaging 22:674–680Waugh SA, Lerski RA, Bidaut L, Thompson AM (2011) The influence of field strength and different clinical breast MRI protocols on the outcome of texture analysis using foam phantoms. Med Phys 38:5058–5066Chan TF, Vese LA (2001) Active contours without edges. IEEE Trans Image Process 10:266–277Collewet G, Strzelecki M, Mariette F (2004) Influence of MRI acquisition protocols and image intensity normalization methods on texture classification. 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Automatic segmentation of the spine by means of a probabilistic atlas with a special focus on ribs suppression

[EN] Purpose: The development of automatic and reliable algorithms for the detection and segmentation of the vertebrae are of great importance prior to any diagnostic task. However, an important problem found to accurately segment the vertebrae is the presence of the ribs in the thoracic region. To overcome this problem, a probabilistic atlas of the spine has been developed dealing with the proximity of other structures, with a special focus on ribs suppression. Methods: The data sets used consist of Computed Tomography images corresponding to 21 patients suffering from spinal metastases. Two methods have been combined to obtain the final result: firstly, an initial segmentation is performed using a fully automatic level-set method; secondly, to refine the initial segmentation, a 3D volume indicating the probability of each voxel of belonging to the spine has been developed. In this way, a probability map is generated and deformed to be adapted to each testing case. Results: To validate the improvement obtained after applying the atlas, the Dice coefficient (DSC), the Hausdorff distance (HD), and the mean surface-to-surface distance (MSD) were used. The results showed up an average of 10 mm of improvement accuracy in terms of HD, obtaining an overall final average of 15.51 2.74 mm. Also, a global value of 91.01 3.18% in terms of DSC and a MSD of 0.66 0.25 mm were obtained. The major improvement using the atlas was achieved in the thoracic region, as ribs were almost perfectly suppressed. Conclusion: The study demonstrated that the atlas is able to detect and appropriately eliminate the ribs while improving the segmentation accuracy.The authors thank the financial support of the Spanish Ministerio de Economia y Competitividad (MINECO) and FEDER funds under Grants TEC2012-33778 and BFU2015-64380-C2-2-R (D.M.) and DPI2013-4572-R (J.D., E.D.)Ruiz-España, S.; Domingo, J.; Díaz-Parra, A.; Dura, E.; D'ocon-Alcaniz, V.; Arana, E.; Moratal, D. (2017). 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Multiatlas whole heart segmentation of CT data using conditional entropy for atlas ranking and selection. Medical Physics, 42(7), 3822-3833. doi:10.1118/1.4921366Zhou, J., Yan, Z., Lasio, G., Huang, J., Zhang, B., Sharma, N., … D’Souza, W. (2015). Automated compromised right lung segmentation method using a robust atlas-based active volume model with sparse shape composition prior in CT. Computerized Medical Imaging and Graphics, 46, 47-55. doi:10.1016/j.compmedimag.2015.07.003Linguraru, M. G., Sandberg, J. K., Li, Z., Shah, F., & Summers, R. M. (2010). Automated segmentation and quantification of liver and spleen from CT images using normalized probabilistic atlases and enhancement estimation. Medical Physics, 37(2), 771-783. doi:10.1118/1.3284530Xu, Y., Xu, C., Kuang, X., Wang, H., Chang, E. I.-C., Huang, W., & Fan, Y. (2016). 3D-SIFT-Flow for atlas-based CT liver image segmentation. Medical Physics, 43(5), 2229-2241. doi:10.1118/1.4945021Michopoulou, S. 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PSPU-Net for Automatic Short Axis Cine MRI Segmentation of Left and Right Ventricles

[EN] Characterization of the heart anatomy and function is mostly done with magnetic resonance image cine series. To achieve a correct characterization, the volume of the right and left ventricle need to be segmented, which is a timeconsuming task. We propose a new convolutional neural network architecture that combines U-net with PSP modules (PSPU-net) for the segmentation of left and right ventricle cavities and left ventricle myocardium in the diastolic frame of short-axis cine MRI images and compare its results against a classic 3D U-net architecture. We used a dataset containing 399 cases in total. The results showed higher quality results in both segmentation and final volume estimation for a test set of 99 cases in the case of the PSPU-net, with global dice metrics of 0.910 and median absolute relative errors in volume estimations of 0.026 and 0.039 for the left ventricle cavity and myocardium and 0.051 for the right ventricles cavity.DM acknowledges financial support from the Conselleria d'Educacio, Investigacio, Cultura i Esport, Generalitat Valenciana (grants AEST/2019/037 and AEST/2020/029), from the Agencia Valenciana de la Innovacion, Generalitat Valenciana (ref. INNCAD00/19/085), and from the Centro para el Desarrollo Tecnologico Industrial (Programa Eurostars-2, actuacion Interempresas Internacional), Spanish Ministerio de Ciencia, Innovacion y Universidades (ref. CIIP20192020). We are grateful to Andres Larroza for his valuable technical assistance in the project.Pérez-Pelegrí, M.; Monmeneu, JV.; López-Lereu, MP.; Ruiz-España, S.; Del-Canto, I.; Bodi, V.; Moratal, D. (2020). PSPU-Net for Automatic Short Axis Cine MRI Segmentation of Left and Right Ventricles. IEEE Computer Society. 1048-1053. https://doi.org/10.1109/BIBE50027.2020.00177S1048105

MRI texture-based radiomics analysis for the identification of altered functional networks in alcoholic patients and animal models

[EN] Alcohol use disorder (AUD) is a complex condition representing a leading risk factor for death, disease and disability. Its high prevalence and severe health consequences make necessary a better understanding of the brain network alterations to improve diagnosis and treatment. The purpose of this study was to evaluate the potential of resting-state fMRI 3D texture features as a novel source of biomarkers to identify AUD brain network alterations following a radiomics approach. A longitudinal study was conducted in Marchigian Sardinian alcoholpreferring msP rats (N = 36) who underwent resting-state functional and structural MRI before and after 30 days of alcohol or water consumption. A cross-sectional human study was also conducted among 33 healthy controls and 35 AUD patients. The preprocessed functional data corresponding to control and alcohol conditions were used to perform a probabilistic independent component analysis, identifying seven independent components as resting-state networks. Forty-three radiomic features extracted from each network were compared using a Wilcoxon signed-rank test with Holm correction to identify the network most affected by alcohol consumption. Features extracted from this network were then used in the machine learning process, evaluating two feature selection methods and six predictive models within a nested cross-validation structure. The classification was evaluated by computing the area under the ROC curve. Images were quantized using different numbers of graylevels to test their influence on the results. The influence of ageing, data preprocessing, and brain iron accumulation were also analyzed. The methodology was validated using structural scans. The striatal network in alcohol-exposed msP rats presented the most significant number of altered features. The radiomics approach supported this result achieving good classification performance in animals (AUC = 0.915 +/- 0.100, with 12 features) and humans (AUC = 0.724 +/- 0.117, with 9 features) using a random forest model. Using the structural scans, high accuracy was achieved with a multilayer perceptron in both species (animals: AUC > 0.95 with 2 features, humans: AUC > 0.82 with 18 features). The best results were obtained using a feature selection method based on the p-value. The proposed radiomics approach is able to identify AUD patients and alcohol-exposed rats with good accuracy, employing a subset of 3D features extracted from fMRI. Furthermore, it can help identify relevant networks in drug addiction.This work was supported by the European Union's Horizon 2020 research and innovation program (668863-SyBil-AA) and the ERA-NET NEURON program (FKZ 01EW1112-TRANSALC and PIM2010ERN-00679), as well as the Spanish State Research Agency through the Severo Ochoa Program for Centres of Excellence in R & D (SEV-2017-0723). S. C. acknowledges financial support from the Ministerio de Economia y Competitividad (MINECO) under grant PGC2018-101055-B-I00. D.M. and S.C. acknowledge financial support from the Generalitat Valenciana through the Prometeo Program (PROMETEO/2019/015). Additional support was given to W.H.S by the Deutsche Forschungsgemeinschaft Center grant TRR 265 (Heinz et al., 2020) and the Bundesministerium fur Bildung und Forschung (BMBF; FKZ: 031L0190A, 01ZX1909CA). We thank Dr. Begona Fernandez for excellent technical assistance and Dr. Cecile Bordier for helping with the human data preprocessing.Ruiz-España, S.; Ortiz-Ramón, R.; Pérez-Ramírez, MÚ.; Díaz-Parra, A.; Ciccocioppo, R.; Bach, P.; Vollstädt-Klein, S.... (2023). MRI texture-based radiomics analysis for the identification of altered functional networks in alcoholic patients and animal models. Computerized Medical Imaging and Graphics. 104. https://doi.org/10.1016/j.compmedimag.2023.10218710

Bacteraemic pneumococcal pneumonia and SARS-CoV-2 pneumonia: differences and similarities

OBJECTIVE: To analyse differences in clinical presentation and outcome between bacteraemic pneumococcal community-acquired pneumonia (B-PCAP) and sSvere Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pneumonia. METHODS: This observational multi-centre study was conducted on patients hospitalized with B-PCAP between 2000 and 2020 and SARS-CoV-2 pneumonia in 2020. Thirty-day survival, predictors of mortality, and intensive care unit (ICU) admission were compared. RESULTS: In total, 663 patients with B-PCAP and 1561 patients with SARS-CoV-2 pneumonia were included in this study. Patients with B-PCAP had more severe disease, a higher ICU admission rate and more complications. Patients with SARS-CoV-2 pneumonia had higher in-hospital mortality (10.8% vs 6.8%; P=0.004). Among patients admitted to the ICU, the need for invasive mechanical ventilation (69.7% vs 36.2%; P<0.001) and mortality were higher in patients with SARS-CoV-2 pneumonia. In patients with B-PCAP, the predictive model found associations between mortality and systemic complications (hyponatraemia, septic shock and neurological complications), lower respiratory reserve and tachypnoea; chest pain and purulent sputum were protective factors in these patients. In patients with SARS-CoV-2 pneumonia, mortality was associated with previous liver and cardiac disease, advanced age, altered mental status, tachypnoea, hypoxaemia, bilateral involvement, pleural effusion, septic shock, neutrophilia and high blood urea nitrogen; in contrast, ≥7 days of symptoms was a protective factor in these patients. In-hospital mortality occurred earlier in patients with B-PCAP. CONCLUSIONS: Although B-PCAP was associated with more severe disease and a higher ICU admission rate, the mortality rate was higher for SARS-CoV-2 pneumonia and deaths occurred later. New prognostic scales and more effective treatments are needed for patients with SARS-CoV-2 pneumonia

MRI texture-based radiomics analysis for the identification of altered functional networks in alcoholic patients and animal models

Alcohol use disorder (AUD) is a complex condition representing a leading risk factor for death, disease and disability. Its high prevalence and severe health consequences make necessary a better understanding of the brain network alterations to improve diagnosis and treatment. The purpose of this study was to evaluate the potential of resting-state fMRI 3D texture features as a novel source of biomarkers to identify AUD brain network alterations following a radiomics approach. A longitudinal study was conducted in Marchigian Sardinian alcohol-preferring msP rats (N = 36) who underwent resting-state functional and structural MRI before and after 30 days of alcohol or water consumption. A cross-sectional human study was also conducted among 33 healthy controls and 35 AUD patients. The preprocessed functional data corresponding to control and alcohol conditions were used to perform a probabilistic independent component analysis, identifying seven independent components as resting-state networks. Forty-three radiomic features extracted from each network were compared using a Wilcoxon signed-rank test with Holm correction to identify the network most affected by alcohol consumption. Features extracted from this network were then used in the machine learning process, evaluating two feature selection methods and six predictive models within a nested cross-validation structure. The classification was evaluated by computing the area under the ROC curve. Images were quantized using different numbers of gray-levels to test their influence on the results. The influence of ageing, data preprocessing, and brain iron accumulation were also analyzed. The methodology was validated using structural scans. The striatal network in alcohol-exposed msP rats presented the most significant number of altered features. The radiomics approach supported this result achieving good classification performance in animals (AUC = 0.915 ± 0.100, with 12 features) and humans (AUC = 0.724 ± 0.117, with 9 features) using a random forest model. Using the structural scans, high accuracy was achieved with a multilayer perceptron in both species (animals: AUC > 0.95 with 2 features, humans: AUC > 0.82 with 18 features). The best results were obtained using a feature selection method based on the p-value. The proposed radiomics approach is able to identify AUD patients and alcohol-exposed rats with good accuracy, employing a subset of 3D features extracted from fMRI. Furthermore, it can help identify relevant networks in drug addiction.This work was supported by the European Union’s Horizon 2020 research and innovation program (668863-SyBil-AA) and the ERA-NET NEURON program (FKZ 01EW1112-TRANSALC and PIM2010ERN-00679), as well as the Spanish State Research Agency through the Severo Ochoa Program for Centres of Excellence in R&D (SEV- 2017–0723). S.C. acknowledges financial support from the Ministerio de Economía y Competitividad (MINECO) under grant PGC2018–101055-B-I00. D.M. and S.C. acknowledge financial support from the Generalitat Valenciana through the Prometeo Program (PROMETEO/2019/015). Additional support was given to W.H.S by the Deutsche Forschungsgemeinschaft Center grant TRR 265 (Heinz et al., 2020) and the Bundesministerium für Bildung und Forschung (BMBF; FKZ: 031L0190A, 01ZX1909CA).Peer reviewe

Treatment with tocilizumab or corticosteroids for COVID-19 patients with hyperinflammatory state: a multicentre cohort study (SAM-COVID-19)

Objectives: The objective of this study was to estimate the association between tocilizumab or corticosteroids and the risk of intubation or death in patients with coronavirus disease 19 (COVID-19) with a hyperinflammatory state according to clinical and laboratory parameters. Methods: A cohort study was performed in 60 Spanish hospitals including 778 patients with COVID-19 and clinical and laboratory data indicative of a hyperinflammatory state. Treatment was mainly with tocilizumab, an intermediate-high dose of corticosteroids (IHDC), a pulse dose of corticosteroids (PDC), combination therapy, or no treatment. Primary outcome was intubation or death; follow-up was 21 days. Propensity score-adjusted estimations using Cox regression (logistic regression if needed) were calculated. Propensity scores were used as confounders, matching variables and for the inverse probability of treatment weights (IPTWs). Results: In all, 88, 117, 78 and 151 patients treated with tocilizumab, IHDC, PDC, and combination therapy, respectively, were compared with 344 untreated patients. The primary endpoint occurred in 10 (11.4%), 27 (23.1%), 12 (15.4%), 40 (25.6%) and 69 (21.1%), respectively. The IPTW-based hazard ratios (odds ratio for combination therapy) for the primary endpoint were 0.32 (95%CI 0.22-0.47; p < 0.001) for tocilizumab, 0.82 (0.71-1.30; p 0.82) for IHDC, 0.61 (0.43-0.86; p 0.006) for PDC, and 1.17 (0.86-1.58; p 0.30) for combination therapy. Other applications of the propensity score provided similar results, but were not significant for PDC. Tocilizumab was also associated with lower hazard of death alone in IPTW analysis (0.07; 0.02-0.17; p < 0.001). Conclusions: Tocilizumab might be useful in COVID-19 patients with a hyperinflammatory state and should be prioritized for randomized trials in this situatio