Personalized 3D reconstruction of the rib cage for clinical assessment of trunk deformities

Scoliosis is a 3D deformity of the spine and rib cage. Extensive validation of 3D reconstruction methods of the spine from biplanar radiography has already been published. In this article, we propose a novel method to reconstruct the rib cage, using the same biplanar views as for the 3D reconstruction of the spine, to allow clinical assessment of whole trunk deformities. This technique uses a semi-automatic segmentation of the ribs in the postero-anterior X-ray view and an interactive segmentation of partial rib edges in the lateral view. The rib midlines are automatically extracted in 2D and reconstructed in 3D using the epipolar geometry. For the ribs not visible in the lateral view, the method predicts their 3D shape. The accuracy of the proposed method has been assessed using data obtained from a synthetic bone model as a gold standard and has also been evaluated using data of real patients with scoliotic deformities. Results show that the reconstructed ribs enable a reliable evaluation of the rib axial rotation, which will allow a 3D clinical assessment of the spine and rib cage deformities.CIHR / IRS

Titanium Cage Fixation in Thoracic and Thoraco-lumbar Anterior Inter-body Fusion

nner by inter body fusion. Study Design:  Prospective Study. Material and Method:  The study was conducted at the department of neurosurgery Lahore general hospital Lahore. Results:  Thirty cases were included during period two years. All cases operated for decompression, fusion and instrumentation, cages of titanium mesh were used. Neurological status of the patients assessed before and after operation. Twenty eight (93.3%) cases improved neurologically. Two (6.7%) did not improved. There were three infected cases which were treated and improved in the long run. Conclusion:  By using anterior interbody fusion (AIF) with cage we can mobilize the patient early. Improvement of the neurological status is excellent. Per operative infection rate is very low. Deformity can be corrected with more accuracy. Key Words:  Anterior cervical corpectomy, anterior dorsal inter body fusion, anterior, posterior and lateral, computed tommography, magnetic resonance imaging

Reconstruction 3D personnalisée de la cage thoracique pour l'amélioration de la simulation de l'effet de la correction du rachis sur l'apparence externe du tronc

Résumé Afin de procéder à une évaluation clinique de la scoliose, les cliniciens se réfèrent souvent à l'angle de Cobb. Celui-ci ne représente malheureusement que la courbure mesurée sur un plan. De plus, les déformations que subit la cage thoracique ne sont pas toujours corrélées à celle de la colonne vertébrale. Plusieurs techniques ont été proposées afin de fournir au clinicien une information quant à la configuration tridimensionnelle de la cage thoracique. Cependant, il doit souvent se limiter à la correction de la colonne vertébrale, ce qui peut entraîner une persistance des gibbosités après l'opération. Un simulateur permettant de prédire l'effet d'une correction du rachis sur l'apparence externe du tronc serait très utile dans la planification de la chirurgie. Le chirurgien pourra ainsi déterminer la stratégie opératoire qui pourra non seulement redresser la colonne mais réduire les gibbosités qui affectent aussi l'apparence externe du patient. Par contre, les modèles tridimensionnels de la cage thoracique existants ne sont pas complètement personnalisés au patient, et donc limitent la précision des résultats de simulation. L'objectif de ce projet est de développer une nouvelle technique de reconstruction 3D personnalisée de la cage thoracique, afin d'améliorer les résultats de simulation de la propagation de l'effet d'une chirurgie du rachis sur l'apparence externe du tronc. Les méthodes actuelles de reconstructions 3D de la cage thoracique ne sont pas précises et n'ont pas été validées avec des modèles représentants fidèlement une cage thoracique en position debout. Dans la littérature, la plupart des modèles de références sont obtenus par tomodensitométrie, qui s'effectue en position couchée. Ces modèles sont donc difficilement recommandables pour une validation clinique des méthodes de reconstruction 3D de la cage thoracique à partir de radiographies acquises en position debout. De plus, ces techniques n'offrent que des reconstructions de cage thoracique par modèles filaires, ou des reconstructions surfaciques par déformation de modèles génériques. Ces modèles ne sont pas adéquats dans un contexte de simulation personnalisée, où le but ultime est de planifier la meilleure stratégie à effectuer afin d'obtenir la meilleure correction à l'interne bien sûr, mais surtout à l'externe puisque c'est un facteur important de satisfaction chez le patient. Une nouvelle méthode a été proposée afin de pallier ces problèmes. Celle-ci se base uniquement sur les radiographies standards, soit la radiographie postéro-antérieure à 0° et la radiographie latérale. Premièrement, une détection semi-automatique des côtes est effectuée sur la radiographie postéro-antérieure, et une identification interactive d'un ensemble de points sur les côtes visibles est faite sur la radiographie latérale. Ensuite, une reconstruction automatique des côtes est réalisée par une mise en correspondance de ces points sur deux vues. De plus, les côtes non détectées sur la radiographie latérale, qui sont en général les côtes de la partie supérieure de la cage thoracique, sont prédites à partir des côtes inférieures, ce qui constitue l'originalité de cette méthode. Finalement, une surface est générée le long de la ligne médiane reconstruite. Cette surface représente l'épaisseur réelle de la côte, et sert de point d'ancrage pour les tissus mous lors des simulations de la correction du rachis. Une validation rigoureuse fut menée, grâce à un modèle de cage thoracique synthétique représentant une vraie cage thoracique en position debout. Cela n'a jamais été fait auparavant. Trois sévérités de déformations ont été considérées, soit 0°, 20° et 40° d'angle de Cobb thoracique droite. Dans chacun des cas, le modèle a été numérisé à l'aide d'un appareil de mesure tridimensionnelle et des radiographies ont été acquises. Des reconstructions effectuées par la nouvelle méthode et l'ancienne méthode de reconstruction de la cage thoracique utilisée à l'hôpital Sainte-Justine ont été comparées aux numérisations du modèle synthétique. La méthode proposée offre une erreur moyenne de 11,95 mm (±6,56 mm), 9,30 mm (±5,86 mm) et 8,27 mm (±5,16 mm), comparativement à l'ancienne méthode qui offre une erreur moyenne de 23,98 mm (±11,09 mm), 11,80 mm (±6,56 mm) et 14,05 mm (±9,59 mm), respectivement pour les configurations à 0°, 20° et 40°. De plus, des simulations ont été effectuées sur trois patients afin de déterminer si la cage thoracique obtenue par la nouvelle méthode améliore les résultats. Les résultats obtenus ont clairement démontré qu'une reconstruction précise de la cage thoracique améliore significativement les résultats de simulation. La principale contribution de ce projet réside dans le fait que la méthode proposée permet de faire une évaluation clinique fiable des déformations de la cage thoracique. L'amélioration de la précision de la reconstruction 3D et la personnalisation plus complète de la cage thoracique permettent non seulement cela, mais ouvrent aussi la voie à différentes opportunités. Notamment, la simulation de la chirurgie des côtes, la reconstruction des poumons ou même l'étude de la corrélation entre la structure osseuse interne et la surface externe du tronc bénéficierait grandement d'une cage thoracique personnalisée. Tous ces projets, globalement, contribuent à diminuer la quantité de radiation infligée aux patients, car ceux-ci auront de moins en moins à subir de radiographies afin de faire un suivi clinique.----------Abstract To evaluate scoliosis severity in the clinical setting, clinicians often refer to the Cobb angle. Unfortunately, this angle only represents a curve on a plane. Furthermore, the deformities sustained by the rib cage are not always correlated to those of the spine. Many techniques have been proposed to help the clinician by providing information about the three dimensional configuration of the rib cage. However, he must sometimes only correct the spine and rib humps may persist. A simulator predicting the effects of a spine correction on the external appearance of the trunk would be useful to plan the surgery. However, three dimensional rib cage models used are not fully personalised to each patient, thus limiting the precision of the results of the simulation. The goal of this project is to develop a new method for personalised 3D reconstruction of the rib cage, in order to improve the results of simulating the propagation of the spinal correction to the external trunk. Current methods of 3D reconstruction of the rib cage are not precise and have not been validated with models that faithfully represent a rib cage in standing position. In the literature, most reference models are obtained by computed tomography (CT) scans, which are acquired in supine position. Such models are thus inappropriate for a clinical assessment of the 3D reconstruction methods based on radiographs acquired in standing position. Furthermore, the existing methods only provide the reconstruction of the rib midlines or complete 3D rib cage models obtained by deforming generic models. These reconstructions are not adequate in the context of personalized simulation, where the ultimate goal is to plan the clinical strategy providing the best correction both of the internal structures and of the external appearance of the trunk, the latter being the main factor contributing to patient satisfaction. We have proposed a new method in order to address these problems. This method is based only on the two standards radiographs, i.e. the postero-anterior view at 0° and the lateral view. First of all, a semi-automatic detection of the ribs is done on the postero-anterior radiograph, followed by an interactive identification of a set of points on the visible ribs in the lateral view. Then, an automatic reconstruction of the ribs is performed by means of stereo matching points. The originality of this method is that it can predict the undetected ribs in the lateral view, which are mostly those of the upper section of the rib cage, based on the reconstruction of the lower ribs. Finally, a surface is generated along the rib's 3D midline. This surface represents the real thickness of the rib and serves as an anchor for the attachment of soft tissues during the simulation of the spine correction's effect on the whole trunk. A thorough validation was conducted with the help of a synthetic rib cage model. This model represents a real rib cage in standing position . This kind of validation has never been done before. Three cases of scoliotic deformation were considered, namely 0°, 20° and 40° of right-thoracic Cobb angle. In each case, the model was digitized with a coordinate measuring machine and radiographed. 3D reconstructions of the rib cage obtained by the proposed method and the existing method used at Sainte-Justine Hospital were compared to the digitized model. The new method yields mean errors of 11,95 mm (±6,56 mm), 9,30 mm (±5,86 mm) and 8,27 mm (±5,16 mm), compared to the old method which yields mean errors of 23,98 mm (±11,09 mm), 11,80 mm (±6,56 mm) and 14,05 mm (±9,59 mm), for the 0°, 20° and 40° deformations, respectively. Furthermore, simulations were performed on three patients to determine if the rib cage produced by the new method improves the results of the simulator. The results clearly demonstrated that a precise reconstruction of the rib cage significantly improves the simulation results. The main contribution of this project lies in the fact that the new method allows a reliable clinical assessment of rib cage deformities. In addition, the enhanced precision of the 3D reconstruction and the more complete personalization of the rib cage model open up new possibilities. In particular, the simulation of other surgical interventions such as rib resection and lung reconstruction, as well as studies on the relationship between internal bone structures and external trunk shape, could all benefit from a personalized rib cage. Globally, all these projects contribute to reducing the amount of radiation inflicted to patients because less radiographs will be required in order to make a clinical follow up

Reconstruction 3D personnalisée de la cage thoracique pour l'amélioration de la simulation de l'effet de la correction du rachis sur l'apparence externe du tronc

Résumé Afin de procéder à une évaluation clinique de la scoliose, les cliniciens se réfèrent souvent à l'angle de Cobb. Celui-ci ne représente malheureusement que la courbure mesurée sur un plan. De plus, les déformations que subit la cage thoracique ne sont pas toujours corrélées à celle de la colonne vertébrale. Plusieurs techniques ont été proposées afin de fournir au clinicien une information quant à la configuration tridimensionnelle de la cage thoracique. Cependant, il doit souvent se limiter à la correction de la colonne vertébrale, ce qui peut entraîner une persistance des gibbosités après l'opération. Un simulateur permettant de prédire l'effet d'une correction du rachis sur l'apparence externe du tronc serait très utile dans la planification de la chirurgie. Le chirurgien pourra ainsi déterminer la stratégie opératoire qui pourra non seulement redresser la colonne mais réduire les gibbosités qui affectent aussi l'apparence externe du patient. Par contre, les modèles tridimensionnels de la cage thoracique existants ne sont pas complètement personnalisés au patient, et donc limitent la précision des résultats de simulation. L'objectif de ce projet est de développer une nouvelle technique de reconstruction 3D personnalisée de la cage thoracique, afin d'améliorer les résultats de simulation de la propagation de l'effet d'une chirurgie du rachis sur l'apparence externe du tronc. Les méthodes actuelles de reconstructions 3D de la cage thoracique ne sont pas précises et n'ont pas été validées avec des modèles représentants fidèlement une cage thoracique en position debout. Dans la littérature, la plupart des modèles de références sont obtenus par tomodensitométrie, qui s'effectue en position couchée. Ces modèles sont donc difficilement recommandables pour une validation clinique des méthodes de reconstruction 3D de la cage thoracique à partir de radiographies acquises en position debout. De plus, ces techniques n'offrent que des reconstructions de cage thoracique par modèles filaires, ou des reconstructions surfaciques par déformation de modèles génériques. Ces modèles ne sont pas adéquats dans un contexte de simulation personnalisée, où le but ultime est de planifier la meilleure stratégie à effectuer afin d'obtenir la meilleure correction à l'interne bien sûr, mais surtout à l'externe puisque c'est un facteur important de satisfaction chez le patient. Une nouvelle méthode a été proposée afin de pallier ces problèmes. Celle-ci se base uniquement sur les radiographies standards, soit la radiographie postéro-antérieure à 0° et la radiographie latérale. Premièrement, une détection semi-automatique des côtes est effectuée sur la radiographie postéro-antérieure, et une identification interactive d'un ensemble de points sur les côtes visibles est faite sur la radiographie latérale. Ensuite, une reconstruction automatique des côtes est réalisée par une mise en correspondance de ces points sur deux vues. De plus, les côtes non détectées sur la radiographie latérale, qui sont en général les côtes de la partie supérieure de la cage thoracique, sont prédites à partir des côtes inférieures, ce qui constitue l'originalité de cette méthode. Finalement, une surface est générée le long de la ligne médiane reconstruite. Cette surface représente l'épaisseur réelle de la côte, et sert de point d'ancrage pour les tissus mous lors des simulations de la correction du rachis. Une validation rigoureuse fut menée, grâce à un modèle de cage thoracique synthétique représentant une vraie cage thoracique en position debout. Cela n'a jamais été fait auparavant. Trois sévérités de déformations ont été considérées, soit 0°, 20° et 40° d'angle de Cobb thoracique droite. Dans chacun des cas, le modèle a été numérisé à l'aide d'un appareil de mesure tridimensionnelle et des radiographies ont été acquises. Des reconstructions effectuées par la nouvelle méthode et l'ancienne méthode de reconstruction de la cage thoracique utilisée à l'hôpital Sainte-Justine ont été comparées aux numérisations du modèle synthétique. La méthode proposée offre une erreur moyenne de 11,95 mm (±6,56 mm), 9,30 mm (±5,86 mm) et 8,27 mm (±5,16 mm), comparativement à l'ancienne méthode qui offre une erreur moyenne de 23,98 mm (±11,09 mm), 11,80 mm (±6,56 mm) et 14,05 mm (±9,59 mm), respectivement pour les configurations à 0°, 20° et 40°. De plus, des simulations ont été effectuées sur trois patients afin de déterminer si la cage thoracique obtenue par la nouvelle méthode améliore les résultats. Les résultats obtenus ont clairement démontré qu'une reconstruction précise de la cage thoracique améliore significativement les résultats de simulation. La principale contribution de ce projet réside dans le fait que la méthode proposée permet de faire une évaluation clinique fiable des déformations de la cage thoracique. L'amélioration de la précision de la reconstruction 3D et la personnalisation plus complète de la cage thoracique permettent non seulement cela, mais ouvrent aussi la voie à différentes opportunités. Notamment, la simulation de la chirurgie des côtes, la reconstruction des poumons ou même l'étude de la corrélation entre la structure osseuse interne et la surface externe du tronc bénéficierait grandement d'une cage thoracique personnalisée. Tous ces projets, globalement, contribuent à diminuer la quantité de radiation infligée aux patients, car ceux-ci auront de moins en moins à subir de radiographies afin de faire un suivi clinique.----------Abstract To evaluate scoliosis severity in the clinical setting, clinicians often refer to the Cobb angle. Unfortunately, this angle only represents a curve on a plane. Furthermore, the deformities sustained by the rib cage are not always correlated to those of the spine. Many techniques have been proposed to help the clinician by providing information about the three dimensional configuration of the rib cage. However, he must sometimes only correct the spine and rib humps may persist. A simulator predicting the effects of a spine correction on the external appearance of the trunk would be useful to plan the surgery. However, three dimensional rib cage models used are not fully personalised to each patient, thus limiting the precision of the results of the simulation. The goal of this project is to develop a new method for personalised 3D reconstruction of the rib cage, in order to improve the results of simulating the propagation of the spinal correction to the external trunk. Current methods of 3D reconstruction of the rib cage are not precise and have not been validated with models that faithfully represent a rib cage in standing position. In the literature, most reference models are obtained by computed tomography (CT) scans, which are acquired in supine position. Such models are thus inappropriate for a clinical assessment of the 3D reconstruction methods based on radiographs acquired in standing position. Furthermore, the existing methods only provide the reconstruction of the rib midlines or complete 3D rib cage models obtained by deforming generic models. These reconstructions are not adequate in the context of personalized simulation, where the ultimate goal is to plan the clinical strategy providing the best correction both of the internal structures and of the external appearance of the trunk, the latter being the main factor contributing to patient satisfaction. We have proposed a new method in order to address these problems. This method is based only on the two standards radiographs, i.e. the postero-anterior view at 0° and the lateral view. First of all, a semi-automatic detection of the ribs is done on the postero-anterior radiograph, followed by an interactive identification of a set of points on the visible ribs in the lateral view. Then, an automatic reconstruction of the ribs is performed by means of stereo matching points. The originality of this method is that it can predict the undetected ribs in the lateral view, which are mostly those of the upper section of the rib cage, based on the reconstruction of the lower ribs. Finally, a surface is generated along the rib's 3D midline. This surface represents the real thickness of the rib and serves as an anchor for the attachment of soft tissues during the simulation of the spine correction's effect on the whole trunk. A thorough validation was conducted with the help of a synthetic rib cage model. This model represents a real rib cage in standing position . This kind of validation has never been done before. Three cases of scoliotic deformation were considered, namely 0°, 20° and 40° of right-thoracic Cobb angle. In each case, the model was digitized with a coordinate measuring machine and radiographed. 3D reconstructions of the rib cage obtained by the proposed method and the existing method used at Sainte-Justine Hospital were compared to the digitized model. The new method yields mean errors of 11,95 mm (±6,56 mm), 9,30 mm (±5,86 mm) and 8,27 mm (±5,16 mm), compared to the old method which yields mean errors of 23,98 mm (±11,09 mm), 11,80 mm (±6,56 mm) and 14,05 mm (±9,59 mm), for the 0°, 20° and 40° deformations, respectively. Furthermore, simulations were performed on three patients to determine if the rib cage produced by the new method improves the results of the simulator. The results clearly demonstrated that a precise reconstruction of the rib cage significantly improves the simulation results. The main contribution of this project lies in the fact that the new method allows a reliable clinical assessment of rib cage deformities. In addition, the enhanced precision of the 3D reconstruction and the more complete personalization of the rib cage model open up new possibilities. In particular, the simulation of other surgical interventions such as rib resection and lung reconstruction, as well as studies on the relationship between internal bone structures and external trunk shape, could all benefit from a personalized rib cage. Globally, all these projects contribute to reducing the amount of radiation inflicted to patients because less radiographs will be required in order to make a clinical follow up

Automatic 3D extraction of pleural plaques and diffuse pleural thickening from lung MDCT images

Pleural plaques (PPs) and diffuse pleural thickening (DPT) are very common asbestos related pleural diseases (ARPD). They are currently identified non-invasively using medical imaging techniques. A fully automatic algorithm for 3D detection of calcified pleura in the diaphragmatic area and thickened pleura on the costal surfaces from multi detector computed tomography (MDCT) images has been developed and tested. The algorithm for detecting diaphragmatic pleura includes estimation of the diaphragm top surface in 3D and identifying those voxels at a certain vertical distance from the estimated diaphragm, and with intensities close to that of bone, as calcified pleura. The algorithm for detecting thickened pleura on the costal surfaces includes: estimation of the pleural costal surface in 3D, estimation of the centrelines of ribs and costal cartilages and the surfaces that they lie on, calculating the mean distance between the two surfaces, and identifying any space between the two surfaces whose distance exceeds the mean distance as thickened pleura. The accuracy and performance of the proposed algorithm was tested on 20 MDCT datasets from patients diagnosed with existing PPs and/or DPT and the results were compared against the ground truth provided by an experienced radiologist. Several metrics were employed and evaluations indicate high performance of both calcified pleura detection in the diaphragmatic area and thickened pleura on the costal surfaces. This work has made significant contributions to both medical image analysis and medicine. For the first time in medical image analysis, the approach uses other stable organs such as the ribs and costal cartilage, besides the lungs themselves, for referencing and landmarking in 3D. It also estimates fat thickness between the rib surface and pleura (which is usually very thin) and excludes it from the detected areas, when identifying the thickened pleura. It also distinguishes the calcified pleura attached to the rib(s), separates them in 3D and detects calcified pleura on the lung diaphragmatic surfaces. The key contribution to medicine is effective detection of pleural thickening of any size and recognition of any changes, however small. This could have a significant impact on managing patient risks

Unsupervised CT lung image segmentation of a mycobacterium tuberculosis infection model

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that produces pulmonary damage. Radiological imaging is the preferred technique for the assessment of TB longitudinal course. Computer-assisted identification of biomarkers eases the work of the radiologist by providing a quantitative assessment of disease. Lung segmentation is the step before biomarker extraction. In this study, we present an automatic procedure that enables robust segmentation of damaged lungs that have lesions attached to the parenchyma and are affected by respiratory movement artifacts in a Mycobacterium Tuberculosis infection model. Its main steps are the extraction of the healthy lung tissue and the airway tree followed by elimination of the fuzzy boundaries. Its performance was compared with respect to a segmentation obtained using: (1) a semi-automatic tool and (2) an approach based on fuzzy connectedness. A consensus segmentation resulting from the majority voting of three experts' annotations was considered our ground truth. The proposed approach improves the overlap indicators (Dice similarity coefficient, 94% ± 4%) and the surface similarity coefficients (Hausdorff distance, 8.64 mm ± 7.36 mm) in the majority of the most difficult-to-segment slices. Results indicate that the refined lung segmentations generated could facilitate the extraction of meaningful quantitative data on disease burden.The research leading to these results received funding from the Innovative Medicines Initiative (www.imi.europa.eu) Joint Undertaking under grant agreement no. 115337, whose resources comprise funding from the European Union’s Seventh Framework Programme (FP7/2007–2013) and EFPIA companies’ in kind contribution. This work was partially funded by projects TEC2013-48552-C2-1-R, RTC-2015-3772-1, TEC2015-73064-EXP and TEC2016-78052-R from the Spanish Ministerio de Economía, Industria y Competitividad, TOPUS S2013/MIT-3024 project from the regional government of Madrid and by the Department of Health, UK

Consensus based recommendations for diagnosis and medical management of Poland syndrome (sequence)

Background Poland syndrome (OMIM: 173800) is a disorder in which affected individuals are born with missing or underdeveloped muscles on one side of the body, resulting in abnormalities that can affect the chest, breast, shoulder, arm, and hand. The extent and severity of the abnormalities vary among affected individuals. Main body The aim of this work is to provide recommendations for the diagnosis and management of people affected by Poland syndrome based on evidence from literature and experience of health professionals from different medical backgrounds who have followed for several years affected subjects. The literature search was performed in the second half of 2019. Original papers, meta-analyses, reviews, books and guidelines were reviewed and final recommendations were reached by consensus. Conclusion Being Poland syndrome a rare syndrome most recommendations here presented are good clinical practice based on the consensus of the participant experts

Unsupervised CT Lung Image Segmentation of a Mycobacterium Tuberculosis Infection Model

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that produces pulmonary damage. Radiological imaging is the preferred technique for the assessment of TB longitudinal course. Computer-assisted identification of biomarkers eases the work of the radiologist by providing a quantitative assessment of disease. Lung segmentation is the step before biomarker extraction. In this study, we present an automatic procedure that enables robust segmentation of damaged lungs that have lesions attached to the parenchyma and are affected by respiratory movement artifacts in a Mycobacterium Tuberculosis infection model. Its main steps are the extraction of the healthy lung tissue and the airway tree followed by elimination of the fuzzy boundaries. Its performance was compared with respect to a segmentation obtained using: (1) a semi-automatic tool and (2) an approach based on fuzzy connectedness. A consensus segmentation resulting from the majority voting of three experts' annotations was considered our ground truth. The proposed approach improves the overlap indicators (Dice similarity coefficient, 94\% +/- 4\%) and the surface similarity coefficients (Hausdorff distance, 8.64 mm +/- 7.36 mm) in the majority of the most difficult-to-segment slices. Results indicate that the refined lung segmentations generated could facilitate the extraction of meaningful quantitative data on disease burden.We thank Estibaliz Gomez de Mariscal, Paula Martin Gonzalez and Mario Gonzalez Arjona for helping with the manual lung annotation. The research leading to these results received funding from the Innovative Medicines Initiative (www.imi.europa.eu) Joint Undertaking under grant agreement no. 115337, whose resources comprise funding from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies' in kind contribution. This work was partially funded by projects TEC2013-48552-C2-1-R, RTC-2015-3772-1, TEC2015-73064-EXP and TEC2016-78052-R from the Spanish Ministerio de Economia, Industria y Competitividad, TOPUS S2013/MIT-3024 project from the regional government of Madrid and by the Department of Health, UK.S