UCI – Das Tumorzentrum Bern - Navigation

Reyes, Mauricio

{"headers":{"title":"Title","year":"Year","type":"Type"},"rows":[{"title":"Kamath, A., Willmann, J., Andratschke, N., \u0026 Reyes, M. (2025). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/218912\u0022\u003EThe impact of U-Net architecture choices and skip connections on the robustness of segmentation across texture variations\u003C\/a\u003E. \u003Ci\u003EComputers in Biology and Medicine\u003C\/i\u003E, \u003Ci\u003E197\u003C\/i\u003E(Pt B), 111056.","year":2025,"type":"Journal Article (Original Article)"},{"title":"Lohmeier, J., Meinhardt, J., Radbruch, H., Reyes, M., Brenner, W., Tietze, A., \u0026 Makowski, M. R. (2025). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/217603\u0022\u003ESpatial tumour characteristics as an indirect marker of metabolic dysregulation: evaluation for non-invasive IDH-genotyping of glioma using hybrid [18\u00a0F]FET-PET\/MRI\u003C\/a\u003E. \u003Ci\u003EEuropean Journal of Nuclear Medicine and Molecular Imaging\u003C\/i\u003E.","year":2025,"type":"Journal Article (Original Article)"},{"title":"de la Rosa, E., Reyes, M., Liew, S.-L., Hutton, A., Wiest, R., Kaesmacher, J., Hanning, U., Hakim, A., Zubal, R., Valenzuela, W., Robben, D., Sima, D. M., Anania, V., Brys, A., Meakin, J. A., Mickan, A., Broocks, G., Heitkamp, C., Gao, S., \u2026 Wiestler, B. (2025). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/214645\u0022\u003EDeepISLES: a clinically validated ischemic stroke segmentation model from the ISLES\u201922 challenge\u003C\/a\u003E. \u003Ci\u003ENature Communications\u003C\/i\u003E, \u003Ci\u003E16\u003C\/i\u003E(1), 7357.","year":2025,"type":"Journal Article (Original Article)"},{"title":"Aumente-Maestro, C., M\u00fcller, M., Remeseiro, B., D\u00edez, J., \u0026 Reyes, M. (2025). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/214888\u0022\u003EAUDIT: An open-source Python library for AI model evaluation with use cases in MRI brain tumor segmentation\u003C\/a\u003E. \u003Ci\u003EComputer Methods and Programs in Biomedicine\u003C\/i\u003E, \u003Ci\u003E271\u003C\/i\u003E, 108991.","year":2025,"type":"Journal Article (Original Article)"},{"title":"Poel, R., R\u00fcfenacht, E., Scheib, S., Hemmatazad, H., Krcek, R., Tran, S., Romano, E., Rogers, S., Stieb, S., Poolakundan, M. R., Al-Abdulla, H. H., Foerster, R., Schr\u00f6der, C., Oehler, C., Hong, J., Breedveld, S., Andratschke, N., Manser, P., Fix, M. K., \u2026 Ermi\u015f, E. (2025). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/214515\u0022\u003EA comprehensive multifaceted technical evaluation framework for implementation of auto-segmentation models in radiotherapy\u003C\/a\u003E. \u003Ci\u003ECommunications Medicine\u003C\/i\u003E, \u003Ci\u003E5\u003C\/i\u003E(1), 319.","year":2025,"type":"Journal Article (Original Article)"},{"title":"R\u00e4z, T., Pahud de Mortanges, A., \u0026 Reyes, M. (2025). [Review of \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/214803\u0022\u003EExplainable AI in medicine: challenges of integrating XAI into the future clinical routine\u003C\/a\u003E\u003C\/i\u003E]. \u003Ci\u003EFrontiers in Radiology\u003C\/i\u003E, \u003Ci\u003E5\u003C\/i\u003E.","year":2025,"type":"Journal Article (Review)"},{"title":"Willmann, J., Kamath, A., Poel, R., Riggenbach, E., Mose, L., Bertholet, J., Muller, S., Schmidhalter, D., Andratschke, N., Ermis, E., \u0026 Reyes, M. (2025). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/212656\u0022\u003EPredicting the impact of target volume contouring variations on the organ at risk dose: results of a qualitative survey\u003C\/a\u003E. \u003Ci\u003ERadiotherapy \u0026 Oncology\u003C\/i\u003E.","year":2025,"type":"Journal Article (Original Article)"},{"title":"Krcek, R., Poel, R., Bachmann, N., Hemmatazad, H., Reinhardt, P., Radojewski, P., Slotboom, J., Reyes, M., \u0026 Ermis, E. (2025, May). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/211901\u0022\u003E7-Tesla vs. 3-Tesla MRI in low grade glioma radiotherapy planning: Can we improve delineation consistency\u003C\/a\u003E? In \u003Ci\u003ERadiotherapy \u0026 Oncology\u003C\/i\u003E (Vols. 206, Issue Supplement 1, pp. S718-S719). ESTRO 2025, Vienna. Elsevier.","year":2025,"type":"Conference Paper (Abstract)"},{"title":"Mahapatra, D., Yepes, A. J., Bozorgtabar, B., Roy, S., Ge, Z., \u0026 Reyes, M. (2025). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/205407\u0022\u003EMulti-Label Generalized Zero Shot Chest Xray Classification By Combining Image-Text Information With Feature Disentanglement\u003C\/a\u003E. \u003Ci\u003EIEEE Transactions on Medical Imaging\u003C\/i\u003E, \u003Ci\u003E44\u003C\/i\u003E(1), 31-43.","year":2025,"type":"Journal Article (Original Article)"},{"title":"Yang, J., Garcia Henao, J. A., Dvornek, N., He, J., Bower, D. V., Depotter, A., Bajercius, H., Pahud de Mortanges, A., You, C., Gange, C., Ledda, R. E., Silva, M., Dela Cruz, C. S., Hautz, W., Bonel, H. M., Reyes, M., Staib, L. H., Poellinger, A., \u0026 Duncan, J. S. (2024). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/189654\u0022\u003EPrior knowledge-guided vision-transformer-based unsupervised domain adaptation for intubation prediction in lung disease at one week\u003C\/a\u003E. \u003Ci\u003EComputerized Medical Imaging and Graphics\u003C\/i\u003E, \u003Ci\u003E118\u003C\/i\u003E, 102442.","year":2024,"type":"Journal Article (Original Article)"},{"title":"Shu, S. Z., Pahud de Mortanges, A., Poellinger, A., Mahapatra, D., \u0026 Reyes, M. (2024). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/190729\u0022\u003EINFORMER- Interpretability Founded Monitoring of\u00a0Medical Image Deep Learning Models\u003C\/a\u003E. \u003Ci\u003EUncertainty for Safe Utilization of Machine Learning in Medical Imaging\u003C\/i\u003E, \u003Ci\u003E15167\u003C\/i\u003E, 215-224.","year":2024,"type":"Conference Paper (Paper)"},{"title":"Mercado, Z., Kamath, A., Poel, R., Willmann, J., Ermis, E., Riggenbach, E., Mose, L., Andratschke, N., \u0026 Reyes, M. (2024). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/189114\u0022\u003EAutomated Dosimetry-informed Segmentation Ranking for Radiotherapy\u003C\/a\u003E. \u003Ci\u003ELecture Notes in Computer Science\u003C\/i\u003E, \u003Ci\u003E15199\u003C\/i\u003E, 221-230.","year":2024,"type":"Conference Paper (Paper)"},{"title":"Mahapatra, D., Tennakoon, R., George, Y., Roy, S., Bozorgtabar, B., Ge, Z., \u0026 Reyes, M. (2024). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/179217\u0022\u003EALFREDO: Active Learning with FeatuRe disEntangelement and DOmain adaptation for medical image classification\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E97\u003C\/i\u003E(103261), 103261.","year":2024,"type":"Journal Article (Original Article)"},{"title":"Pahud de Mortanges, A. H. C., Luo, H., Shu, Z., Kamath, A. J., Suter, Y. R., Shelan, M., P\u00f6llinger, A., \u0026 Reyes, M. (2024). [Review of \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/179273\u0022\u003EOrchestrating explainable artificial intelligence for multimodal and longitudinal data in medical imaging.\u003C\/a\u003E\u003C\/i\u003E]. \u003Ci\u003ENPJ Digital Medicine\u003C\/i\u003E, \u003Ci\u003E7\u003C\/i\u003E(1).","year":2024,"type":"Journal Article (Review)"},{"title":"Poel, R., R\u00fcfenacht, E., Fix, M., Scheib, S., Reyes, M., \u0026 Ermis, E. (2024). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/178859\u0022\u003EClinical evaluation of a deep learning based auto-segmentation model for intracranial organs at risk\u003C\/a\u003E. In \u003Ci\u003ERadiotherapy and oncology\u003C\/i\u003E (Vols. 194, Issue 1, pp. S821-S822). ESTRO 2024, Glasgow,UK. Elsevier.","year":2024,"type":"Conference Paper"},{"title":"Mahapatra, D., Bozorgtabar, B., Ge, Z., \u0026 Reyes, M. (2024). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/173277\u0022\u003EGANDALF: Graph-based transformer and Data Augmentation Active Learning Framework with interpretable features for multi-label chest Xray classification\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E93\u003C\/i\u003E(103075), 103075.","year":2024,"type":"Journal Article (Original Article)"},{"title":"Alwan, L., Benz, D. C., Cuddy, S. A. M., Dobner, S., Shiri Lord, I., Caobelli, F., Bernhard, B., St\u00e4mpfli, S. F., Eberli, F., Reyes, M., Kwong, R. Y., Falk, R. H., Dorbala, S., \u0026 Gr\u00e4ni, C. (2024). [Review of \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/172496\u0022\u003ECurrent and Evolving Multimodality Cardiac Imaging in Managing Transthyretin Amyloid Cardiomyopathy.\u003C\/a\u003E\u003C\/i\u003E]. \u003Ci\u003EJACC. Cardiovascular Imaging\u003C\/i\u003E, \u003Ci\u003E17\u003C\/i\u003E(2), 195-211.","year":2024,"type":"Journal Article (Review)"},{"title":"Maier-Hein, L., Reinke, A., Godau, P., Tizabi, M. D., Buettner, F., Christodoulou, E., Glocker, B., Isensee, F., Kleesiek, J., Kozubek, M., Reyes, M., Riegler, M. A., Wiesenfarth, M., Kavur, A. E., Sudre, C. H., Baumgartner, M., Eisenmann, M., Heckmann-N\u00f6tzel, D., R\u00e4dsch, T., \u2026 J\u00e4ger, P. F. (2024). [Review of \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/174380\u0022\u003EMetrics reloaded: recommendations for image analysis validation.\u003C\/a\u003E\u003C\/i\u003E]. \u003Ci\u003ENature Methods\u003C\/i\u003E, \u003Ci\u003E21\u003C\/i\u003E(2), 195-212.","year":2024,"type":"Journal Article (Review)"},{"title":"Reinke, A., Tizabi, M. D., Baumgartner, M., Eisenmann, M., Heckmann-N\u00f6tzel, D., Kavur, A. E., R\u00e4dsch, T., Sudre, C. H., Acion, L., Antonelli, M., Arbel, T., Bakas, S., Benis, A., Buettner, F., Cardoso, M. J., Cheplygina, V., Chen, J., Christodoulou, E., Cimini, B. A., \u2026 Maier-Hein, L. (2024). [Review of \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/174381\u0022\u003EUnderstanding metric-related pitfalls in image analysis validation.\u003C\/a\u003E\u003C\/i\u003E]. \u003Ci\u003ENature Methods\u003C\/i\u003E, \u003Ci\u003E21\u003C\/i\u003E(2), 182-194.","year":2024,"type":"Journal Article (Review)"},{"title":"Lerch, L., Huber, L. S., Kamath, A., P\u00f6llinger, A., Pahud de Mortanges, A., Obmann, V. C., Dammann, F., Senn, W., \u0026 Reyes, M. (2024). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/202793\u0022\u003EDreamOn: a data augmentation strategy to narrow the robustness gap between expert radiologists and deep learning classifiers\u003C\/a\u003E. \u003Ci\u003EFrontiers in Radiology\u003C\/i\u003E, \u003Ci\u003E4\u003C\/i\u003E, 1420545.","year":2024,"type":"Journal Article (Original Article)"},{"title":"Luo, H., Pahud de Mortanges, A., Inel, O., Bernstein, A., \u0026 Reyes, M. (2024). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/190733\u0022\u003EDWARF: Disease-weighted network for attention map refinement\u003C\/a\u003E\u003C\/i\u003E. Cornell University.","year":2024,"type":"Working Paper"},{"title":"You, S., Wiest, R. G. R., \u0026 Reyes, M. (2024). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/170817\u0022\u003ESaRF: Saliency regularized feature learning improves MRI sequence classification\u003C\/a\u003E. \u003Ci\u003EComputer Methods and Programs in Biomedicine\u003C\/i\u003E, \u003Ci\u003E243\u003C\/i\u003E(107867), 107867.","year":2024,"type":"Journal Article (Original Article)"},{"title":"Kamath, A., Mercado, Z., Poel, R., Willmann, J., Ermis, E., Riggenbach, E., Andratschke, N., \u0026 Reyes, M. (2024). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/190797\u0022\u003EComparing the Performance of Radiation Oncologists versus a Deep Learning Dose Predictor to Estimate Dosimetric Impact of Segmentation Variations for Radiotherapy\u003C\/a\u003E\u003C\/i\u003E. Medical Imaging with Deep Learning \u2013 045 2024, Paris, France.","year":2024,"type":"Conference Paper (Paper)"},{"title":"Garcia Henao, J. A., Depotter, A. G. A., Bower, D. V., Bajercius, H., Todorova, P. T., Saint-James, H., de Mortanges, A. P., Barroso, M. C., He, J., Yang, J., You, C., Staib, L. H., Gange, C., Ledda, R. E., Caminiti, C., Silva, M., Cortopassi, I. O., Dela Cruz, C. S., Hautz, W., \u2026 P\u00f6llinger, A. (2023). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/168956\u0022\u003EA Multiclass Radiomics Method-Based WHO Severity Scale for Improving COVID-19 Patient Assessment and Disease Characterization From CT Scans\u003C\/a\u003E. \u003Ci\u003EInvestigative Radiology\u003C\/i\u003E, \u003Ci\u003E58\u003C\/i\u003E(12), 882-893.","year":2023,"type":"Journal Article (Original Article)"},{"title":"Mahapatra, D., Jimeno Yepes, A. J., Kuanar, S., Roy, S., Bozorgtabar, B., Reyes, M., \u0026 Ge, Z. (2023). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/202418\u0022\u003EClass Specific Feature Disentanglement and Text Embeddings for Multi-label Generalized Zero Shot CXR Classification\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E14221\u003C\/i\u003E, 276-286.","year":2023,"type":"Conference Paper (Paper)"},{"title":"Kamath, A. J., Willmann, J., Andratschke, N., \u0026 Reyes, M. (2023). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/202419\u0022\u003EDo We Really Need that Skip-Connection? Understanding Its Interplay with Task Complexity\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E14223\u003C\/i\u003E, 302-311.","year":2023,"type":"Conference Paper (Paper)"},{"title":"Gassner, M., Barranco Garcia, J., Tanadini-Lang, S., Bertoldo, F., Fr\u00f6hlich, F., Guckenberger, M., Haueis, S., Pelzer, C., Reyes, M., Schmithausen, P., Simic, D., Staeger, R., Verardi, F., Andratschke, N., Adelmann, A., \u0026 Braun, R. P. (2023). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/169497\u0022\u003ESaliency-Enhanced Content-Based Image Retrieval for Diagnosis Support in Dermatology Consultation: Reader Study\u003C\/a\u003E. \u003Ci\u003EJMIR Dermatology\u003C\/i\u003E, \u003Ci\u003E6\u003C\/i\u003E(e42129), e42129.","year":2023,"type":"Journal Article (Original Article)"},{"title":"Oca\u00f1a-Tienda, B., P\u00e9rez-Beteta, J., Villanueva-Garc\u00eda, J. D., Romero-Rosales, J. A., Molina-Garc\u00eda, D., Suter, Y. R., Asenjo, B., Albillo, D., Ortiz de Mendivil, A., P\u00e9rez-Romasanta, L. A., Gonz\u00e1lez-Del Portillo, E., Llorente, M., Carballo, N., Nagib-Raya, F., Vidal-Denis, M., Luque, B., Reyes, M., Arana, E., \u0026 P\u00e9rez-Garc\u00eda, V. M. (2023). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/202417\u0022\u003EA comprehensive dataset of annotated brain metastasis MR images with clinical and radiomic data\u003C\/a\u003E. \u003Ci\u003EScientific Data\u003C\/i\u003E, \u003Ci\u003E10\u003C\/i\u003E(1), 208.","year":2023,"type":"Journal Article (Original Article)"},{"title":"R\u00fcfenacht, E., Kamath, A. J., Suter, Y. R., Poel, R., Ermis, E., Scheib, S., \u0026 Reyes Aguirre, M. A. (2023). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/121311\u0022\u003EPyRaDiSe: A Python package for DICOM-RT-based auto-segmentation pipeline construction and DICOM-RT data conversion\u003C\/a\u003E. \u003Ci\u003EComputer Methods and Programs in Biomedicine\u003C\/i\u003E, \u003Ci\u003E231\u003C\/i\u003E(107374), 107374.","year":2023,"type":"Journal Article (Original Article)"},{"title":"Mahapatra, D., P\u00f6llinger, A., \u0026 Reyes Aguirre, M. A. (2023). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/88799\u0022\u003EGraph Node Based Interpretability Guided Sample Selection for Active Learning\u003C\/a\u003E. \u003Ci\u003EIEEE Transactions on Medical Imaging\u003C\/i\u003E, \u003Ci\u003E42\u003C\/i\u003E(3), 661-673.","year":2023,"type":"Journal Article (Original Article)"},{"title":"Rebsamen, M. A., McKinley, R. I., Radojewski, P., Pistor, M., Friedli, C. D., Hoepner, R., Salmen, A., Chan, A. H.-K., Reyes, M., Wagner, F., Wiest, R. G. R., \u0026 Rummel, C. (2023). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/88156\u0022\u003EReliable brain morphometry from contrast-enhanced T1w-MRI in patients with multiple sclerosis\u003C\/a\u003E. \u003Ci\u003EHuman Brain Mapping\u003C\/i\u003E, \u003Ci\u003E44\u003C\/i\u003E(3), 970-979.","year":2023,"type":"Journal Article (Original Article)"},{"title":"Silva, W., Gon\u00e7alves, T., H\u00e4rm\u00e4, K. H., Schr\u00f6der, E. A., Obmann, V. C., Barroso, M. C., P\u00f6llinger, A., Reyes Aguirre, M. A., \u0026 Cardoso, J. S. (2023). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/202164\u0022\u003EAuthor Correction: Computer-aided diagnosis through medical image retrieval in radiology\u003C\/a\u003E. \u003Ci\u003EScientific Reports\u003C\/i\u003E, \u003Ci\u003E13\u003C\/i\u003E(1), 1470.","year":2023,"type":"Journal Article (Further Contribution)"},{"title":"Pati, S., Baid, U., Edwards, B., Sheller, M., Wang, S.-H., Reina, G. A., Foley, P., Gruzdev, A., Karkada, D., Davatzikos, C., Sako, C., Ghodasara, S., Bilello, M., Mohan, S., Vollmuth, P., Brugnara, G., Preetha, C. J., Sahm, F., Maier-Hein, K., \u2026 Bakas, S. (2023). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/120975\u0022\u003EAuthor Correction: Federated learning enables big data for rare cancer boundary detection\u003C\/a\u003E. \u003Ci\u003ENature Communications\u003C\/i\u003E, \u003Ci\u003E14\u003C\/i\u003E(1), 436.","year":2023,"type":"Journal Article (Further Contribution)"},{"title":"Krcek, R., Poel, R., Hemmatazad, H., Reyes, M., \u0026 Ermis, E. (2023, January 17). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/168687\u0022\u003EVariations in contouring brain target volumes and Organs at Risk on 3 T vs. 7 T MRI: An intra-rater\/inter-rater analysis study\u003C\/a\u003E. In \u003Ci\u003EStrahlentherapie und Onkologie\u003C\/i\u003E (p. 215). 26th Annual SASRO Meeting 2022, Trafohalle - CH-5400 Baden. Springer.","year":2023,"type":"Conference Paper (Abstract)"},{"title":"You, S., Tomar, D., Bozorgtabar, B., \u0026 Reyes, M. (2023). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/171606\u0022\u003ESagtta: saliency guided test time augmentation for medical image segmentation across vendor domain shift\u003C\/a\u003E\u003C\/i\u003E. 1-4.","year":2023,"type":"Conference Paper (Paper)"},{"title":"Poel, R., Kamath, A. J., Willmann, J., Andratschke, N., Ermis, E., Aebersold, D. M., Manser, P., \u0026 Reyes, M. (2023). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/169838\u0022\u003EDeep-Learning-Based Dose Predictor for Glioblastoma\u2013Assessing the Sensitivity and Robustness for Dose Awareness in Contouring\u003C\/a\u003E. \u003Ci\u003ECancers\u003C\/i\u003E, \u003Ci\u003E15\u003C\/i\u003E(17).","year":2023,"type":"Journal Article (Original Article)"},{"title":"Suter, Y. R., Notter, M., Meier, R., Loosli, T., Schucht, P., Wiest, R. G. R., Reyes, M., \u0026 Knecht, U. (2023). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/170193\u0022\u003EEvaluating automated longitudinal tumor measurements for glioblastoma response assessment\u003C\/a\u003E. \u003Ci\u003EFrontiers in Radiology\u003C\/i\u003E, \u003Ci\u003E3\u003C\/i\u003E(1211859), 1211859.","year":2023,"type":"Journal Article (Original Article)"},{"title":"Kamath, A. J., Poel, R., Willmann, J., Andratschke, N., \u0026 Reyes, M. (2023). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/202415\u0022\u003EHow Sensitive Are Deep Learning Based Radiotherapy Dose Prediction Models To Variability In Organs At Risk Segmentation\u003C\/a\u003E?\u003C\/i\u003E 1-4.","year":2023,"type":"Conference Paper (Paper)"},{"title":"Kamath, A. J., Poel, R., Willmann, J., Ermis, E., Andratschke, N., \u0026 Reyes, M. (2023). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/172985\u0022\u003EASTRA: Atomic Surface Transformations for Radiotherapy Quality Assurance\u003C\/a\u003E\u003C\/i\u003E (pp. 1-4). 2023 45th Annual International Conference of the IEEE Engineering in Medicine \u0026 Biology Society (EMBC), Sydney, Australia. IEEE.","year":2023,"type":"Conference Paper (Abstract)"},{"title":"R\u00fcfenacht, E., Poel, R., Kamath, A. J., Ermis, E., Scheib, S., Fix, M., \u0026 Reyes, M. (2023). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/202438\u0022\u003EDose Guidance for Radiotherapy-Oriented Deep Learning Segmentation\u003C\/a\u003E. \u003Ci\u003ELecture Notes in Computer Science\u003C\/i\u003E, \u003Ci\u003E14228\u003C\/i\u003E, 525-534.","year":2023,"type":"Conference Paper (Paper)"},{"title":"Reyes, M. (2023). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/171607\u0022\u003EMedShapeNet--A Large-Scale Dataset of 3D Medical Shapes for Computer Vision\u003C\/a\u003E\u003C\/i\u003E. Cornell University.","year":2023,"type":"Working Paper"},{"title":"Abayazeed, A. H., Abbassy, A., M\u00fcller, M., Hill, M., Qayati, M., Mohamed, S., Mekhaimar, M., Raymond, C., Dubey, P., Nael, K., Rohatgi, S., Kapare, V., Kulkarni, A., Shiang, T., Kumar, A., Andratschke, N., Willmann, J., Brawanski, A., De Jesus, R., \u2026 Reyes, M. (2023). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/120864\u0022\u003ENS-HGlio: A generalizable and repeatable HGG segmentation and volumetric measurement AI algorithm for the longitudinal MRI assessment to inform RANO in trials and clinics\u003C\/a\u003E. \u003Ci\u003ENeuro-Oncology Advances\u003C\/i\u003E, \u003Ci\u003E5\u003C\/i\u003E(1), vdac184.","year":2023,"type":"Journal Article (Original Article)"},{"title":"Suter, Y. R., Knecht, U., Valenzuela, W. E., Notter, M., Hewer, E., Schucht, P., Wiest, R. G. R., \u0026 Reyes, M. (2022). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/116216\u0022\u003EThe LUMIERE dataset: Longitudinal Glioblastoma MRI with expert RANO evaluation\u003C\/a\u003E. \u003Ci\u003EScientific Data\u003C\/i\u003E, \u003Ci\u003E9\u003C\/i\u003E(1), 768.","year":2022,"type":"Journal Article (Original Article)"},{"title":"Hernandez Petzsche, M. R., de la Rosa, E., Hanning, U., Wiest, R. G. R., Valenzuela, W. E., Reyes Aguirre, M. A., Meyer, M., Liew, S.-L., Kofler, F., Ezhov, I., Robben, D., Hutton, A., Friedrich, T., Zarth, T., B\u00fcrkle, J., Baran, T. A., Menze, B., Broocks, G., Meyer, L., \u2026 Kirschke, J. S. (2022). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/116041\u0022\u003EISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset\u003C\/a\u003E. \u003Ci\u003EScientific Data\u003C\/i\u003E, \u003Ci\u003E9\u003C\/i\u003E(1), 762.","year":2022,"type":"Journal Article (Original Article)"},{"title":"Pati, S., Baid, U., Edwards, B., Sheller, M., Wang, S.-H., Reina, G. A., Foley, P., Gruzdev, A., Karkada, D., Davatzikos, C., Sako, C., Ghodasara, S., Bilello, M., Mohan, S., Vollmuth, P., Brugnara, G., Preetha, C. J., Sahm, F., Maier-Hein, K., \u2026 Bakas, S. (2022). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/115892\u0022\u003EFederated learning enables big data for rare cancer boundary detection\u003C\/a\u003E. \u003Ci\u003ENature Communications\u003C\/i\u003E, \u003Ci\u003E13\u003C\/i\u003E(1), 7346.","year":2022,"type":"Journal Article (Original Article)"},{"title":"Silva, W., Gon\u00e7alves, T., H\u00e4rm\u00e4, K. H., Schr\u00f6der, E. A., Obmann, V. C., Barroso, M. C., P\u00f6llinger, A., Reyes Aguirre, M. A., \u0026 Cardoso, J. S. (2022). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/115812\u0022\u003EComputer-aided diagnosis through medical image retrieval in radiology\u003C\/a\u003E. \u003Ci\u003EScientific Reports\u003C\/i\u003E, \u003Ci\u003E12\u003C\/i\u003E(1), 20732.","year":2022,"type":"Journal Article (Original Article)"},{"title":"You, S., \u0026 Reyes, M. (2022). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/169164\u0022\u003EInfluence of contrast and texture based image modifications on the performance and attention shift of U-Net models for brain tissue segmentation\u003C\/a\u003E. \u003Ci\u003EFrontiers in Neuroimaging\u003C\/i\u003E, \u003Ci\u003E1\u003C\/i\u003E(1012639), 1012639.","year":2022,"type":"Journal Article (Original Article)"},{"title":"Poel, R., R\u00fcfenacht, E., Ermis, E., M\u00fcller, M., Fix, M., Aebersold, D. M., Manser, P., \u0026 Reyes Aguirre, M. A. (2022). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/88292\u0022\u003EImpact of random outliers in auto-segmented targets on radiotherapy treatment plans for glioblastoma\u003C\/a\u003E. \u003Ci\u003ERadiation Oncology\u003C\/i\u003E, \u003Ci\u003E17\u003C\/i\u003E(1), 170.","year":2022,"type":"Journal Article (Original Article)"},{"title":"Mahapatra, D., P\u00f6llinger, A., \u0026 Reyes, M. (2022). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/86499\u0022\u003EInterpretability-Guided Inductive Bias For Deep Learning Based Medical Image\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E81\u003C\/i\u003E, 102551.","year":2022,"type":"Journal Article (Original Article)"},{"title":"Liew, S.-L., Lo, B. P., Donnelly, M. R., Zavaliangos-Petropulu, A., Jeong, J. N., Barisano, G., Hutton, A., Simon, J. P., Juliano, J. M., Suri, A., Wang, Z., Abdullah, A., Kim, J., Ard, T., Banaj, N., Borich, M. R., Boyd, L. A., Brodtmann, A., Buetefisch, C. M., \u2026 Yu, C. (2022). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/85707\u0022\u003EA large, curated, open-source stroke neuroimaging dataset to improve lesion segmentation algorithms\u003C\/a\u003E. \u003Ci\u003EScientific Data\u003C\/i\u003E, \u003Ci\u003E9\u003C\/i\u003E(1), 320.","year":2022,"type":"Journal Article (Original Article)"},{"title":"Kang, M., Hu, X., Huang, W., Scott, M. R., \u0026 Reyes, M. (2022). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/116853\u0022\u003EDual-stream pyramid registration network\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E78\u003C\/i\u003E, 102379.","year":2022,"type":"Journal Article (Original Article)"},{"title":"Rebsamen, M. A., Radojewski, P., McKinley, R. I., Reyes Aguirre, M. A., Wiest, R. G. R., \u0026 Rummel, C. (2022). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/68304\u0022\u003EA Quantitative Imaging Biomarker Supporting Radiological Assessment of Hippocampal Sclerosis Derived From Deep Learning-Based Segmentation of T1w-MRI\u003C\/a\u003E. \u003Ci\u003EFrontiers in Neurology\u003C\/i\u003E, \u003Ci\u003E13\u003C\/i\u003E, 812432.","year":2022,"type":"Journal Article (Original Article)"},{"title":"Rizzo, R., Dziadosz, M., Kyathanahally, S. P., Reyes Aguirre, M. A., \u0026 Kreis, R. (2022). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/202147\u0022\u003EReliability of Quantification Estimates in MR Spectroscopy: CNNs vs Traditional Model Fitting\u003C\/a\u003E. \u003Ci\u003ELecture Notes in Computer Science\u003C\/i\u003E, \u003Ci\u003E13438\u003C\/i\u003E, 715-724.","year":2022,"type":"Journal Article (Original Article)"},{"title":"Mahapatra, D., P\u00f6llinger, A., Shao, L., \u0026 Reyes Aguirre, M. A. (2021). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/41190\u0022\u003EInterpretability-Driven Sample Selection Using Self Supervised Learning For Disease Classification And Segmentation\u003C\/a\u003E. \u003Ci\u003EIEEE Transactions on Medical Imaging\u003C\/i\u003E, \u003Ci\u003E40\u003C\/i\u003E(10), 2548-2562.","year":2021,"type":"Journal Article (Original Article)"},{"title":"Poel, R., R\u00fcfenacht, E., Herrmann, E., Scheib, S., Manser, P., Aebersold, D. M., \u0026 Reyes Aguirre, M. A. (2021). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/57124\u0022\u003EThe predictive value of segmentation metrics on dosimetry in organs at risk of the brain\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E73\u003C\/i\u003E, 102161.","year":2021,"type":"Journal Article (Original Article)"},{"title":"Hakim, A., Christensen, S., Winzeck, S., Lansberg, M. G., Parsons, M. W., Lucas, C., Robben, D., Wiest, R. G. R., Reyes Aguirre, M. A., \u0026 Zaharchuk, G. (2021). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/42562\u0022\u003EPredicting Infarct Core From Computed Tomography Perfusion in Acute Ischemia With Machine Learning: Lessons From the ISLES Challenge\u003C\/a\u003E. \u003Ci\u003EStroke\u003C\/i\u003E, \u003Ci\u003E52\u003C\/i\u003E(7), 2328-2337.","year":2021,"type":"Journal Article (Original Article)"},{"title":"Pinto, A., Pereira, S., Meier, R., Wiest, R. G. R., Alves, V., Reyes Aguirre, M. A., \u0026 Silva, C. A. (2021). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/39788\u0022\u003ECombining unsupervised and supervised learning for predicting the final stroke lesion\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E69\u003C\/i\u003E(101888), 101888.","year":2021,"type":"Journal Article (Original Article)"},{"title":"Menze, B., Isensee, F., Wiest, R. G. R., Wiestler, B., Maier-Hein, K., Reyes Aguirre, M. A., \u0026 Bakas, S. (2021). [Review of \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/45328\u0022\u003EAnalyzing Magnetic Resonance Imaging Data from Glioma Patients using Deep Learning\u003C\/a\u003E\u003C\/i\u003E]. \u003Ci\u003EComputerized Medical Imaging and Graphics\u003C\/i\u003E, \u003Ci\u003E88\u003C\/i\u003E, 101828.","year":2021,"type":"Journal Article (Review)"},{"title":"McKinley, R. I., Wepfer, R., Aschwanden, F., Grunder, L. N., Muri, R., Rummel, C., Verma, R., Weisstanner, C., Reyes Aguirre, M. A., Salmen, A., Chan, A. H.-K., Wagner, F., \u0026 Wiest, R. G. R. (2021). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/39789\u0022\u003ESimultaneous lesion and brain segmentation in multiple sclerosis using deep neural networks\u003C\/a\u003E. \u003Ci\u003EScientific Reports\u003C\/i\u003E, \u003Ci\u003E11\u003C\/i\u003E(1), 1087.","year":2021,"type":"Journal Article (Original Article)"},{"title":"Jungo, A., Scheidegger, O., Reyes Aguirre, M. A., \u0026 Balsiger, F. (2021). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/55503\u0022\u003Epymia: A Python package for data handling and evaluation in deep learning-based medical image analysis\u003C\/a\u003E. \u003Ci\u003EComputer Methods and Programs in Biomedicine\u003C\/i\u003E, \u003Ci\u003E198\u003C\/i\u003E, 105796.","year":2021,"type":"Journal Article (Original Article)"},{"title":"Suter, Y. R., Knecht, U., Wiest, R. G. R., \u0026 Reyes Aguirre, M. A. (2021). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/85517\u0022\u003EOverall Survival Prediction for Glioblastoma on Pre-treatment MRI Using Robust Radiomics and Priors\u003C\/a\u003E. \u003Ci\u003ELecture Notes in Computer Science\u003C\/i\u003E, \u003Ci\u003E12658\u003C\/i\u003E, 307-317.","year":2021,"type":"Journal Article (Original Article)"},{"title":"Rebsamen, M. A., Rummel, C., Reyes Aguirre, M. A., Wiest, R. G. R., \u0026 McKinley, R. I. (2020). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/55262\u0022\u003EDirect cortical thickness estimation using deep learning-based anatomy segmentation and cortex parcellation\u003C\/a\u003E. \u003Ci\u003EHuman Brain Mapping\u003C\/i\u003E, \u003Ci\u003E41\u003C\/i\u003E(17), 4804-4814.","year":2020,"type":"Journal Article (Original Article)"},{"title":"Balsiger, F., Jungo, A., Scheidegger, O., Marty, B., \u0026 Reyes Aguirre, M. A. (2020). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/55502\u0022\u003ELearning Bloch Simulations for MR Fingerprinting by Invertible Neural Networks\u003C\/a\u003E. In F. Deeba, P. Johnson, T. W\u00fcrfl, \u0026 J. C. Ye (Eds.), \u003Ci\u003EMachine Learning for Medical Image Reconstruction\u003C\/i\u003E (Vols. 12450, pp. 60-69). Springer.","year":2020,"type":"Book Section"},{"title":"Suter, Y. R., Knecht, U., Alao, M., Valenzuela, W. E., Hewer, E. W., Schucht, P., Wiest, R. G. R., \u0026 Reyes Aguirre, M. A. (2020). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/55210\u0022\u003ERadiomics for glioblastoma survival analysis in pre-operative MRI: exploring feature robustness, class boundaries, and machine learning techniques\u003C\/a\u003E. \u003Ci\u003ECancer Imaging : The Official Publication of the International Cancer Imaging Society\u003C\/i\u003E, \u003Ci\u003E20\u003C\/i\u003E(55), 1-13.","year":2020,"type":"Journal Article (Original Article)"},{"title":"Balsiger, F., Jungo, A., Scheidegger, O., Carlier, P. G., Reyes Aguirre, M. A., \u0026 Marty, B. (2020). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/55488\u0022\u003ESpatially regularized parametric map reconstruction for fast magnetic resonance fingerprinting\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E64\u003C\/i\u003E(101741), 101741.","year":2020,"type":"Journal Article (Original Article)"},{"title":"Reyes Aguirre, M. A., Meier, R., Pereira, S., Silva, C. A., Dahlweid, F.-M., von Tengg-Kobligk, H., Summers, R. M., \u0026 Wiest, R. G. R. (2020). [Review of \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/36165\u0022\u003EOn the Interpretability of Artificial Intelligence in Radiology: Challenges and Opportunities.\u003C\/a\u003E\u003C\/i\u003E]. \u003Ci\u003ERadiology: Artificial Intelligence\u003C\/i\u003E, \u003Ci\u003E2\u003C\/i\u003E(3), e190043.","year":2020,"type":"Journal Article (Review)"},{"title":"Ermis, E., Jungo, A., Poel, R., Blatti, M. J., Meier, R., Knecht, U., Aebersold, D. M., Fix, M., Manser, P., Reyes Aguirre, M. A., \u0026 Herrmann, E. (2020). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/54862\u0022\u003EFully automated brain resection cavity delineation for radiation target volume definition in glioblastoma patients using deep learning\u003C\/a\u003E. \u003Ci\u003ERadiation Oncology\u003C\/i\u003E, \u003Ci\u003E15\u003C\/i\u003E(1), 100.","year":2020,"type":"Journal Article (Original Article)"},{"title":"Jungo, A., Balsiger, F., \u0026 Reyes Aguirre, M. A. (2020). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/55510\u0022\u003EAnalyzing the Quality and Challenges of Uncertainty Estimations for Brain Tumor Segmentation\u003C\/a\u003E. \u003Ci\u003EFrontiers in Neuroscience\u003C\/i\u003E, \u003Ci\u003E14\u003C\/i\u003E(282), 282.","year":2020,"type":"Journal Article (Original Article)"},{"title":"Rebsamen, M. A., Suter, Y. R., Wiest, R. G. R., Reyes Aguirre, M. A., \u0026 Rummel, C. (2020). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/54842\u0022\u003EBrain Morphometry Estimation: From Hours to Seconds Using Deep Learning\u003C\/a\u003E. \u003Ci\u003EFrontiers in Neurology\u003C\/i\u003E, \u003Ci\u003E11\u003C\/i\u003E(244), 244.","year":2020,"type":"Journal Article (Original Article)"},{"title":"Hu, X., Luo, W., Hu, J., Guo, S., Huang, W., Scott, M. R., Wiest, R. G. R., Dahlweid, M., \u0026 Reyes Aguirre, M. A. (2020). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/44837\u0022\u003EBrain SegNet: 3D local refinement network for brain lesion segmentation\u003C\/a\u003E. \u003Ci\u003EBMC Medical Imaging\u003C\/i\u003E, \u003Ci\u003E20\u003C\/i\u003E(1), 17.","year":2020,"type":"Journal Article (Original Article)"},{"title":"McKinley, R. I., Wepfer, R., Aschwanden, F., Grunder, L. N., Muri, R., Rummel, C., Verma, R. K., Weisstanner, C., Reyes Aguirre, M. A., Salmen, A., Chan, A. H.-K., Wagner, F., \u0026 Wiest, R. G. R. (2020). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/55048\u0022\u003ERobustness of Simultaneous Lesion and Neuroanatomy Segmentation in Multiple Sclerosis Using Deep Neural Networks\u003C\/a\u003E. \u003Ci\u003ESSRN Electronic Journal\u003C\/i\u003E.","year":2020,"type":"Journal Article (Original Article)"},{"title":"Jin, B. Z., De Stefano, P., Petroulia, V. D., Rummel, C., Kiefer, C., Reyes Aguirre, M. A., Schindler, K., van Mierlo, P., Seeck, M., \u0026 Wiest, R. G. R. (2020). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/37783\u0022\u003EDiagnosis of epilepsy after first seizure. Introducing the SWISS FIRST study\u003C\/a\u003E. \u003Ci\u003EClinical and Translational Neuroscience\u003C\/i\u003E, \u003Ci\u003E4\u003C\/i\u003E(2), 2514183X2093944.","year":2020,"type":"Journal Article (Original Article)"},{"title":"Silva, W., P\u00f6llinger, A., Cardoso, J. S., \u0026 Reyes Aguirre, M. A. (2020). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/45330\u0022\u003EInterpretability-Guided Content-Based Medical Image Retrieval\u003C\/a\u003E. \u003Ci\u003ELecture Notes in Computer Science\u003C\/i\u003E, \u003Ci\u003E12261\u003C\/i\u003E, 305-314.","year":2020,"type":"Conference Paper (Paper)"},{"title":"McKinley, R. I., Wepfer, R., Grunder, L. N., Aschwanden, F., Fischer, T., Friedli, C. D., Muri, R., Rummel, C., Verma, R. K., Weisstanner, C., Wiestler, B., Berger, C., Eichinger, P., Muehlau, M., Reyes Aguirre, M. A., Salmen, A., Chan, A. H.-K., Wiest, R. G. R., \u0026 Wagner, F. (2020). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/185088\u0022\u003EAutomatic detection of lesion load change in Multiple Sclerosis using convolutional neural networks with segmentation confidence\u003C\/a\u003E. \u003Ci\u003ENeuroImage: Clinical\u003C\/i\u003E, \u003Ci\u003E25\u003C\/i\u003E, 102104.","year":2020,"type":"Journal Article (Original Article)"},{"title":"R\u00fcfenacht, E., Jungo, A., Ermis, E., Hemmatazad, H., Blatti, M. J., Aebersold, D. M., Manser, P., Fix, M., Reyes Aguirre, M. A., \u0026 Herrmann, E. (2019, December). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/183964\u0022\u003EFully automated organs at risk delineation for brain tumor radiation planning in patients with glioblastoma using deep learning\u003C\/a\u003E. In \u003Ci\u003EStrahlentherapie und Onkologie\u003C\/i\u003E (Vols. 195, Issues 12, p. 1149). SASRO ANNUAL MEETING, Lausanne. Springer.","year":2019,"type":"Conference Paper (Abstract)"},{"title":"da Silva Mendes Pedrosa de Barros, N. M., Meier, R., Pletscher, M., Stettler, S., Knecht, U., Reyes Aguirre, M. A., Gralla, J., Wiest, R. G. R., \u0026 Slotboom, J. (2019). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/193388\u0022\u003EAnalysis of metabolic abnormalities in high-grade glioma using MRSI and convex NMF\u003C\/a\u003E. \u003Ci\u003ENMR in Biomedicine\u003C\/i\u003E, \u003Ci\u003E32\u003C\/i\u003E(8), e4109.","year":2019,"type":"Journal Article (Original Article)"},{"title":"Suter, Y. R., Jungo, A., Rebsamen, M., Knecht, U., Herrmann, E., Wiest, R. G. R., \u0026 Reyes Aguirre, M. A. (2019). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/184581\u0022\u003EDeep Learning Versus Classical Regression for Brain Tumor Patient Survival Prediction\u003C\/a\u003E. \u003Ci\u003ELecture Notes in Computer Science\u003C\/i\u003E, \u003Ci\u003E11384\u003C\/i\u003E, 429-440.","year":2019,"type":"Conference Paper (Paper)"},{"title":"Rebsamen, M. A., Knecht, U., Reyes Aguirre, M. A., Wiest, R. G. R., Meier, R., \u0026 McKinley, R. (2019). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/193444\u0022\u003EDivide and Conquer: Stratifying Training Data by Tumor Grade Improves Deep Learning-Based Brain Tumor Segmentation\u003C\/a\u003E. \u003Ci\u003EFrontiers in Neuroscience\u003C\/i\u003E, \u003Ci\u003E13\u003C\/i\u003E, 1182.","year":2019,"type":"Journal Article (Original Article)"},{"title":"Chandran, V., Maquer, G. B., Gerig, T., Zysset, P., \u0026 Reyes Aguirre, M. A. (2019). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/65259\u0022\u003ESupervised learning for bone shape and cortical thickness estimation from CT images for finite element analysis\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E52\u003C\/i\u003E, 42-55.","year":2019,"type":"Journal Article (Original Article)"},{"title":"Balsiger, F., Soom, Y., Scheidegger, O., \u0026 Reyes Aguirre, M. A. (2019). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/185837\u0022\u003ELearning Shape Representation on Sparse Point Clouds for Volumetric Image Segmentation\u003C\/a\u003E. In \u003Ci\u003EMedical Image Computing and Computer Assisted Intervention \u2013 MICCAI 2019\u003C\/i\u003E (Vols. 11765, pp. 273-281). Springer International Publishing.","year":2019,"type":"Book Section"},{"title":"McKinley, R. I., Grunder, L. N., Wepfer, R., Aschwanden, F., Fischer, T., Friedli, C. D., Muri, R., Rummel, C., Verma, R., Weisstanner, C., Reyes Aguirre, M. A., Salmen, A., Chan, A. H.-K., Wiest, R. G. R., \u0026 Wagner, F. (2019). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/184321\u0022\u003EAutomatic detection of lesion load change in Multiple Sclerosis using convolutional neural networks with segmentation con\ufb01dence\u003C\/a\u003E\u003C\/i\u003E. Cornell University.","year":2019,"type":"Working Paper"},{"title":"R\u00fcfenacht, E., Jungo, A., Ermis, E., Blatti, M. J., Hemmatazad, H., Aebersold, D. M., Fix, M., Manser, P., Reyes Aguirre, M. A., \u0026 Herrmann, E. (2019). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/183221\u0022\u003EOrgans at Risk Delineation for Brain Tumor Radiation Planning in Patients with Glioblastoma Using Deep Learning\u003C\/a\u003E. In \u003Ci\u003EInternational journal of radiation oncology, biology, physics\u003C\/i\u003E (Vols. 105, Issue 1, pp. E718-E719). ASTRO Annual Meeting, Chicago. Elsevier.","year":2019,"type":"Conference Paper (Abstract)"},{"title":"Meier, R., Lux, P., Jung, S., Fischer, U. M., Gralla, J., Reyes Aguirre, M. A., Wiest, R. G. R., McKinley, R. I., \u0026 Kaesmacher, J. (2019). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/182126\u0022\u003ENeural network-derived perfusion Maps for the assessment of lesions in patients with acute ischemic stroke\u003C\/a\u003E. \u003Ci\u003ERadiology: Artificial Intelligence\u003C\/i\u003E.","year":2019,"type":"Journal Article (Original Article)"},{"title":"Jungo, A., \u0026 Reyes Aguirre, M. A. (2019). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/185839\u0022\u003EAssessing Reliability and Challenges of Uncertainty Estimations for Medical Image Segmentation\u003C\/a\u003E. \u003Ci\u003ELecture Notes in Computer Science\u003C\/i\u003E, \u003Ci\u003E11765\u003C\/i\u003E, 48-56.","year":2019,"type":"Conference Paper (Paper)"},{"title":"da Silva Mendes Pedrosa de Barros, N. M., Meier, R., Pletscher, M., Stettler, S., Knecht, U., Herrmann, E., Schucht, P., Reyes Aguirre, M. A., Gralla, J., Wiest, R. G. R., \u0026 Slotboom, J. (2018). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/193202\u0022\u003EOn the relation between MR spectroscopy features and the distance to MRI-visible solid tumor in GBM patients\u003C\/a\u003E. \u003Ci\u003EMagnetic Resonance in Medicine\u003C\/i\u003E, \u003Ci\u003E80\u003C\/i\u003E(6), 2339-2355.","year":2018,"type":"Journal Article (Original Article)"},{"title":"Hlushchuk, R., Zubler, C. O., Barr\u00e9, S., Correa Shokiche, C., Schaad, L., R\u00f6thlisberger, R., Wnuk, M. L., Daniel, C., Khoma, O.-Z., Tschanz, S. A., Reyes Aguirre, M. A., \u0026 Djonov, V. G. (2018). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/156833\u0022\u003ECutting-edge microangio-CT: new dimensions in vascular imaging and kidney morphometry\u003C\/a\u003E. \u003Ci\u003EAmerican Journal of Physiology - Renal Physiology\u003C\/i\u003E, \u003Ci\u003E314\u003C\/i\u003E(3), F493-F499.","year":2018,"type":"Journal Article (Original Article)"},{"title":"Kjer, H. M., Fagertun, J., Wimmer, W., Gerber, N., Vera, S., Barazzetti, L., Mangado, N., Ceresa, M., Piella, G., Stark, T., Stauber, M., Reyes Aguirre, M. A., Weber, S., Caversaccio, M., Gonz\u00e1lez Ballester, M. \u00c1., \u0026 Paulsen, R. R. (2018). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/156893\u0022\u003EPatient-specific estimation of detailed cochlear shape from clinical CT images\u003C\/a\u003E. \u003Ci\u003EInternational Journal of Computer Assisted Radiology and Surgery\u003C\/i\u003E, \u003Ci\u003E13\u003C\/i\u003E(3), 389-396.","year":2018,"type":"Journal Article (Original Article)"},{"title":"Pereira, S., Meier, R., McKinley, R., Wiest, R. G. R., Alves, V., Silva, C. A., \u0026 Reyes Aguirre, M. A. (2018). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/193082\u0022\u003EEnhancing interpretability of automatically extracted machine learning features: application to a RBM-Random Forest system on brain lesion segmentation\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E44\u003C\/i\u003E, 228-244.","year":2018,"type":"Journal Article (Original Article)"},{"title":"Jungo, A., McKinley, R. I., Meier, R., Knecht, U., Vera, L., P\u00e9rez-Beteta, J., Molina-Garc\u00eda, D., P\u00e9rez-Garc\u00eda, V. M., Wiest, R. G. R., \u0026 Reyes Aguirre, M. A. (2018). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/180457\u0022\u003ETowards uncertainty-assisted brain tumor segmentation and survival prediction\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E10670\u003C\/i\u003E, 474-485.","year":2018,"type":"Conference Paper (Paper)"},{"title":"Balsiger, F., Shridhar Konar, A., Chikop, S., Chandran, V., Scheidegger, O., Geethanath, S., \u0026 Reyes Aguirre, M. A. (2018). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/60226\u0022\u003EMagnetic Resonance Fingerprinting Reconstruction via Spatiotemporal Convolutional Neural Networks\u003C\/a\u003E. In \u003Ci\u003EMachine Learning for Medical Image Reconstruction\u003C\/i\u003E (Vols. 11074, pp. 39-46). Springer International Publishing.","year":2018,"type":"Book Section"},{"title":"Pinto, A., McKinley, R., Alves, V., Wiest, R. G. R., Silva, C. A., \u0026 Reyes Aguirre, M. A. (2018). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/193279\u0022\u003EStroke Lesion Outcome Prediction Based on MRI Imaging Combined With Clinical Information\u003C\/a\u003E. \u003Ci\u003EFrontiers in Neurology\u003C\/i\u003E, \u003Ci\u003E9\u003C\/i\u003E(1060), 1060.","year":2018,"type":"Journal Article (Original Article)"},{"title":"Pinto, A., Pereira, S., Meier, R., Alves, V., Wiest, R. G. R., Silva, C. A., \u0026 Reyes Aguirre, M. A. (2018). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/181471\u0022\u003EEnhancing Clinical MRI Perfusion Maps with Data-Driven Maps of Complementary Nature for Lesion Outcome Prediction\u003C\/a\u003E\u003C\/i\u003E (A. F. Frangi, J. A. Schnabel, C. Davatzikos, C. Alberola-L\u00f3pez, \u0026 G. Fichtinger, Eds.; Vols. 11072, pp. 107-115). Springer International Publishing.","year":2018,"type":"Conference Paper (Paper)"},{"title":"Habegger, S., Wiest, R. G. R., Weder, B., Mordasini, P. R., Gralla, J., H\u00e4ni, L., Jung, S., Reyes Aguirre, M. A., \u0026 McKinley, R. (2018). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/193239\u0022\u003ERelating Acute Lesion Loads to Chronic Outcome in Ischemic Stroke-An Exploratory Comparison of Mismatch Patterns and Predictive Modeling\u003C\/a\u003E. \u003Ci\u003EFrontiers in Neurology\u003C\/i\u003E, \u003Ci\u003E9\u003C\/i\u003E(737), 737.","year":2018,"type":"Journal Article (Original Article)"},{"title":"Lu, P., Barazzetti, L., Chandran, V., Gerber, K., Weber, S., Gerber, N., \u0026 Reyes Aguirre, M. A. (2018). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/155057\u0022\u003EHighly accurate Facial Nerve Segmentation Refinement from CBCT\/CT Imaging using a Super Resolution Classification Approach\u003C\/a\u003E. \u003Ci\u003EIEEE Transactions on Biomedical Engineering\u003C\/i\u003E, \u003Ci\u003E65\u003C\/i\u003E(1), 178-188.","year":2018,"type":"Journal Article (Original Article)"},{"title":"Pereira, S., Meier, R., Alves, V., Reyes Aguirre, M. A., \u0026 Silva, C. A. (2018). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/181472\u0022\u003EAutomatic Brain Tumor Grading from MRI Data Using Convolutional Neural Networks and Quality Assessment\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E11038\u003C\/i\u003E, 106-114.","year":2018,"type":"Conference Paper (Paper)"},{"title":"Herrmann, E., Ermis, E., Meier, R., Blatti, M. J., Knecht, U., Aebersold, D. M., Manser, P., \u0026 Reyes Aguirre, M. A. (2018). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/62462\u0022\u003EFully Automated Segmentation of the Brain Resection Cavity for Radiation Target Volume Definition in Glioblastoma Patients\u003C\/a\u003E. In \u003Ci\u003EInternational journal of radiation oncology, biology, physics\u003C\/i\u003E (Vols. 102, Issues 3, p. S194). ASTRO Annual Meeting. Elsevier.","year":2018,"type":"Conference Paper (Abstract)"},{"title":"Balsiger, F., Steindel, C., Arn, M., Wagner, B., Grunder, L. N., El-Koussy, M., Valenzuela, W. E., Reyes Aguirre, M. A., \u0026 Scheidegger, O. (2018). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/60010\u0022\u003ESegmentation of Peripheral Nerves From Magnetic Resonance Neurography: A Fully-Automatic, Deep Learning-Based Approach\u003C\/a\u003E. \u003Ci\u003EFrontiers in Neurology\u003C\/i\u003E, \u003Ci\u003E9\u003C\/i\u003E(777), 777.","year":2018,"type":"Journal Article (Original Article)"},{"title":"Winzeck, S., Hakim, A., McKinley, R., Pinto, J. A. A. D. S. R., Alves, V., Silva, C., Pisov, M., Krivov, E., Belyaev, M., Monteiro, M., Oliveira, A., Choi, Y., Paik, M. C., Kwon, Y., Lee, H., Kim, B. J., Won, J.-H., Islam, M., Ren, H., \u2026 Reyes Aguirre, M. A. (2018). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/193240\u0022\u003EISLES 2016 and 2017-Benchmarking Ischemic Stroke Lesion Outcome Prediction Based on Multispectral MRI\u003C\/a\u003E. \u003Ci\u003EFrontiers in Neurology\u003C\/i\u003E, \u003Ci\u003E9\u003C\/i\u003E(679), 679.","year":2018,"type":"Journal Article (Original Article)"},{"title":"Jungo, A., Meier, R., Ermis, E., Herrmann, E., \u0026 Reyes Aguirre, M. A. (2018). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/180456\u0022\u003EUncertainty-driven Sanity Check: Application to Postoperative Brain Tumor Cavity Segmentation\u003C\/a\u003E\u003C\/i\u003E. International Conference on Medical Imaging with Deep Learning.","year":2018,"type":"Conference Paper (Paper)"},{"title":"Suter, Y. R., Rummel, C., Wiest, R. G. R., \u0026 Reyes Aguirre, M. A. (2018). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/63556\u0022\u003EFast and uncertainty-aware cerebral cortex morphometry estimation using random forest regression\u003C\/a\u003E\u003C\/i\u003E. 1052-1055.","year":2018,"type":"Conference Paper (Paper)"},{"title":"Jungo, A., Meier, R., Ermis, E., Blatti, M. J., Herrmann, E., Wiest, R. G. R., \u0026 Reyes Aguirre, M. A. (2018). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/180458\u0022\u003EOn the Effect of Inter-observer Variability for a Reliable Estimation of Uncertainty of Medical Image Segmentation\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E11070\u003C\/i\u003E, 682-690.","year":2018,"type":"Conference Paper (Paper)"},{"title":"Mahapatra, D., Bozorgtabar, B., Thiran, J.-P., \u0026 Reyes Aguirre, M. A. (2018). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/181470\u0022\u003EEfficient Active Learning for Image Classification and Segmentation Using a Sample Selection and Conditional Generative Adversarial Network\u003C\/a\u003E\u003C\/i\u003E (A. F. Frangi, J. A. Schnabel, C. Davatzikos, C. Alberola-L\u00f3pez, \u0026 G. Fichtinger, Eds.; Vols. 11071, pp. 580-588). Springer International Publishing.","year":2018,"type":"Conference Paper (Paper)"},{"title":"Kellner-Weldon, F., Stippich, C., Wiest, R. G. R., Lehmann, V., Meier, R., Beck, J., Schucht, P., Raabe, A., Reyes Aguirre, M. A., \u0026 Bink, A. (2017). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/190334\u0022\u003EComparison of perioperative automated versus manual two-dimensional tumor analysis in glioblastoma patients\u003C\/a\u003E. \u003Ci\u003EEuropean Journal of Radiology\u003C\/i\u003E, \u003Ci\u003E95\u003C\/i\u003E, 75-81.","year":2017,"type":"Journal Article (Original Article)"},{"title":"Taghizadeh, E., Chandran, V., Reyes Aguirre, M. A., Zysset, P., \u0026 B\u00fcchler, P. (2017). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/199207\u0022\u003EStatistical analysis of the inter-individual variations of the bone shape, volume fraction and fabric and their correlations in the proximal femur\u003C\/a\u003E. \u003Ci\u003EBone\u003C\/i\u003E, \u003Ci\u003E103\u003C\/i\u003E, 252-261.","year":2017,"type":"Journal Article (Original Article)"},{"title":"Meier, R., Porz, N., Knecht, U., Schucht, P., Beck, J., Slotboom, J., Wiest, R. G. R., \u0026 Reyes Aguirre, M. A. (2017). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/147921\u0022\u003EAutomatic estimation of extent of resection and residual tumor volume of patients with glioblastoma\u003C\/a\u003E. \u003Ci\u003EJournal of Neurosurgery\u003C\/i\u003E, \u003Ci\u003E127\u003C\/i\u003E(4), 798-806.","year":2017,"type":"Journal Article (Original Article)"},{"title":"Chandran, V., Reyes Aguirre, M. A., \u0026 Zysset, P. (2017). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/158721\u0022\u003EA novel registration-based methodology for prediction of trabecular bone fabric from clinical QCT: A comprehensive analysis\u003C\/a\u003E. \u003Ci\u003EPLoS ONE\u003C\/i\u003E, \u003Ci\u003E12\u003C\/i\u003E(11), e0187874.","year":2017,"type":"Journal Article (Original Article)"},{"title":"Gerber, N., Reyes Aguirre, M. A., Barazzetti, L., Kjer, H. M., Vera, S., Stauber, M., Mistrik, P., Ceresa, M., Mangado, N., Wimmer, W., Stark, T., Paulsen, R. R., Weber, S., Caversaccio, M., \u0026 Ballester, M. A. G. (2017). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/154580\u0022\u003EA multiscale imaging and modelling dataset of the human inner ear\u003C\/a\u003E. \u003Ci\u003EScientific Data\u003C\/i\u003E, \u003Ci\u003E4\u003C\/i\u003E(170132), 170132.","year":2017,"type":"Journal Article (Original Article)"},{"title":"Porz, N., Habegger, S., Meier, R., Verma, R. K., Jilch, A., Fichtner, J., Knecht, U., Radina, C., Schucht, P., Beck, J., Raabe, A., Slotboom, J., Reyes Aguirre, M. A., \u0026 Wiest, R. G. R. (2016). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/147275\u0022\u003EFully Automated Enhanced Tumor Compartmentalization: Man vs. Machine Reloaded\u003C\/a\u003E. \u003Ci\u003EPLoS ONE\u003C\/i\u003E, \u003Ci\u003E11\u003C\/i\u003E(11), e0165302.","year":2016,"type":"Journal Article (Original Article)"},{"title":"Correa Shokiche, C., Baumann, P., Hlushchuk, R., Djonov, V. G., \u0026 Reyes Aguirre, M. A. (2016). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/151263\u0022\u003EHigh-Throughput Glomeruli Analysis of micro-CT Kidney Images Using Tree Priors and Scalable Sparse Computation\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E9901\u003C\/i\u003E, 370-378.","year":2016,"type":"Conference Paper (Paper)"},{"title":"Maier, O., Menze, B. H., von der Gablentz, J., H\u00e4ni, L., Heinrich, M. P., Liebrand, M., Winzeck, S., Basit, A., Bentley, P., Chen, L., Christiaens, D., Dutil, F., Egger, K., Feng, C., Glocker, B., G\u00f6tz, M., Haeck, T., Halme, H.-L., Havaei, M., \u2026 Reyes Aguirre, M. A. (2016). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/192730\u0022\u003EISLES 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral MRI\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E35\u003C\/i\u003E, 250-269.","year":2016,"type":"Journal Article (Original Article)"},{"title":"Taghizadeh, E., \u0026 Reyes Aguirre, M. A. (2016). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/198916\u0022\u003EStatistical Shape Model of the Leg to Improve the Treatment of Patella Pathology in Total Knee Arthroplasty\u003C\/a\u003E\u003C\/i\u003E. BORIS Portal.","year":2016,"type":"Thesis"},{"title":"Seif, M., Mani, L.-Y., Lu, H., Boesch, C. H., Reyes Aguirre, M. A., Vogt, B., \u0026 Vermathen, P. (2016). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/140675\u0022\u003EDiffusion tensor imaging of the human kidney: Does image registration permit scanning without respiratory triggering\u003C\/a\u003E? \u003Ci\u003EJournal of Magnetic Resonance Imaging\u003C\/i\u003E, \u003Ci\u003E44\u003C\/i\u003E(2), na.","year":2016,"type":"Journal Article (Original Article)"},{"title":"Taghizadeh, E., Reyes Aguirre, M. A., Zysset, P., Latypova, A., Terrier, A., \u0026 B\u00fcchler, P. (2016). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/198215\u0022\u003EBiomechanical Role of Bone Anisotropy Estimated on Clinical CT Scans by Image Registration\u003C\/a\u003E. \u003Ci\u003EAnnals of Biomedical Engineering\u003C\/i\u003E, \u003Ci\u003E44\u003C\/i\u003E(8), 2505-2517.","year":2016,"type":"Journal Article (Original Article)"},{"title":"Valenzuela, W. E., Ferguson, S. J., Ignasiak, D., Diserens, G., H\u00e4ni, L., Wiest, R. G. R., Vermathen, P., Boesch, C. H., \u0026 Reyes Aguirre, M. A. (2016). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/142629\u0022\u003EFISICO: Fast Image SegmentatIon COrrection\u003C\/a\u003E. \u003Ci\u003EPLoS ONE\u003C\/i\u003E, \u003Ci\u003E11\u003C\/i\u003E(5), e0156035.","year":2016,"type":"Journal Article (Original Article)"},{"title":"Meier, R., Knecht, U., Loosli, T., Bauer, S., Slotboom, J., Wiest, R. G. R., \u0026 Reyes Aguirre, M. A. (2016). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/141431\u0022\u003EClinical Evaluation of a Fully-automatic Segmentation Method for Longitudinal Brain Tumor Volumetry\u003C\/a\u003E. \u003Ci\u003EScientific Reports\u003C\/i\u003E, \u003Ci\u003E6\u003C\/i\u003E(23376), 23376.","year":2016,"type":"Journal Article (Original Article)"},{"title":"McKinley, R., H\u00e4ni, L., Gralla, J., El-Koussy, M., Bauer, S., Arnold, M., Fischer, U. M., Jung, S., Mattmann, K., Reyes Aguirre, M. A., \u0026 Wiest, R. G. R. (2016). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/192804\u0022\u003EFully automated stroke tissue estimation using random forest classifiers (FASTER)\u003C\/a\u003E. \u003Ci\u003EJournal of Cerebral Blood Flow and Metabolism\u003C\/i\u003E, \u003Ci\u003E37\u003C\/i\u003E(8), 2728-2741.","year":2016,"type":"Journal Article (Original Article)"},{"title":"Taghizadeh, E., Kistler, M., B\u00fcchler, P., \u0026 Reyes Aguirre, M. A. (2016). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/198217\u0022\u003EFast Prediction of Femoral Biomechanics Using Supervised Machine Learning and Statistical Shape Modeling\u003C\/a\u003E. In G. Joldes, B. Doyle, A. Wittek, P. Nielsen, \u0026 K. Miller (Eds.), \u003Ci\u003EComputational Biomechanics for Medicine X\u003C\/i\u003E (pp. 115-127). Springer-Verlag New York.","year":2016,"type":"Book Section"},{"title":"Lu, P., Barazzetti, L., Chandran, V., Gerber, K., Weber, S., Gerber, N., \u0026 Reyes Aguirre, M. A. (2016). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/147926\u0022\u003ESuper-Resolution Classification Improves Facial Nerve Segmentation from CBCT Imaging\u003C\/a\u003E\u003C\/i\u003E (pp. 143-144). CURAC 2016 : 15. Jahrestagung der Deutschen Gesellschaft f\u00fcr Computer- und Roboterassistierte Chirurgie. BORIS Portal.","year":2016,"type":"Conference Paper (Abstract)"},{"title":"Meier, R., Karamitsou, V., Habegger, S., Wiest, R. G. R., \u0026 Reyes Aguirre, M. A. (2016). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/150811\u0022\u003EParameter Learning for CRF-Based Tissue Segmentation of Brain Tumors\u003C\/a\u003E. In \u003Ci\u003EBrainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries\u003C\/i\u003E (Vols. 9556, pp. 156-167). Springer International Publishing.","year":2016,"type":"Book Section"},{"title":"Taghizadeh, E., Reyes Aguirre, M. A., \u0026 B\u00fcchler, P. (2015, October 2). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/198415\u0022\u003EStatistical Model of Bone Mechanical Properties\u003C\/a\u003E\u003C\/i\u003E (p. 18). Shape Symposium. BORIS Portal.","year":2015,"type":"Conference Paper (Abstract)"},{"title":"Cerrolaza, J. J., Reyes Aguirre, M. A., Summers, R. M., Gonz\u00e1lez-Ballester, M. \u00c1., \u0026 Linguraru, M. G. (2015). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/135800\u0022\u003EAutomatic multi-resolution shape modeling of multi-organ structures\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E25\u003C\/i\u003E(1), 11-21.","year":2015,"type":"Journal Article (Original Article)"},{"title":"Chandran, V., Zysset, P., \u0026 Reyes Aguirre, M. A. (2015). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/137752\u0022\u003EPrediction of Trabecular Bone Anisotropy from Quantitative Computed Tomography using Supervised Learning and a Novel Morphometric Feature Descriptor\u003C\/a\u003E. \u003Ci\u003EMedical Image Computing and Computer-Assisted Intervention - MICCAI 2015. 18th International Conference, Munich, Germany, October 5-9, 2015, Proceedings, Part I\u003C\/i\u003E, \u003Ci\u003E9349\u003C\/i\u003E, 621-628.","year":2015,"type":"Conference Paper (Paper)"},{"title":"Chappuis, V., Engel, O., Shahim, K., Reyes Aguirre, M. A., Katsaros, C., \u0026 Buser, D. A. (2015). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/135801\u0022\u003ESoft Tissue Alterations in Esthetic Postextraction Sites: A 3-Dimensional Analysis\u003C\/a\u003E. \u003Ci\u003EJournal of Dental Research\u003C\/i\u003E, \u003Ci\u003E94\u003C\/i\u003E(9), 187S-193S.","year":2015,"type":"Journal Article (Original Article)"},{"title":"Lu, P., Barazzetti, L., Chandran, V., Gerber, K., Weber, S., Gerber, N., \u0026 Reyes Aguirre, M. A. (2015). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/134934\u0022\u003EFacial Nerve Image Enhancement from CBCT using Supervised Learning Technique\u003C\/a\u003E. \u003Ci\u003EIEEE Engineering in Medicine and Biology Society Conference Proceedings\u003C\/i\u003E, \u003Ci\u003E2015\u003C\/i\u003E, 2964-2967.","year":2015,"type":"Conference Paper (Paper)"},{"title":"Seif, M., Lu, H., Boesch, C. H., Reyes Aguirre, M. A., \u0026 Vermathen, P. (2015). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127908\u0022\u003EImage registration for triggered and non-triggered DTI of the human kidney: Reduced variability of diffusion parameter estimation\u003C\/a\u003E. \u003Ci\u003EJournal of Magnetic Resonance Imaging\u003C\/i\u003E, \u003Ci\u003E41\u003C\/i\u003E(5), 1228-1235.","year":2015,"type":"Journal Article (Original Article)"},{"title":"Taghizadeh, E., Latypova, A., Maquer, G. B., Reyes Aguirre, M. A., \u0026 B\u00fcchler, P. (2015). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/198220\u0022\u003EIncluding anisotropic information of trabecular bone using image registration\u003C\/a\u003E\u003C\/i\u003E. 21h Congress of the European Society of Biomechanics, Prague, Czech Republic. BORIS Portal.","year":2015,"type":"Conference Paper (Abstract)"},{"title":"Menze, B., Reyes Aguirre, M. A., Van Leemput, K., Porz, N., \u0026 Wiest, R. G. R. (2015). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/130252\u0022\u003EThe Multimodal Brain TumorImage Segmentation Benchmark (BRATS)\u003C\/a\u003E. \u003Ci\u003EIEEE Transactions on Medical Imaging\u003C\/i\u003E, \u003Ci\u003E34\u003C\/i\u003E(10), 199-2024.","year":2015,"type":"Journal Article (Original Article)"},{"title":"Valenzuela, W. E., Ferguson, S. J., Ignasiak, D., Diserens, G., Vermathen, P., Boesch, C. H., \u0026 Reyes Aguirre, M. A. (2015). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/139116\u0022\u003ECorrection tool for Active Shape Model based lumbar muscle segmentation\u003C\/a\u003E. \u003Ci\u003EIEEE Engineering in Medicine and Biology Society Conference Proceedings\u003C\/i\u003E, 3033-3036.","year":2015,"type":"Conference Paper (Paper)"},{"title":"Rios Velazquez, E., Meier, R., Dunn, W. D., Alexander, B., Wiest, R. G. R., Bauer, S., Gutman, D. A., Reyes Aguirre, M. A., \u0026 Aerts, H. J. W. L. (2015). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/137035\u0022\u003EFully automatic GBM segmentation in the TCGA-GBM dataset: Prognosis and correlation with VASARI features\u003C\/a\u003E. \u003Ci\u003EScientific Reports\u003C\/i\u003E, \u003Ci\u003E5\u003C\/i\u003E(16822), 16822.","year":2015,"type":"Journal Article (Original Article)"},{"title":"Bonaretti, S., Seiler, C., Boichon, C., Reyes Aguirre, M. A., \u0026 B\u00fcchler, P. (2014). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/197351\u0022\u003EImage-based vs. mesh-based statistical appearance models of the human femur: Implications for finite element simulations\u003C\/a\u003E. \u003Ci\u003EMedical Engineering \u0026 Physics\u003C\/i\u003E, \u003Ci\u003E36\u003C\/i\u003E(12), 1626-1635.","year":2014,"type":"Journal Article (Original Article)"},{"title":"Cerrolaza, J. J., Villanueva, A., Reyes Aguirre, M. A., Cabeza, R., Gonz\u00e1lez Ballester, M. A., \u0026 Linguraru, M. G. (2014). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127909\u0022\u003EGeneralized Multiresolution Hierarchical Shape Models via Automatic Landmark Clusterization\u003C\/a\u003E\u003C\/i\u003E (P. Golland, N. Hata, C. Barillot, J. Hornegger, \u0026 R. Howe, Eds.; Vols. 8675, pp. 1-8). BORIS Portal.","year":2014,"type":"Conference Paper (Paper)"},{"title":"Meier, R., Bauer, S., Slotboom, J., Wiest, R. G. R., \u0026 Reyes Aguirre, M. A. (2014). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127910\u0022\u003EPatient-Specific Semi-Supervised Learning for Postoperative Brain Tumor Segmentation\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E17\u003C\/i\u003E(Pt 1), 714-721.","year":2014,"type":"Conference Paper (Paper)"},{"title":"Gerig, T., Shahim, K., Reyes Aguirre, M. A., Vetter, T., \u0026 L\u00fcthi, M. (2014). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127911\u0022\u003ESpatially Varying Registration using Gaussian Processes.\u003C\/a\u003E\u003C\/i\u003E (P. Golland, N. Hata, C. Barillot, J. Hornegger, \u0026 R. Howe, Eds.; Vols. 8674, pp. 413-420). Springer.","year":2014,"type":"Conference Paper (Paper)"},{"title":"Taghizadeh, E., Maquer, G. B., Reyes Aguirre, M. A., \u0026 B\u00fcchler, P. (2014). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/197515\u0022\u003EIncluding the trabecular anisotropy from registered microCT data in homogenized FE model improves the bone\u2019s mechanical predictions\u003C\/a\u003E\u003C\/i\u003E. CMBBE 2014. BORIS Portal.","year":2014,"type":"Conference Paper (Speech)"},{"title":"Bauer, S., Wiest, R., Slotboom, J., \u0026 Reyes Aguirre, M. A. (2014). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/124484\u0022\u003EAtlas-based Segmentation of Tumor-bearing Brain Images\u003C\/a\u003E. In M. Hayat (Ed.), \u003Ci\u003EMolecular Mechanisms, Children\u2019s Cancer, Treatments, and Radiosurgery\u003C\/i\u003E (Vols. 12, pp. 159-169). Springer.","year":2014,"type":"Book Section"},{"title":"Seiler, C., Gazdhar, A., Reyes Aguirre, M. A., Benneker, L. M., Geiser, T., Siebenrock, K.-A., \u0026 Gantenbein, B. (2014). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/81704\u0022\u003ETime-lapse microscopy and classification of 2D human mesenchymal stem cells based on cell shape picks up myogenic from osteogenic and adipogenic differentiation\u003C\/a\u003E. \u003Ci\u003EJournal of Tissue Engineering and Regenerative Medicine\u003C\/i\u003E, \u003Ci\u003E8\u003C\/i\u003E(9), 737-746.","year":2014,"type":"Journal Article (Original Article)"},{"title":"Bauer, S., Porz, N., Meier, R., Pica, A., Slotboom, J., Wiest, R. G. R., \u0026 Reyes Aguirre, M. A. (2014). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127912\u0022\u003EInteractive Segmentation of MR Images from Brain Tumor Patients\u003C\/a\u003E\u003C\/i\u003E. 862-865.","year":2014,"type":"Conference Paper (Paper)"},{"title":"Bauer, S., Gratz, P. P., Gralla, J., Reyes Aguirre, M. A., \u0026 Wiest, R. G. R. (2014). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127913\u0022\u003ETowards Automatic MRI Volumetry for Treatment Selection in Acute Ischemic Stroke Patients\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E2014\u003C\/i\u003E, 1521-1524.","year":2014,"type":"Conference Paper (Paper)"},{"title":"Chappuis, V., Engel, O., Reyes Aguirre, M. A., Shahim, K., Nolte, L.-P., \u0026 Buser, D. A. (2013). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/112732\u0022\u003ERidge alterations post-extraction in the esthetic zone: a 3D analysis with CBCT\u003C\/a\u003E. \u003Ci\u003EJournal of Dental Research\u003C\/i\u003E, \u003Ci\u003E92\u003C\/i\u003E(12 Sup), 195S-201S.","year":2013,"type":"Journal Article (Original Article)"},{"title":"Shahim, K., J\u00fcrgens, P., Cattin, P. C., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2013). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/117972\u0022\u003EPrediction of Cranio-Maxilofacial Surgical Planning using an Inverse Soft Tissue Modelling Approach\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E7908\u003C\/i\u003E, 18-25.","year":2013,"type":"Conference Paper (Paper)"},{"title":"Valenzuela, W. E., Vermathen, P., Boesch, C. H., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2013). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/124483\u0022\u003EiSix - Image Segmentation in Osirix\u003C\/a\u003E\u003C\/i\u003E. 30th Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology, Toulouse, France. BORIS Portal.","year":2013,"type":"Conference Paper"},{"title":"J\u00fcrgens, P., Shahim, K., Cattin, P., Zeilhofer, H. F., \u0026 Reyes Aguirre, M. A. (2013). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/117976\u0022\u003EBackward-planning for orthognatic surgery - a new inverse modelling algorithm to define the hard-tissue position from a desired soft-tissue surface\u003C\/a\u003E. \u003Ci\u003EInternational Journal of Oral \u0026 Maxillofacial Surgery\u003C\/i\u003E, \u003Ci\u003E42\u003C\/i\u003E(10), 1331.","year":2013,"type":"Conference Paper (Paper)"},{"title":"Lu, H., Beisteiner, R., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2013). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/117975\u0022\u003EHierarchical segmentation-assisted multimodal registration for MR brain images\u003C\/a\u003E. \u003Ci\u003EComputerized Medical Imaging and Graphics\u003C\/i\u003E, \u003Ci\u003E37\u003C\/i\u003E(3), 234-244.","year":2013,"type":"Journal Article (Original Article)"},{"title":"Bauer, S., Lu, H., May, C., Nolte, L.-P., B\u00fcchler, P., \u0026 Reyes Aguirre, M. A. (2013). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/197004\u0022\u003EIntegrated Segmentation of Brain Tumor Images for Radiotherapy and Neurosurgery\u003C\/a\u003E. \u003Ci\u003EInternational Journal of Imaging Systems and Technology\u003C\/i\u003E, \u003Ci\u003E23\u003C\/i\u003E(1), 59-63.","year":2013,"type":"Journal Article (Original Article)"},{"title":"Bauer, S., Fejes, T., \u0026 Reyes Aguirre, M. A. (2013). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/112256\u0022\u003EA Skull-Stripping Filter for ITK\u003C\/a\u003E. \u003Ci\u003EInsight Journal\u003C\/i\u003E, \u003Ci\u003E2012\u003C\/i\u003E.","year":2013,"type":"Journal Article (Original Article)"},{"title":"Bou Sleiman, H., Paul, L., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2013). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/117974\u0022\u003EComparative Evaluation of Pelvic Allograft Selection Methods\u003C\/a\u003E. \u003Ci\u003EAnnals of Biomedical Engineering\u003C\/i\u003E, \u003Ci\u003E41\u003C\/i\u003E(5), 931-938.","year":2013,"type":"Journal Article (Original Article)"},{"title":"Oliveira Dos Santos, T., Baumberger, C., Constantinescu, M. A., Olariu, R., Nolte, L.-P., Alaraibi, S., \u0026 Reyes Aguirre, M. A. (2013). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/117973\u0022\u003E3D Face Reconstruction from 2D Pictures: First Results of a Web-Based Computer Aided System for Aesthetic Procedures\u003C\/a\u003E. \u003Ci\u003EAnnals of Biomedical Engineering\u003C\/i\u003E, \u003Ci\u003E41\u003C\/i\u003E(5), 952-966.","year":2013,"type":"Journal Article (Original Article)"},{"title":"Bou Sleiman, H., Iizuka, T., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2013). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/89162\u0022\u003EPopulation-based design of mandibular fixation plates with bone quality and morphology considerations\u003C\/a\u003E. \u003Ci\u003EAnnals of Biomedical Engineering\u003C\/i\u003E, \u003Ci\u003E41\u003C\/i\u003E(2), 377-384.","year":2013,"type":"Journal Article (Original Article)"},{"title":"Kim, B.-R., Oh, K.-M., Cevidanes, L. H., Park, J.-E., Sim, H.-S., Seo, S.-K., Reyes Aguirre, M. A., Kim, Y.-J., \u0026 Park, Y.-H. (2013). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/81635\u0022\u003EAnalysis of 3D Soft Tissue Changes After 1- and 2-Jaw Orthognathic Surgery in Mandibular Prognathism Patients\u003C\/a\u003E. \u003Ci\u003EJournal of Oral and Maxillofacial Surgery\u003C\/i\u003E, \u003Ci\u003E71\u003C\/i\u003E(1), 151-161.","year":2013,"type":"Journal Article (Original Article)"},{"title":"Bauer, S., Wiest, R. G. R., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2013). [Review of \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/89781\u0022\u003EA survey of MRI-based medical image analysis for brain tumor studies\u003C\/a\u003E\u003C\/i\u003E]. \u003Ci\u003EPhysics in Medicine and Biology\u003C\/i\u003E, \u003Ci\u003E58\u003C\/i\u003E(13), R97-R129.","year":2013,"type":"Journal Article (Review)"},{"title":"Bauer, S., Tessier, J., Krieter, O., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2013). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127914\u0022\u003EIntegrated Spatio-Temporal Segmentation of Longitudinal Brain Tumor Imaging Studies\u003C\/a\u003E\u003C\/i\u003E (B. Menze, G. Langs, A. Montillo, M. Kelm, H. M\u00fcller, \u0026 Z. Tu, Eds.; Vols. 8331, pp. 74-83). Springer International Publishing.","year":2013,"type":"Conference Paper (Paper)"},{"title":"Shahim, K., Goksel, O., J\u00fcrgens, P., \u0026 Reyes Aguirre, M. A. (2013). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/117977\u0022\u003EAccuracy Improvement In Cranio-Maxillofacial Soft Tissue Simulation Using A Muscle Embedded Meshing Approach\u003C\/a\u003E. \u003Ci\u003EIEEE Engineering in Medicine and Biology Society Conference Proceedings\u003C\/i\u003E, \u003Ci\u003E2013\u003C\/i\u003E, 7156-7159.","year":2013,"type":"Conference Paper (Paper)"},{"title":"Ritacco, L. E., Seiler, C., Farfalli, G. L., Nolte, L.-P., Reyes Aguirre, M. A., Muscolo, D. L., \u0026 Tinao, L. A. (2013). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71345\u0022\u003EValidity of an automatic measure protocol in distal femur for allograft selection from a three-dimensional virtual bone bank system\u003C\/a\u003E. \u003Ci\u003ECell and Tissue Banking\u003C\/i\u003E, \u003Ci\u003E14\u003C\/i\u003E(2), 213-220.","year":2013,"type":"Journal Article (Original Article)"},{"title":"Schulz, A. P., Reimers, N., Wipf, F., Vallotton, M., Bonaretti, S., Kozic, N., Reyes Aguirre, M. A., \u0026 Kienast, B. J. (2012). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/81636\u0022\u003EEvidence Based Development of a Novel Lateral Fibula Plate (VariAx Fibula) Using a Real CT Bone Data Based Optimization Process During Device Development\u003C\/a\u003E. \u003Ci\u003EOpen Orthopaedics Journal\u003C\/i\u003E, \u003Ci\u003E6\u003C\/i\u003E(1), 1-7.","year":2012,"type":"Journal Article (Original Article)"},{"title":"Seif, M., Lu, H., Boesch, C. H., Reyes Aguirre, M. A., \u0026 Vermathen, P. (2012). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/81634\u0022\u003EImage co-registration for triggered and non-triggered DTI of the human kidney: Reduced variability of diffusion parameter estimation\u003C\/a\u003E\u003C\/i\u003E. Proceedings of ESMRMB 2012, Lisbon, Portugal.","year":2012,"type":"Conference Paper (Paper)"},{"title":"L\u00fcthi, M., Blanc, R., Albrecht, T., Gass, T., Goksel, O., B\u00fcchler, P., Kistler, M., Bou Sleiman, H., Reyes Aguirre, M. A., Cattin, P., \u0026 Vetter, T. (2012). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/195949\u0022\u003EStatismo - A framework for PCA based statistical models\u003C\/a\u003E. \u003Ci\u003EInsight Journal\u003C\/i\u003E, 1.","year":2012,"type":"Journal Article (Original Article)"},{"title":"Bauer, S., Ritacco, L. E., Boesch, C. H., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2012). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/78097\u0022\u003EAutomatic Scan Planning for Magnetic Resonance Imaging of the Knee Joint\u003C\/a\u003E. \u003Ci\u003EAnnals of Biomedical Engineering\u003C\/i\u003E, \u003Ci\u003E40\u003C\/i\u003E(9), 2033-42.","year":2012,"type":"Journal Article (Original Article)"},{"title":"Seiler, C., Pennec, X., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2012). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/81641\u0022\u003ECapturing the Multiscale Anatomical Shape Variability with Polyaffine Transformation Trees\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E16\u003C\/i\u003E(7), 1371-1384.","year":2012,"type":"Journal Article (Original Article)"},{"title":"De Heras Ciechomski, P., Constantinescu, M. A., Garcia, J., Olariu, R., Dindoyal, I., Le Huu, S., \u0026 Reyes Aguirre, M. A. (2012). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/90316\u0022\u003EDevelopment and implementation of a web-enabled 3D consultation tool for breast augmentation surgery based on 3D-image reconstruction of 2D pictures\u003C\/a\u003E. \u003Ci\u003EJournal of Medical Internet Research\u003C\/i\u003E, \u003Ci\u003E14\u003C\/i\u003E(1), e21.","year":2012,"type":"Journal Article (Original Article)"},{"title":"Seiler, C., Pennec, X., \u0026 Reyes Aguirre, M. A. (2012). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/81639\u0022\u003ESimultaneous Multiscale Polyaffine Registration by Incorporating Deformation Statistics\u003C\/a\u003E\u003C\/i\u003E (N. Ayache, H. Delingette, \u0026 P. Golland, Eds.; Vols. 15, Issue Pt 2, pp. 130-137). Springer.","year":2012,"type":"Conference Paper (Paper)"},{"title":"Lu, H., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2012). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/81637\u0022\u003EInterest points localization for brain image using landmark-annotated atlas\u003C\/a\u003E. \u003Ci\u003EInternational Journal of Imaging Systems and Technology\u003C\/i\u003E, \u003Ci\u003E22\u003C\/i\u003E(2), 145.","year":2012,"type":"Journal Article (Original Article)"},{"title":"Blanc, R., Seiler, C., Sz\u00e9kely, G., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2012). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/81640\u0022\u003EStatistical Model Based Shape Prediction from a Combination of Direct Observations and Various Surrogates. Application to Orthopaedic Research\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E16\u003C\/i\u003E(6), 1156-1166.","year":2012,"type":"Journal Article (Original Article)"},{"title":"Lu, H., Van der Zwaag, W., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2012). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/81633\u0022\u003EGeometric and Intensity EPI Distortion Correction for 7T fMRI Using Simultaneous Classification and Registration\u003C\/a\u003E\u003C\/i\u003E. Proceedings of ESMRMB 2012, Lisbon, Portugal.","year":2012,"type":"Conference Paper (Paper)"},{"title":"Bou Sleiman, H., Seiler, C., Iizuka, T., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2012). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/81638\u0022\u003EPopulation-Based Design of Mandibular Plates Based on Bone Quality and Morphology\u003C\/a\u003E\u003C\/i\u003E (N. Ayache, H. Delingette, P. Golland, \u0026 K. Mori, Eds.; Vols. 15, Issue Pt 1, pp. 66-73). Springer.","year":2012,"type":"Conference Paper (Paper)"},{"title":"Gerber, K., Oliveira Dos Santos, T., Peterhans, M., Reyes Aguirre, M. A., Kim, H., Weber, S., \u0026 Weber, S. (2012). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/82378\u0022\u003EEvaluation of a portable image overlay projector for the visualisation of surgical navigation data: phantom studies\u003C\/a\u003E. \u003Ci\u003EInternational Journal of Computer Assisted Radiology and Surgery\u003C\/i\u003E, \u003Ci\u003E7\u003C\/i\u003E(4), 547-56.","year":2012,"type":"Journal Article (Original Article)"},{"title":"Kim, Y.-J., Oh, K.-M., Hong, J.-S., Lee, J.-H., Kim, H.-M., Reyes Aguirre, M. A., Cevidanes, L. H., \u0026 Park, Y.-H. (2011). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127917\u0022\u003EDo Patients Treated With Bimaxillary Surgery Have More Stable Condylar Positions Than Those Who Have Undergone Single-Jaw Surgery\u003C\/a\u003E? \u003Ci\u003EJournal of Oral and Maxillofacial Surgery\u003C\/i\u003E, \u003Ci\u003E70\u003C\/i\u003E(9), 2143-2152.","year":2011,"type":"Journal Article (Original Article)"},{"title":"Lu, H., Cattin, P. C., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2011). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/75305\u0022\u003EDiffusion weighted imaging distortion correction using hybrid multimodal image registration\u003C\/a\u003E\u003C\/i\u003E. 594-597.","year":2011,"type":"Conference Paper (Paper)"},{"title":"Bou Sleiman, H., Ritacco, L. E., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2011). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/75300\u0022\u003EMinimization of Intra-Operative Shaping of Orthopaedic Fixation Plates: A Population-Based Design\u003C\/a\u003E\u003C\/i\u003E (G. Fichtinger, A. Martel, \u0026 T. Peters, Eds.; Vols. 14, Issue Pt 2, pp. 409-416). Springer.","year":2011,"type":"Conference Paper (Paper)"},{"title":"J\u00fcrgens, P., Kim, H., \u0026 Reyes Aguirre, M. A. (2011). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127916\u0022\u003EApplication of a new soft-tissue simulation strategy based on a mimic muscle template model to predict the outcome in orthognatic surgery\u003C\/a\u003E. In \u003Ci\u003EInternational journal of oral \u0026 maxillofacial surgery\u003C\/i\u003E (Vols. 40, Issues 10, p. 1064). Abstracts of the 20th International Conference on Oral and Maxillofacial Surgery. Elsevier.","year":2011,"type":"Conference Paper (Abstract)"},{"title":"Marias, K., Dionysiou, D., Sakkalis, V., Graf, N., Bohle, R., Coveney, P., Wan, S., Folarin, A., B\u00fcchler, P., Reyes Aguirre, M. A., Clapworthy, G., Liu, E., Sabczynski, J., Bily, T., Roniotis, A., Tsiknakis, M., Kolokotroni, E., Giatili, S., Veith, C., \u2026 Stamatakos, G. S. (2011). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/195632\u0022\u003EClinically driven design of multi-scale cancer models : the ContraCancrum project paradigm\u003C\/a\u003E. \u003Ci\u003EInterface - Journal of the Royal Society\u003C\/i\u003E, \u003Ci\u003E1\u003C\/i\u003E(3), 450-461.","year":2011,"type":"Journal Article (Original Article)"},{"title":"Juergens, P., Klug, C., Krol, Z., Beinemann, J., Kim, H., Reyes Aguirre, M. A., Guevara-Rojas, G., Zeilhofer, H.-F., Ewers, R., \u0026 Schicho, K. (2011). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/75302\u0022\u003ENavigation-Guided Harvesting of Autologous Iliac Crest Graft for Mandibular Reconstruction\u003C\/a\u003E. \u003Ci\u003EJournal of Oral and Maxillofacial Surgery\u003C\/i\u003E, \u003Ci\u003E69\u003C\/i\u003E(11), 2915-2923.","year":2011,"type":"Journal Article (Original Article)"},{"title":"Bonaretti, S., Seiler, C., Boichon, C., B\u00fcchler, P., \u0026 Reyes Aguirre, M. A. (2011). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/195618\u0022\u003EMesh-based vs. Image-based Statistical Appearance Model of the Human Femur: a Preliminary Comparison Study for the Creation of Finite Element Meshes\u003C\/a\u003E\u003C\/i\u003E. Proceedings of the MICCAI Workshop on Mesh Processing in Medical Image Analysis, Westin Harbor Castle, Toronto, Canada.","year":2011,"type":"Conference Paper (Paper)"},{"title":"Bauer, S., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2011). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/75299\u0022\u003EFully Automatic Segmentation of Brain Tumor Images using Support Vector Machine Classiffication in Combination with Hierarchical Conditional Random Field Regularization\u003C\/a\u003E\u003C\/i\u003E (G. Fichtinger, A. Martel, \u0026 T. Peters, Eds.; Vols. 6893, pp. 354-361). Springer.","year":2011,"type":"Conference Paper (Paper)"},{"title":"Bauer, S., May, C., Dionysiou, D., Stamatakos, G., B\u00fcchler, P., \u0026 Reyes Aguirre, M. A. (2011). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/195619\u0022\u003EMulti-Scale Modeling for Image Analysis of Brain Tumor Studies\u003C\/a\u003E. \u003Ci\u003EIEEE Transactions on Biomedical Engineering\u003C\/i\u003E, \u003Ci\u003E59\u003C\/i\u003E(1), 25-29.","year":2011,"type":"Journal Article (Original Article)"},{"title":"J\u00fcrgens, P., Kim, H., Forter, S., Beinemann, J., Zeilhofer, H., Reyes Aguirre, M. A., \u0026 Schwenzer, K. (2011). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127915\u0022\u003EThree-dimensional control of maxillary position--validation of a 3-d real time navigational prototype system for routine application in orthognathic surgery\u003C\/a\u003E. In \u003Ci\u003EInternational journal of oral \u0026 maxillofacial surgery\u003C\/i\u003E (Vols. 40, Issues 10, p. 1064). Abstracts of the 20th International Conference on Oral and Maxillofacial Surgery. Elsevier.","year":2011,"type":"Conference Paper (Abstract)"},{"title":"Peterhans, M., Frei, D., Manser, P., Reyes Aguirre, M. A., \u0026 Fix, M. (2011). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/75319\u0022\u003EMonte Carlo Dose Calculation on Deforming Anatomy\u003C\/a\u003E. \u003Ci\u003EZeitschrift F\u00fcr Medizinische Physik\u003C\/i\u003E, \u003Ci\u003E21\u003C\/i\u003E(2), 113-23.","year":2011,"type":"Journal Article (Original Article)"},{"title":"Kim, H. M., J\u00fcrgens, P., \u0026 Reyes Aguirre, M. A. (2011). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/75297\u0022\u003ESoft-Tissue Simulation for Cranio-Maxillofacial Surgery: Clinical Needs and Technical Aspects\u003C\/a\u003E. In A. Gefen (Ed.), \u003Ci\u003EPatient-Specific Modeling in Tomorrow\u2019s Medicine\u003C\/i\u003E (Vols. 09, pp. 413-440). Springer.","year":2011,"type":"Book Section"},{"title":"Seiler, C., Pennec, X., Ritacco, L. E., \u0026 Reyes Aguirre, M. A. (2011). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/75298\u0022\u003EFemur Specific Polyaffine Model to Regularize the Log-Domain Demons Registration\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E7962\u003C\/i\u003E, 79620G.","year":2011,"type":"Conference Paper (Paper)"},{"title":"Bou Sleiman, H., Ritacco, L. E., Aponte-Tinao, L., Muscolo, D. L., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2011). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/75304\u0022\u003EAllograft Selection for Transepiphyseal Tumor Resection Around the Knee Using Three-Dimensional Surface Registration\u003C\/a\u003E. \u003Ci\u003EAnnals of Biomedical Engineering\u003C\/i\u003E, \u003Ci\u003E39\u003C\/i\u003E(6), 1720-1727.","year":2011,"type":"Journal Article (Original Article)"},{"title":"Bauer, S., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2011). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/75303\u0022\u003ESegmentation of brain tumor images based on atlas-registration combined with a Markov-Random-Field lesion growth model\u003C\/a\u003E\u003C\/i\u003E. 2018-2021.","year":2011,"type":"Conference Paper (Paper)"},{"title":"Seiler, C., Pennec, X., \u0026 Reyes Aguirre, M. A. (2011). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/75301\u0022\u003EGeometry-Aware Multiscale Image Registration via OBBTree-Based Polyaffine Log-Demons\u003C\/a\u003E\u003C\/i\u003E (F. Gabor, A. Martel, \u0026 T. Peters, Eds.; Vols. 6892, pp. 631-638). Springer.","year":2011,"type":"Conference Paper (Paper)"},{"title":"Seiler, C., Gazdhar, A., Geiser, T., Reyes Aguirre, M. A., \u0026 Gantenbein, B. (2010, June). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127922\u0022\u003EMesenchymal Stem Cell Classification during Differentiation Based on Shape Information\u003C\/a\u003E\u003C\/i\u003E. TERMIS -- Tissue Engineering and Regenerative Medicine International Society. BORIS Portal.","year":2010,"type":"Conference Paper (Abstract)"},{"title":"Lu, H., Reyes Aguirre, M. A., S\u030cerifovic\u0301 A., Weber, S., Sakurai, Y., Yamagata, H., \u0026 Cattin, P. C. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71350\u0022\u003EMulti-modal diffeomorphic demons registration based on point-wise mutual information\u003C\/a\u003E\u003C\/i\u003E. 372-375.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Kim, H. M., J\u00fcrgens, P., Cattin, P., Weber, S., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71343\u0022\u003EPatient-specific, Fast Soft-Tissue Simulation for Cranio-Maxillofacial Surgery\u003C\/a\u003E\u003C\/i\u003E. 17th Congress of the European Society of Biomechanics, Edinburgh, U.K.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Kozic, N., Weber, S., B\u00fcchler, P., Lutz, C., Reimers, N., Gonz\u00e1lez Ballester, M. A., \u0026 Reyes Aguirre, M. A. (2010). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/195589\u0022\u003EOptimisation of orthopaedic implant design using statistical shape space analysis based on level sets\u003C\/a\u003E. \u003Ci\u003EMedical Image Analysis\u003C\/i\u003E, \u003Ci\u003E14\u003C\/i\u003E(3), 265-275.","year":2010,"type":"Journal Article (Original Article)"},{"title":"Bonaretti, S., Reyes Aguirre, M. A., Kistler, M., Seiler, C., \u0026 B\u00fcchler, P. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/195588\u0022\u003ECombined statistical model of bone shape and mechanical properties for bone and implant modeling\u003C\/a\u003E\u003C\/i\u003E. 9th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering, Valencia\/Spain, Feb 24-27.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Oliveira Dos Santos, T., Weitzel, T., Klaeser, B., Krause, T., Nolte, L.-P., Weber, S., \u0026 Reyes Aguirre, M. A. (2010). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/73553\u0022\u003EMultimodal target correction by local bone registration: a PET\/CT evaluation\u003C\/a\u003E. \u003Ci\u003EIEEE Engineering in Medicine and Biology Society Conference Proceedings\u003C\/i\u003E, \u003Ci\u003E2010\u003C\/i\u003E, 5616-5619.","year":2010,"type":"Journal Article (Original Article)"},{"title":"Marias, K., Sakkalis, V., Roniotis, A., Karatzanis, I., Stamatakos, G., Dionysiou, D., Giatili, S., Uzunoglou, N., Graf, N., Bohle, R., Meese, E., Stenzhorn, H., Kim, Y.-J., Coveney, P., Zasada, S., Wan, S., Folarin, A., B\u00fcchler, P., Bardyn, T., \u2026 Sabczynski, J. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127919\u0022\u003EClinically Oriented Translational Cancer Multilevel Modelling: The ContraCancrum project\u003C\/a\u003E\u003C\/i\u003E. Proceedings of the Virtual Physiological Human Conference 2010. BORIS Portal.","year":2010,"type":"Conference Paper (Abstract)"},{"title":"Bonaretti, S., Helgason, B., Seiler, C., Kistler, M., Reyes Aguirre, M. A., \u0026 B\u00fcchler, P. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/195601\u0022\u003EA statistical shape model of bone anatomical variability for finite element assessment of bone mechanics\u003C\/a\u003E\u003C\/i\u003E (p. 2008). Proceedings of the 17th Congress of the European Society of Biomechanics, University of Edinburgh, UK. BORIS Portal.","year":2010,"type":"Conference Paper"},{"title":"Bauer, S., Seiler, C., Bardyn, T., B\u00fcchler, P., \u0026 Reyes Aguirre, M. A. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/195587\u0022\u003EAtlas-Based Segmentation of Brain Tumor Images Using a Markov Random Field-Based Tumor Growth Model and Non-Rigid Registration\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E2010\u003C\/i\u003E, 4080-4083.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Stamatakos, G., Dionysiou, D., Kolokotroni, E., Georgiadi, E., Roniotis, A., Sakkalis, V., Coveney, P., Wan, S., Manos, S., Zasada, S., Folarin, A., B\u00fcchler, P., Bardyn, T., Bauer, S., Reyes Aguirre, M. A., Bily, T., Bednar, V., Karasek., M., Graf, N., \u2026 Marias, K. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127918\u0022\u003ECONTRA CANCRUM AT THE PROJECT LEVEL: The ContraCancrum Oncosimulator: Integrating Biomechanisms Across Scales in the Clinical Context\u003C\/a\u003E\u003C\/i\u003E (G. Stamatakos \u0026 D. Dionysiou, Eds.). BORIS Portal.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Bou Sleiman, H., Ritacco, L. E., \u0026 Reyes Aguirre, M. A. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71340\u0022\u003EComputer-assisted allograft selection for transepiphyseal tumor resection at the knee\u003C\/a\u003E\u003C\/i\u003E. 10th Annual Meeting of the International Society for Computer Assisted Surgery, Paris, France, June 16-19.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Lu, H., Cattin, P. C., \u0026 Reyes Aguirre, M. A. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71339\u0022\u003EA Hybrid Multimodal Non-Rigid Registration of MR Images Based on Diffeomorphic Demons\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E2010\u003C\/i\u003E, 5951-5954.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Tucker, S., Cevidanes, L., Styner, M., Kim, H. M., Reyes Aguirre, M. A., Proffit, W., \u0026 Turvey, T. (2010). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71347\u0022\u003EComparison of actual surgical outcomes and 3-dimensional surgical simulations\u003C\/a\u003E. \u003Ci\u003EJournal of Oral and Maxillofacial Surgery\u003C\/i\u003E, \u003Ci\u003E68\u003C\/i\u003E(10), 2412-2421.","year":2010,"type":"Journal Article (Original Article)"},{"title":"May, C., Bardyn, T., Reyes Aguirre, M. A., \u0026 B\u00fcchler, P. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/195596\u0022\u003EBiomechanical model of tumor growth: application to the European ContraCancrum project\u003C\/a\u003E\u003C\/i\u003E (G. Stamatakos \u0026 D. Dionysiou, Eds.; Vols. 2010, p. 73). BORIS Portal.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Cevidanes, L., Tucker, S., Styner, M., Kim, H. M., Chapuis, J., Reyes Aguirre, M. A., Proffit, W., Turvey, T., \u0026 Jaskolka, M. (2010). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71344\u0022\u003EThree-dimensional surgical simulation\u003C\/a\u003E. \u003Ci\u003EAmerican Journal of Orthodontics and Dentofacial Orthopedics\u003C\/i\u003E, \u003Ci\u003E138\u003C\/i\u003E(3), 361-371.","year":2010,"type":"Journal Article (Original Article)"},{"title":"Bardyn, T., Reyes Aguirre, M. A., Larrea, X., \u0026 B\u00fcchler, P. (2010). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/195606\u0022\u003EInfluence of Smoothing on Voxel-Based Mesh Accuracy in Micro-Finite Element\u003C\/a\u003E. In K. Miller \u0026 P. M. F. Nielsen (Eds.), \u003Ci\u003EComputational Biomechanics for Medicine\u003C\/i\u003E (pp. 85-93). Springer.","year":2010,"type":"Book Section"},{"title":"Kim, H. M., J\u00fcrgens, P., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71348\u0022\u003EAnatomically-Driven Soft-Tissue Simulation Strategy for Cranio-Maxillofacial Surgery Using Facial Muscle Template Model\u003C\/a\u003E\u003C\/i\u003E (T. Jiang, N. Navab, J. Pluim, \u0026 M. Viergever, Eds.; Vols. 6361, pp. 61-68). Springer.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Seiler, C., Pennec, X., \u0026 Reyes Aguirre, M. A. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71351\u0022\u003EParametric regression of 3D medical images through the exploration of non-parametric regression models\u003C\/a\u003E\u003C\/i\u003E. 452-455.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Seiler, C., Gazdhar, A., Geiser, T., Reyes Aguirre, M. A., \u0026 Gantenbein, B. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71349\u0022\u003EMesenchymal Stem Cell Classification during Differentiation Based on Shape Information\u003C\/a\u003E\u003C\/i\u003E.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Bauer, S., \u0026 Reyes Aguirre, M. A. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127921\u0022\u003EA Markov-Random-Field-Based Biomechanical Tumor Growth Model for Atlas-Based Segmentation of Brain Tumor Images\u003C\/a\u003E\u003C\/i\u003E. Proceedings of the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Reyes Aguirre, M. A., Gonz\u00e1lez Ballester, M. A., Kozic, N., Summers, R. M., \u0026 Linguraru, M. G. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71342\u0022\u003EHierarchical Patch Generation for Multi-level Statistical Shape Analysis by Principal Factor Analysis Decomposition\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E7626\u003C\/i\u003E(762617), 157-167.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Kim, H. M., J\u00fcrgens, P., Weber, S., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2010). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71346\u0022\u003EA New Soft-Tissue Simulation Strategy for Cranio-Maxillofacial Surgery Using Facial Muscle Template Model\u003C\/a\u003E. \u003Ci\u003EProgress in Biophysics and Molecular Biology\u003C\/i\u003E, \u003Ci\u003E103\u003C\/i\u003E(2-3), 284-291.","year":2010,"type":"Journal Article (Original Article)"},{"title":"Kim, H. M., J\u00fcrgens, P., Cattin, P., Weber, S., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71341\u0022\u003EFast soft-tissue simulation method for cranio-maxillofacial surgery using facial muscle template models\u003C\/a\u003E\u003C\/i\u003E. 14th Annual Conference of the International Society for Computer Aided Surgery, Geneva, Switzerland, June.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Oliveira Dos Santos, T., Peterhans, M., Roth, B., Thalmann, G., Reyes Aguirre, M. A., Nolte, L.-P., \u0026 Weber, S. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71364\u0022\u003EComputer Aided Surgery for Percutaneous Nephrolithotomy: Clinical Requirement Analysis and System Design\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E1\u003C\/i\u003E, 442-445.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Dong, X., Lu, H., Sakurai, Y., Yamagata, H., Zheng, G., \u0026 Reyes Aguirre, M. A. (2010). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/71381\u0022\u003EAutomated Intervertebral Disc Detection from Low Resolution, Sparse MRI Images for the Planning of Scan Geometries\u003C\/a\u003E. In F. Wang, P. Yan, K. Suzuki, \u0026 D. Shen (Eds.), \u003Ci\u003EMachine Learning in Medical Imaging\u003C\/i\u003E.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Marias, K., Sakkalis, V., Roniotis, A., Karatzanis, I., Stamatakos, G., Dionysiou, D., Giatili, S., Uzunoglou, N., Graf, N., Bohle, R., Meese, E., Stenzhorn, H., Kim, Y.-J., Coveney, P., Zasada, S., Wan, S., Folarin, A., B\u00fcchler, P., Bardyn, T., \u2026 Sabczynski, J. (2010). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127920\u0022\u003ECONTRACANCRUM AT THE PROJECT LEVEL: Clinically Oriented Translational Cancer Multilevel Modelling\u003C\/a\u003E\u003C\/i\u003E (G. Stamatakos \u0026 D. Dionysiou, Eds.). BORIS Portal.","year":2010,"type":"Conference Paper (Paper)"},{"title":"Kozic, N., Weber, S., Gonzalez Ballester, M. A., Abdo, G., Rufenacht, D., Ferguson, S. J., \u0026 Reyes Aguirre, M. A. (2010). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/73496\u0022\u003EAutomated cement segmentation in vertebroplasty\u003C\/a\u003E. \u003Ci\u003EComputer Aided Surgery\u003C\/i\u003E, \u003Ci\u003E15\u003C\/i\u003E(1-3), 49-55.","year":2010,"type":"Journal Article (Original Article)"},{"title":"Santos, T., Weitzel, T., Klaeser, B., Reyes Aguirre, M. A., \u0026 Weber, S. (2009). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/104031\u0022\u003EIntroducing computer-assisted surgery into combined PET\/CT based biopsy treatments\u003C\/a\u003E\u003C\/i\u003E. 308-311.","year":2009,"type":"Conference Paper (Paper)"},{"title":"Kim, H. M., J\u00fcrgens, P., Nolte, L.-P., Weber, S., Zeilhofer, H.-F., \u0026 Reyes Aguirre, M. A. (2009). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/104018\u0022\u003EAnatomically considered, fast soft-tissue simulation for cranio-maxillofacial surgery\u003C\/a\u003E\u003C\/i\u003E. Computer Aided Surgery around the Head.","year":2009,"type":"Conference Paper (Paper)"},{"title":"Bonaretti, S., B\u00fcchler, P., Reimers, N., Schmidt, W., Seiler, C., Weber, S., \u0026 Reyes Aguirre, M. A. (2009). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/196470\u0022\u003EAutomatic bone density evaluation from CT images\u003C\/a\u003E\u003C\/i\u003E. 625-627.","year":2009,"type":"Conference Paper (Paper)"},{"title":"Bardyn, T., Reyes Aguirre, M. A., Boyd, S., \u0026 B\u00fcchler, P. (2009). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/196474\u0022\u003EAutomatic Finite Element Mesh Generation and Correction from 3D Image Data\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E25\/IV\u003C\/i\u003E, 1873.","year":2009,"type":"Conference Paper (Paper)"},{"title":"Bardyn, T., Reyes Aguirre, M. A., Boyd, S., \u0026 B\u00fcchler, P. (2009). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/196469\u0022\u003EInfluence of smoothing on voxel-based mesh accuracy in micro finite-element\u003C\/a\u003E\u003C\/i\u003E. 78-86.","year":2009,"type":"Conference Paper (Paper)"},{"title":"Schmidt, W., Reyes Aguirre, M. A., Fischer, F., Geesink, R., Nolte, L.-P., Racanelli, J., \u0026 Reimers, N. (2009). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/104022\u0022\u003EQuantifying human knee anthropometric differences between ethnic groups and gender using shape analysis\u003C\/a\u003E\u003C\/i\u003E. 26-29.","year":2009,"type":"Conference Paper (Paper)"},{"title":"Reyes Aguirre, M. A., Gonzalez Ballester, M. A., Li, Z., Kozic, N., Chin, S., Summers, R. M., \u0026 Linguraru, M. G. (2009). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/104019\u0022\u003EAnatomical variability of organs via principal factor analysis from the construction of an abdominal probabilistic atlas\u003C\/a\u003E\u003C\/i\u003E. 682-685.","year":2009,"type":"Conference Paper (Paper)"},{"title":"Marias, K., Sakkalis, V., Roniotis, A., Farmaki, C., Stamatakos, G., Dionysiou, D., Giatili, S., Uzunoglou, N., Graf, N., Bohle, R., Messe, E., Coveney, P., Manos, S., Wan, S., Folarin, A., Nagl, S., B\u00fcchler, P., Bardyn, T., Reyes Aguirre, M. A., \u2026 Carlsen, I. (2009). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/196478\u0022\u003EClinically Oriented Translational Cancer Multilevel Modeling: The ContraCancrum Project\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E25\/IV\u003C\/i\u003E, 2124-2127.","year":2009,"type":"Conference Paper (Paper)"},{"title":"Kozic, N., Gonzalez Ballester, M. A., B\u00fcchler, P., Reimers, N., Nolte, L.-P., Linguraru, M. G., \u0026 Reyes Aguirre, M. A. (2009). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/196468\u0022\u003EPopulation-specific evaluation of implant bone fitting using PCA shape space and level sets\u003C\/a\u003E\u003C\/i\u003E. 883-886.","year":2009,"type":"Conference Paper (Paper)"},{"title":"Seiler, C., Weber, S., Schmidt, W., Fischer, F., Reimers, N., \u0026 Reyes Aguirre, M. A. (2009). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/104021\u0022\u003EAutomatic landmark propagation for left and right symmetry assessment of tibia and femur: A computational anatomy based approach\u003C\/a\u003E\u003C\/i\u003E. 195-198.","year":2009,"type":"Conference Paper (Paper)"},{"title":"Blanc, R., Reyes Aguirre, M. A., Seiler, C., \u0026 Sz\u00e9kely, G. (2009). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/104020\u0022\u003EConditional variability of statistical shape models based on surrogate variables\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E5762\u003C\/i\u003E, 84-91.","year":2009,"type":"Conference Paper (Paper)"},{"title":"Seiler, C., B\u00fcchler, P., Nolte, L.-P., Reyes Aguirre, M. A., \u0026 Paulsen, R. (2009). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/196480\u0022\u003EHierarchical Markov Random Fields Applied to Model Soft Tissue Deformations on Graphics Hardware\u003C\/a\u003E. In N. Magnenat-Thalmann, J. J. Zhang, \u0026 D. D. Feng (Eds.), \u003Ci\u003ERecent Advances in the 3D Physiological Human\u003C\/i\u003E (Issue al. N., pp. 133-148). Springer Verlag.","year":2009,"type":"Book Section"},{"title":"Kozic, N., Reyes Aguirre, M. A., Tannast, M., Nolte, L.-P., \u0026 Gonzalez Ballester, M. A. (2008, June). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127931\u0022\u003EAssesment of anatomical criteria across populations using statistical shape models and level sets\u003C\/a\u003E\u003C\/i\u003E (pp. 46-49). 8th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery. BORIS Portal.","year":2008,"type":"Conference Paper (Abstract)"},{"title":"Bonaretti, S., Reimers, N., Reyes Aguirre, M. A., Nikitsin, A., Joensson, A., Nolte, L.-P., \u0026 B\u00fcchler, P. (2008). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/196451\u0022\u003EAssessment of Peri-Articular Implant Fitting Based on Statistical Finite Element Modeling\u003C\/a\u003E\u003C\/i\u003E. 138-147.","year":2008,"type":"Conference Paper (Paper)"},{"title":"Reyes Aguirre, M. A., Gonzalez Ballester, M. A., Li, Z., Kozic, N., Summers, R. M., \u0026 Linguraru, M. G. (2008). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/100534\u0022\u003EInterpretability of anatomical variability analysis of abdominal organs via clusterization of decomposition modes\u003C\/a\u003E\u003C\/i\u003E. 355-358.","year":2008,"type":"Conference Paper (Paper)"},{"title":"Reyes Aguirre, M. A., Linguraru, M., Nolte, L.-P., \u0026 Gonzalez Ballester, M. A. (2008). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/102020\u0022\u003EClusterization of deformation modes for quantitative evaluation on factor analysis techniques on statistical shape modelling\u003C\/a\u003E\u003C\/i\u003E. 185-192.","year":2008,"type":"Conference Paper (Paper)"},{"title":"Larrea, X., Reyes Aguirre, M. A., Boyd, S., B\u00fcchler, P., \u0026 Gonzalez Ballester, M. A. (2008). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/196444\u0022\u003EAutomatic Mesh Smoothing For Finite Element Modeling From 3d Image Data\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E41\u003C\/i\u003E(S1), S275.","year":2008,"type":"Conference Paper (Paper)"},{"title":"Kozic, N., Reyes Aguirre, M. A., Tannast, M., Nolte, L.-P., \u0026 Gonzalez Ballester, M. A. (2008). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/101910\u0022\u003EAssessment of anatomical criteria across populations using statistical shape models and level sets\u003C\/a\u003E\u003C\/i\u003E. 46-49.","year":2008,"type":"Conference Paper (Paper)"},{"title":"Bonaretti, S., Reimers, N., Rueckert, D., Reyes Aguirre, M. A., Gonzalez Ballester, M. A., \u0026 B\u00fcchler, P. (2008). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/196439\u0022\u003EStatistical finite element analysis for bone modeling\u003C\/a\u003E. \u003Ci\u003EJournal of Biomechanics\u003C\/i\u003E, \u003Ci\u003E41\u003C\/i\u003E(S1), S369.","year":2008,"type":"Conference Paper (Paper)"},{"title":"Larrea, X., Reyes Aguirre, M. A., Boyd, S., B\u00fcchler, P., \u0026 Gonzalez Ballester, M. A. (2008). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/197355\u0022\u003EAutomatic mesh smoothing for finite element modelling from 3D image data\u003C\/a\u003E.\u003C\/i\u003E 16th Congress of the European Society of Biomechanics. BORIS Portal.","year":2008,"type":"Conference Paper (Abstract)"},{"title":"Kozic, N., Gonzalez Ballester, M. A., Tannast, M., Nolte, L.-P., \u0026 Reyes Aguirre, M. A. (2008). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/100532\u0022\u003EStatistical Shape Space Analysis Based on Level Sets\u003C\/a\u003E\u003C\/i\u003E (T. Dohi, I. Sakuma, \u0026 H. Liao, Eds.; Vols. 5128, pp. 160-167). BORIS Portal.","year":2008,"type":"Conference Paper (Paper)"},{"title":"Reyes Aguirre, M. A., Bonaretti, S., Reimers, N., Lutz, C., \u0026 Gonzalez Ballester, M. A. (2008). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/100535\u0022\u003EEvidence-based implant design using statistical bone model and automated implant fitting\u003C\/a\u003E\u003C\/i\u003E. 379-381.","year":2008,"type":"Conference Paper (Paper)"},{"title":"Reyes Aguirre, M. A., Larrea, X., Boyd, S., Gonzalez Ballester, M. A., \u0026 B\u00fcchler, P. (2008). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/196441\u0022\u003EConstrained hexahedral mesh smoothing for finite element modelling from 3D image datag\u003C\/a\u003E\u003C\/i\u003E. Proceedings of the 8th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering.","year":2008,"type":"Conference Paper (Paper)"},{"title":"Linguraru, M., Vercauteren, T., Reyes Aguirre, M. A., Gonzalez Ballester, M. A., \u0026 Ayache, N. (2008). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/100537\u0022\u003ESegmentation Propagation from Deformable Atlases for Brain Mapping and Analysis\u003C\/a\u003E\u003C\/i\u003E. \u003Ci\u003E1\u003C\/i\u003E(4), 269-287.","year":2008,"type":"Conference Paper (Paper)"},{"title":"Kozic, N., Reyes Aguirre, M. A., Nolte, L.-P., \u0026 Gonzalez Ballester, M. A. (2008). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/100533\u0022\u003EGlobal Optimisation in PCA Shape Space Using Level Sets\u003C\/a\u003E\u003C\/i\u003E. S109-S110.","year":2008,"type":"Conference Paper (Paper)"},{"title":"Reyes Aguirre, M. A., \u0026 Gonzalez Ballester, M. A. (2007). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/97822\u0022\u003EClustering of deformation modes for quantitative evaluation of statistical shape models\u003C\/a\u003E\u003C\/i\u003E. 271-273.","year":2007,"type":"Conference Paper (Paper)"},{"title":"Reyes Aguirre, M. A., Linguraru, M. G., Marias, K., Ayache, N., Nolte, L.-P., \u0026 Gonzalez Ballester, M. A. (2007). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/97825\u0022\u003EStatistical shape analysis via principal factor analysis\u003C\/a\u003E\u003C\/i\u003E. 1216-1219.","year":2007,"type":"Conference Paper (Paper)"},{"title":"Reyes Aguirre, M. A., Malandain, G., Koulibaly, P., Gonzalez Ballester, M. A., \u0026 Darcourt, J. (2007). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/97818\u0022\u003EModel-based respiratory motion compensation for emission tomography image reconstruction\u003C\/a\u003E. \u003Ci\u003EPhysics in Medicine and Biology\u003C\/i\u003E, \u003Ci\u003E52\u003C\/i\u003E(12), 3579-3600.","year":2007,"type":"Journal Article (Original Article)"},{"title":"Linguraru, M. G., Vercauteren, T., Reyes Aguirre, M. A., Gonz\u00e1lez-Ballester, M. \u00c1., \u0026 Ayache, N. (2007). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127924\u0022\u003ESegmentation propagation from deformable atlases for brain mapping and analysis\u003C\/a\u003E. \u003Ci\u003EBrain Research Journal\u003C\/i\u003E, \u003Ci\u003E1\u003C\/i\u003E(4), 269-287.","year":2007,"type":"Journal Article (Original Article)"},{"title":"Reyes Aguirre, M. A., Gonz\u00e1lez-Ballester, M., \u0026 Linguraru, M. (2007). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127925\u0022\u003EStatistical Bone Shape Analysis for Image Free Surgery\u003C\/a\u003E. \u003Ci\u003EActa Universitatis Cibiniensis, Technical Series\u003C\/i\u003E, \u003Ci\u003ELV\u003C\/i\u003E, 121-129.","year":2007,"type":"Journal Article (Original Article)"},{"title":"Malandain, G., \u0026 Reyes Aguirre, M. A. (2005, December). \u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127930\u0022\u003ELa tomographie en mouvement\u003C\/a\u003E. \u003Ci\u003EPour la Science\u003C\/i\u003E, \u003Ci\u003E338\u003C\/i\u003E, 132-137.","year":2005,"type":"Magazine Article"},{"title":"Reyes Aguirre, M. A., Malandain, G., Koulibaly, P. M., \u0026 Darcourt, J. (2005, July). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127926\u0022\u003ERespiratory motion correction in emission tomography imaging\u003C\/a\u003E\u003C\/i\u003E. Fully Three-Dimensional Image Reconstruction Meeting in Radiology and Nuclear Medicine, Salt Lake City, Utah, USA.","year":2005,"type":"Conference Paper (Paper)"},{"title":"Gonzalez Ballester, M. A., Linguraru, M. G., Reyes Aguirre, M. A., \u0026 Ayache, N. (2005). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127928\u0022\u003EOn the adequacy of principal factor analysis for the study of shape variability\u003C\/a\u003E\u003C\/i\u003E (J. M. Fitzpatrick \u0026 J. M. Reinhardt, Eds.; Vols. 5747, p. 1392). SPIE Publishing.","year":2005,"type":"Conference Paper (Paper)"},{"title":"Reyes Aguirre, M. A., Malandain, G., Ayache, N., Darcourt, J., \u0026 Koulibaly, P. (2005). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127929\u0022\u003ERespiratory motion compensation within emission tomographic reconstruction\u003C\/a\u003E\u003C\/i\u003E. 52nd Annual Meeting of the Society of Nuclear Medicine, Toronto, Canada. BORIS Portal.","year":2005,"type":"Conference Paper (Abstract)"},{"title":"Reyes Aguirre, M. A. (2005). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127923\u0022\u003ERespiratory Motion Compensation in Emission Tomography\u003C\/a\u003E\u003C\/i\u003E. BORIS Portal.","year":2005,"type":"Thesis"},{"title":"Reyes Aguirre, M. A., Malandain, G., Koulibaly, P. M., Gonzalez Ballester, M. A., \u0026 Darcourt, J. (2005). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127927\u0022\u003ERespiratory motion correction in emission tomography image reconstruction\u003C\/a\u003E\u003C\/i\u003E (J. Duncan \u0026 G. Gerig, Eds.; Vols. 3750, pp. 369-376). Springer.","year":2005,"type":"Conference Paper (Paper)"},{"title":"Reyes Aguirre, M. A., Malandain, G., \u0026 Darcourt, J. (2004). \u003Ci\u003E\u003Ca target=\u0022_blank\u0022 href=\u0022https:\/\/boris-portal.unibe.ch\/handle\/20.500.12422\/127932\u0022\u003ERespiratory movement correction in emission tomography\u003C\/a\u003E\u003C\/i\u003E (Th\u00e8me BIO, Vols. 5279). Inria Sophia Antipolis.","year":2004,"type":"Report"}]}