Research

My research interests are focused on medical image analysis, a general list of topics include (in no specific order):

Supervision of PhD Theses:

 

Nina Kozic (2009) "Statistical shape space analysis based on level sets for optimization of orthopaedic implant design"

Hyungmin Kim (2011) "Computer-Assistance in Cranio-Maxillofacial Surgery: A Clinically-Driven Approach"

Thiago Oliveira dos Santos (2011) "A Soft Tissue Image Guidance System for Percutaneous Needle Interventions Based on Multimodal Images"

Serena Bonaretti (2012) "Statistical Finite Element Modeling: Application to Orthopaedic Implant Design"

Christof Seiler (2012) "Trees on Geometrical Deformations to Model the Statistical Variability of Organs in Medical Images"

Huanxiang Lu (2012) "Multi-modal Deformable Registration for Magnetic Resonance Image"

Habib Bou-Sleiman (2012) "A Computational Anatomy Approach to Orthopaedic Research"

Stefan Bauer (2013) "Medical Image Analysis and Image-based Modeling for Brain Tumor Studies"

Elham Taghizadeh (2016) "Statistical Shape Model of the Leg to Improve the Treatment of Patella Pathology in Total Knee Arthroplasty"

Waldo Valenzuela (2016) "Effective Human Machine Interfaces for Medical Image Analysis"

Carlos Correa Schokiche (2016) “MicroCT based kidney morphometry: A machine learning approach”

Vimal Chandran (2017) “Comprehensive and Effective Machine Learning based Computational Modelling of the Human Proximal Femur”

Raphael Meier (2017) “Towards Automatic Segmentation of Longitudinal Brain Tumor Imaging Data”

Ping Lu (2017) “Advanced Medical Image Analysis of the Human Facial Nerve based on Machine Learning Technologies”

Alain Jungo (2020) “Applications and Insights of Uncertainty Estimates in Automated Brain Tumor Segmentation”

Fabian Balsiger (2020) “Quantitative Magnetic Resonance Imaging to Monitor and Diagnose Neuromuscular Diseases”

Yannick Suter (2021) “Advanced Machine Learning Technologies for Robust Longitudinal Radiomics and Response Assessment in Glioblastoma Multiforme”

Suhang You (2023) “Segmentation and Quality Control, Understanding Confounders Leading to Failure Modes in Medical Image Analysis with Deep Learning”

Robert Poel 2023) “Radiotherapy Oriented Quality Control for Deep Learning Based Fully Automated Segmentation of Intracranial Targets and Organs at Risk”

Elias Ruefenacht (2023) “Data-centric and Clinically-relevant AI-based Segmentation of Intracranial Tumors and Organs-at-Risk for Radiotherapy”

 

Publications

For a Google Scholar version, please click here

Journal Articles

Peer-reviewed Conference Articles

ConferenceAbstracts

BookChapters

 

 

Journal Articles

Aurelie Pahud de Mortanges, Haozhe Luo, Shelley Zixin Shu, Amith Kamath, Yannick Suter, Mohamed Shelan, Alexander Pllinger, and Mauricio Reyes.  Orchestrating explainable artificial intelligence for multimodal and longitudinal data in medical imaging.  NPJ digital medicine, 7, 195, 2024.
Bibtex-Entry
Dwarikanath Mahapatra, Behzad Bozorgtabar, Zongyuan Ge, and Mauricio Reyes.  GANDALF: Graph-based transformer and Data Augmentation Active Learning Framework with interpretable features for multi-label chest Xray classification.  Medical image analysis, 93, 103075, 2024.
Bibtex-Entry
Dwarikanath Mahapatra, Ruwan Tennakoon, Yasmeen George, Sudipta Roy, Behzad Bozorgtabar, Zongyuan Ge, and Mauricio Reyes.  ALFREDO: Active Learning with FeatuRe disEntangelement and DOmain adaptation for medical image classification.  Medical image analysis, 97, 103261, 2024.
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Dwarikanath Mahapatra, Antonio Jimeno Yepes, Behzad Bozorgtabar, Sudipta Roy, Zongyuan Ge, and Mauricio Reyes.  Multi-Label Generalized Zero Shot Chest Xray Classification By Combining Image-Text Information With Feature Disentanglement.  IEEE Transactions on Medical Imaging, 2024.
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Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, and others.  Metrics reloaded: recommendations for image analysis validation.  Nature methods, 21, 195--212, 2024.
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Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Ntzel, A Emre Kavur, Tim Rdsch, Carole H Sudre, Laura Acion, Michela Antonelli, and others.  Understanding metric-related pitfalls in image analysis validation.  Nature methods, 21, 182--194, 2024.
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Suhang You, Roland Wiest, and Mauricio Reyes.  SaRF: Saliency regularized feature learning improves MRI sequence classification.  Computer methods and programs in biomedicine, 243, 107867, 2024.
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Junlin Yang, John Anderson Garcia Henao, Nicha Dvornek, Jianchun He, Danielle V Bower, Arno Depotter, Herkus Bajercius, Aurlie Pahud de Mortanges, Chenyu You, Christopher Gange, and others.  Prior knowledge-guided vision-transformer-based unsupervised domain adaptation for intubation prediction in lung disease at one week.  Computerized Medical Imaging and Graphics, 102442, 2024.
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Louhai Alwan, Dominik C Benz, Sarah AM Cuddy, Stephan Dobner, Isaac Shiri, Federico Caobelli, Benedikt Bernhard, Simon F Stmpfli, Franz Eberli, Mauricio Reyes, and others.  Current and evolving multimodality cardiac imaging in managing transthyretin amyloid cardiomyopathy.  Cardiovascular Imaging, 17, 195--211, 2024.
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Robert Poel, Amith J Kamath, Jonas Willmann, Nicolaus Andratschke, Ekin Ermi\cs, Daniel M Aebersold, Peter Manser, and Mauricio Reyes.  Deep-Learning-Based Dose Predictor for Glioblastoma--Assessing the Sensitivity and Robustness for Dose Awareness in Contouring.  Cancers, 15, 4226, 2023.
Bibtex-Entry
Aly H Abayazeed, Ahmed Abbassy, Michael Mueller, Michael Hill, Mohamed Qayati, Shady Mohamed, Mahmoud Mekhaimar, Catalina Raymond, Prachi Dubey, Kambiz Nael, Saurabh Rohatgi, Vaishali Kapare, Ashwini Kulkarni, Tina Shiang, Atul Kumar, Nicolaus Andratschke, Jonas Willmann, Alexander Brawanski, Reordan De Jesus, Ibrahim Tuna, Steve H Fung, Joseph C Landolfi, Benjamin M Ellingson, and Mauricio Reyes.  NS-HGlio: A Generalizable and Repeatable HGG Segmentation and Volumetric measurement AI Algorithm for the Longitudinal MRI Assessment to Inform RANO in Trials and Clinics.  Neuro-Oncology Advances, 2023.
https://doi.org/10.1093/noajnl/vdac184 Bibtex-Entry
Yannick Suter, Michelle Notter, Raphael Meier, Tina Loosli, Philippe Schucht, Roland Wiest, Mauricio Reyes, and Urspeter Knecht.  Evaluating automated longitudinal tumor measurements for glioblastoma response assessment.  Frontiers in radiology, 3, 2023.
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Elias Rüfenacht, Amith Kamath, Yannick Suter, Robert Poel, Ekin Ermiş, Stefan Scheib, and Mauricio Reyes.  PyRaDiSe: A Python package for DICOM-RT-based auto-segmentation pipeline construction and DICOM-RT data conversion.  Computer Methods and Programs in Biomedicine, 231, 107374, 2023.
https://www.sciencedirect.com/science/article/pii/S016926072300041X Bibtex-Entry
Beatriz Ocaña-Tienda, Julián Pérez-Beteta, JoséD. Villanueva-García, JoséA. Romero-Rosales, David Molina-García, Yannick Suter, Beatriz Asenjo, David Albillo, Ana Ortiz de Mendivil, Luis A. Pérez-Romasanta, Elisabet González-Del Portillo, Manuel Llorente, Natalia Carballo, Fátima Nagib-Raya, Maria Vidal-Denis, Belén Luque, Mauricio Reyes, Estanislao Arana, and Víctor M. Pérez-García.  A comprehensive dataset of annotated brain metastasis MR images with clinical and radiomic data.  Scientific Data, 10, 208, 2023.
https://doi.org/10.1038/s41597-023-02123-0 Bibtex-Entry
John Anderson Garcia Henao, Arno Depotter, Danielle V Bower, Herkus Bajercius, Plamena Teodosieva Todorova, Hugo Saint-James, Aurélie Pahud de Mortanges, Maria Cecilia Barroso, Jianchun He, Junlin Yang, and others.  A multiclass radiomics method--based WHO severity scale for improving COVID-19 patient assessment and disease characterization from CT scans.  Investigative radiology, 58, 882--893, 2023.
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Mathias Gassner, Javier Barranco Garcia, Stephanie Tanadini-Lang, Fabio Bertoldo, Fabienne Fröhlich, Matthias Guckenberger, Silvia Haueis, Christin Pelzer, Mauricio Reyes, Patrick Schmithausen, and others.  Saliency-enhanced content-based image retrieval for diagnosis support in dermatology consultation: Reader study.  JMIR dermatology, 6, e42129, 2023.
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Michael Rebsamen, Richard McKinley, Piotr Radojewski, Maximilian Pistor, Christoph Friedli, Robert Hoepner, Anke Salmen, Andrew Chan, Mauricio Reyes, Franca Wagner, Wiest Roland, and Rummel Christian.  Reliable brain morphometry from contrast-enhanced T1w-MRI in patients with multiple sclerosis.  Human brain mapping, 44, 970--979, 2023.
Bibtex-Entry
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Acion, Michela Antonelli, and others.  Understanding metric-related pitfalls in image analysis validation.  ArXiv, 2023.
Bibtex-Entry
Yannick Suter, Urspeter Knecht, Waldo Valenzuela, Michelle Notter, Ekkehard Hewer, Philippe Schucht, Roland Wiest, and Mauricio Reyes.  The LUMIERE dataset: Longitudinal Glioblastoma MRI with expert RANO evaluation.  Scientific Data, 9, 768, 2022.
https://doi.org/10.1038/s41597-022-01881-7 Bibtex-Entry
Moritz R. Hernandez Petzsche, Ezequiel de la Rosa, Uta Hanning, Roland Wiest, Waldo Valenzuela, Mauricio Reyes, Maria Meyer, Sook-Lei Liew, Florian Kofler, Ivan Ezhov, David Robben, Alexandre Hutton, Tassilo Friedrich, Teresa Zarth, Johannes Bürkle, The Anh Baran, Björn Menze, Gabriel Broocks, Lukas Meyer, Claus Zimmer, Tobias Boeckh-Behrens, Maria Berndt, Benno Ikenberg, Benedikt Wiestler, and Jan S. Kirschke.  ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset.  Scientific Data, 9, 762, 2022.
https://doi.org/10.1038/s41597-022-01875-5 Bibtex-Entry
Sarthak Pati, Ujjwal Baid, Brandon Edwards, Micah Sheller, Shih-Han Wang, G. Anthony Reina, Patrick Foley, Alexey Gruzdev, Deepthi Karkada, Christos Davatzikos, Chiharu Sako, Satyam Ghodasara, Michel Bilello, Suyash Mohan, Philipp Vollmuth, Gianluca Brugnara, Chandrakanth J. Preetha, Felix Sahm, Klaus Maier-Hein, Maximilian Zenk, Martin Bendszus, Wolfgang Wick, Evan Calabrese, Jeffrey Rudie, Javier Villanueva-Meyer, Soonmee Cha, Madhura Ingalhalikar, Manali Jadhav, Umang Pandey, Jitender Saini, John Garrett, Matthew Larson, Robert Jeraj, Stuart Currie, Russell Frood, Kavi Fatania, Raymond Y. Huang, Ken Chang, Carmen Balaña, Jaume Capellades, Josep Puig, Johannes Trenkler, Josef Pichler, Georg Necker, Andreas Haunschmidt, Stephan Meckel, Gaurav Shukla, Spencer Liem, Gregory S. Alexander, Joseph Lombardo, Joshua D. Palmer, Adam E. Flanders, Adam P. Dicker, Haris I. Sair, Craig K. Jones, Archana Venkataraman, Meirui Jiang, Tiffany Y. So, Cheng Chen, Pheng Ann Heng, Qi Dou, Michal Kozubek, Filip Lux, Jan Michálek, Petr Matula, Miloš Keřkovský, Tereza Kopřivová, Marek Dostál, Václav Vybíhal, Michael A. Vogelbaum, J. Ross Mitchell, Joaquim Farinhas, Joseph A. Maldjian, Chandan Ganesh Bangalore Yogananda, Marco C. Pinho, Divya Reddy, James Holcomb, Benjamin C. Wagner, Benjamin M. Ellingson, Timothy F. Cloughesy, Catalina Raymond, Talia Oughourlian, Akifumi Hagiwara, Chencai Wang, Minh-Son To, Sargam Bhardwaj, Chee Chong, Marc Agzarian, Alexandre Xavier Falcão, Samuel B. Martins, Bernardo C. A. Teixeira, Flávia Sprenger, David Menotti, Diego R. Lucio, Pamela LaMontagne, Daniel Marcus, Benedikt Wiestler, Florian Kofler, Ivan Ezhov, Marie Metz, Rajan Jain, Matthew Lee, Yvonne W. Lui, Richard McKinley, Johannes Slotboom, Piotr Radojewski, Raphael Meier, Roland Wiest, Derrick Murcia, Eric Fu, Rourke Haas, John Thompson, David Ryan Ormond, Chaitra Badve, Andrew E. Sloan, Vachan Vadmal, Kristin Waite, Rivka R. Colen, Linmin Pei, Murat Ak, Ashok Srinivasan, J. Rajiv Bapuraj, Arvind Rao, Nicholas Wang, Ota Yoshiaki, Toshio Moritani, Sevcan Turk, Joonsang Lee, Snehal Prabhudesai, Fanny Morón, Jacob Mandel, Konstantinos Kamnitsas, Ben Glocker, Luke V. M. Dixon, Matthew Williams, Peter Zampakis, Vasileios Panagiotopoulos, Panagiotis Tsiganos, Sotiris Alexiou, Ilias Haliassos, Evangelia I. Zacharaki, Konstantinos Moustakas, Christina Kalogeropoulou, Dimitrios M. Kardamakis, Yoon Seong Choi, Seung-Koo Lee, Jong Hee Chang, Sung Soo Ahn, Bing Luo, Laila Poisson, Ning Wen, Pallavi Tiwari, Ruchika Verma, Rohan Bareja, Ipsa Yadav, Jonathan Chen, Neeraj Kumar, Marion Smits, Sebastian R. van der Voort, Ahmed Alafandi, Fatih Incekara, Maarten M. J. Wijnenga, Georgios Kapsas, Renske Gahrmann, Joost W. Schouten, Hendrikus J. Dubbink, Arnaud J. P. E. Vincent, Martin J. van den Bent, Pim J. French, Stefan Klein, Yading Yuan, Sonam Sharma, Tzu-Chi Tseng, Saba Adabi, Simone P. Niclou, Olivier Keunen, Ann-Christin Hau, Martin Vallières, David Fortin, Martin Lepage, Bennett Landman, Karthik Ramadass, Kaiwen Xu, Silky Chotai, Lola B. Chambless, Akshitkumar Mistry, Reid C. Thompson, Yuriy Gusev, Krithika Bhuvaneshwar, Anousheh Sayah, Camelia Bencheqroun, Anas Belouali, Subha Madhavan, Thomas C. Booth, Alysha Chelliah, Marc Modat, Haris Shuaib, Carmen Dragos, Aly Abayazeed, Kenneth Kolodziej, Michael Hill, Ahmed Abbassy, Shady Gamal, Mahmoud Mekhaimar, Mohamed Qayati, Mauricio Reyes, Ji Eun Park, Jihye Yun, Ho Sung Kim, Abhishek Mahajan, Mark Muzi, Sean Benson, Regina G. H. Beets-Tan, Jonas Teuwen, Alejandro Herrera-Trujillo, Maria Trujillo, William Escobar, Ana Abello, Jose Bernal, Jhon Gómez, Joseph Choi, Stephen Baek, Yusung Kim, Heba Ismael, Bryan Allen, John M. Buatti, Aikaterini Kotrotsou, Hongwei Li, Tobias Weiss, Michael Weller, Andrea Bink, Bertrand Pouymayou, Hassan F. Shaykh, Joel Saltz, Prateek Prasanna, Sampurna Shrestha, Kartik M. Mani, David Payne, Tahsin Kurc, Enrique Pelaez, Heydy Franco-Maldonado, Francis Loayza, Sebastian Quevedo, Pamela Guevara, Esteban Torche, Cristobal Mendoza, Franco Vera, Elvis Ríos, Eduardo López, Sergio A. Velastin, Godwin Ogbole, Mayowa Soneye, Dotun Oyekunle, Olubunmi Odafe-Oyibotha, Babatunde Osobu, Mustapha Shu’aibu, Adeleye Dorcas, Farouk Dako, Amber L. Simpson, Mohammad Hamghalam, Jacob J. Peoples, Ricky Hu, Anh Tran, Danielle Cutler, Fabio Y. Moraes, Michael A. Boss, James Gimpel, Deepak Kattil Veettil, Kendall Schmidt, Brian Bialecki, Sailaja Marella, Cynthia Price, Lisa Cimino, Charles Apgar, Prashant Shah, Bjoern Menze, Jill S. Barnholtz-Sloan, Jason Martin, and Spyridon Bakas.  Federated learning enables big data for rare cancer boundary detection.  Nature Communications, 13, 7346, 2022.
https://doi.org/10.1038/s41467-022-33407-5 Bibtex-Entry
Wilson Silva, Tiago Gonçalves, Kirsi Härmä, Erich Schröder, Verena Carola Obmann, María Cecilia Barroso, Alexander Poellinger, Mauricio Reyes, and Jaime S. Cardoso.  Computer-aided diagnosis through medical image retrieval in radiology.  Scientific Reports, 12, 20732, 2022.
https://doi.org/10.1038/s41598-022-25027-2 Bibtex-Entry
Robert Poel, Elias Rüfenacht, Ekin Ermis, Michael Müller, Michael K Fix, Daniel M Aebersold, Peter Manser, and Mauricio Reyes.  Impact of random outliers in auto-segmented targets on radiotherapy treatment plans for glioblastoma.  Radiation Oncology, 17, 1--18, 2022.
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Dwarikanath Mahapatra, Alexander Poellinger, and Mauricio Reyes.  Graph Node Based Interpretability Guided Sample Selection for Active Learning.  IEEE Transactions on Medical Imaging, 2022.
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Dwarikanath Mahapatra, Alexander Poellinger, and Mauricio Reyes.  Interpretability-Guided Inductive Bias For Deep Learning Based Medical Image.  Medical image analysis, 81, 102551, 2022.
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Sook-Lei Liew, Bethany P Lo, Miranda R Donnelly, Artemis Zavaliangos-Petropulu, Jessica N Jeong, Giuseppe Barisano, Alexandre Hutton, Julia P Simon, Julia M Juliano, Anisha Suri, and others.  A large, curated, open-source stroke neuroimaging dataset to improve lesion segmentation algorithms.  Scientific data, 9, 1--12, 2022.
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Mahapatra D., Zongyuan G., and Reyes M..  Self-Supervised Generalized Zero Shot Learning For Medical Image Classification Using Novel Interpretable Saliency Maps.  IEEE Transactions on Medical Imaging, 1-1, 2022.
https://doi.org/10.1109/TMI.2022.3163232 Bibtex-Entry
Miao Kang, Xiaojun Hu, Weilin Huang, Matthew R. Scott, and Mauricio Reyes.  Dual-stream pyramid registration network.  Medical Image Analysis, 78, 102379, 2022.
https://www.sciencedirect.com/science/article/pii/S1361841522000317 Bibtex-Entry
Michael Rebsamen, Richard McKinley, Piotr Radojewski, Maximilian Pistor, Christoph Friedli, Robert Hoepner, Anke Salmen, Andrew Chan, Mauricio Reyes, Franca Wagner, and others.  Reliable brain morphometry from contrast-enhanced T1w-MRI in patients with multiple sclerosis.  Human brain mapping, 2022.
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Rebsamen M., Radojewski P., McKinley R., Reyes M., Wiest R., and Rummel C..  A Quantitative Imaging Biomarker Supporting Radiological Assessment of Hippocampal Sclerosis Derived From Deep Learning-Based Segmentation of T1w-MRI.  Frontiers in Neurology, 13, 2022.
https://www.frontiersin.org/article/10.3389/fneur.2022.812432 Bibtex-Entry
Poel R., Rufenacht E., Herrmann E., Scheib S., Manser P., Aebersold D., and Reyes M..  The predictive value of segmentation metrics on dosimetry in organs at risk of the brain.  Medical Image Analysis, 73, 102161, 2021.
https://www.sciencedirect.com/science/article/pii/S1361841521002073 Bibtex-Entry
Mahapatra D., Pollinger A., Shao L., and Reyes M..  Interpretability-Driven Sample Selection Using Self Supervised Learning For Disease Classification And Segmentation..  IEEE Trans Med Imaging, PP, 2021.
https://doi.org/10.1109/TMI.2021.3061724 Bibtex-Entry
Pinto A., Pereira S., Meier R., Wiest R., Alves V., Reyes M., and Silva C..  Combining unsupervised and supervised learning for predicting the final stroke lesion.  Medical Image Analysis, 69, 101888, 2021.
https://www.sciencedirect.com/science/article/pii/S1361841520302528 Bibtex-Entry
Pinto A., Amorim J., Hakim A., Alves V., Reyes M., and Silva C..  Prediction of Stroke Lesion at 90-Day Follow-Up by Fusing Raw DSC-MRI With Parametric Maps Using Deep Learning.  IEEE Access, 9, 26260-26270, 2021.
https://doi.org/10.1109/ACCESS.2021.3058297 Bibtex-Entry
Amorim J., Abreu H., and Fernández A., Reyes M., Santos J., and Abreu M..  Interpreting Deep Machine Learning Models: An Easy Guide for Oncologists.  IEEE Reviews in Biomedical Engineering, 1-1, 2021.
https://doi.org/10.1109/RBME.2021.3131358 Bibtex-Entry
Arsany Hakim, Søren Christensen, Stefan Winzeck, Maarten G Lansberg, Mark W Parsons, Christian Lucas, David Robben, Roland Wiest, Mauricio Reyes, and Greg Zaharchuk.  Predicting Infarct Core From Computed Tomography Perfusion in Acute Ischemia With Machine Learning: Lessons From the ISLES Challenge.  Stroke, STROKEAHA--120, 2021.
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Richard McKinley, Rik Wepfer, Fabian Aschwanden, Lorenz Grunder, Raphaela Muri, Christian Rummel, Rajeev Verma, Christian Weisstanner, Mauricio Reyes, Anke Salmen, Andrew Chan, Franca Wagner, and Roland Wiest.  Simultaneous lesion and brain segmentation in multiple sclerosis using deep neural networks.  Scientific Reports, 11, 1087, 2021.
https://doi.org/10.1038/s41598-020-79925-4 Bibtex-Entry
Georgios S. Ioannidis, Søren Christensen, Katerina Nikiforaki, Eleftherios Trivizakis, Kostas Perisinakis, Adam Hatzidakis, Apostolos Karantanas, Mauricio Reyes, Maarten Lansberg, and Kostas Marias.  Cerebral CT Perfusion in Acute Stroke: The Effect of Lowering the Tube Load and Sampling Rate on the Reproducibility of Parametric Maps.  Diagnostics, 11, 2021.
https://www.mdpi.com/2075-4418/11/6/1121 Bibtex-Entry
Jungo A., Scheidegger O., Reyes M., and Balsiger F..  pymia: A Python package for data handling and evaluation in deep learning-based medical image analysis.  Computer Methods and Programs in Biomedicine, 198, 105796, 2021.
https://www.sciencedirect.com/science/article/pii/S0169260720316291 Bibtex-Entry
Balsiger F., Jungo A., Scheidegger O., Carlier P., Reyes M., and Marty B..  Spatially Regularized Parametric Map Reconstruction for Fast Magnetic Resonance Fingerprinting.  Medical Image Analysis, 64, 101741, 2020.
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Suter Y., Knecht U., Alao M., Valenzuela W., Hewer E., Schucht P., Wiest R., and Reyes M..  Radiomics for Glioblastoma Survival Analysis in Pre-operative MRI: Exploring Feature Robustness, Class Boundaries, and Machine Learning Techniques.  Cancer Imaging, 20, 1--13, 2020.
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Zongxin-Jin B., De Stefano P., Petroulia V., Rummel C., Kiefer C., Reyes M., Schindler K., van Mierlo P., Seeck M., and Wiest R..  Diagnosis of epilepsy after first seizure. Introducing the SWISS FIRST study.  Clinical and Translational Neuroscience, 4, 2514183X20939448, 2020.
https://doi.org/10.1177/2514183X20939448 Bibtex-Entry
Ermis E., Jungo A., Poel R., Blatti-Moreno M., Meier R., Knecht U., Aebersold D., Fix M., Manser P., Reyes M., and Herrmann E..  Fully automated brain resection cavity delineation for radiation target volume definition in glioblastoma patients using deep learning.  Radiation oncology, 15, 1--10, 2020.
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Hu X., Luo W., Hu J., Guo S., Huang W., Scott M., Wiest R., Dahlweid M., and Reyes M..  Brain SegNet: 3D local refinement network for brain lesion segmentation.  BMC Medical Imaging, 20, 17, 2020.
https://doi.org/10.1186/s12880-020-0409-2 Bibtex-Entry
Jungo A., Balsiger F., and Reyes M..  Analyzing the Quality and Challenges of Uncertainty Estimations for Brain Tumor Segmentation.  Frontiers in Neuroscience, 14, 282, 2020.
https://www.frontiersin.org/article/10.3389/fnins.2020.00282 Bibtex-Entry
McKinley R., Wepfer R., Grunder L., Aschwanden F., Fischer T., Friedli C., Muri R., Rummel C., Verma R.K., Weisstanner C., Wiestler B., Berger C., Eichinger P., Muhlau M., Reyes M., Salmen A., Chan A., Wiest R., and Wagner F.  Automatic detection of lesion load change in Multiple Sclerosis using convolutional neural networks with segmentation confidence.  NeuroImage: Clinical, 25, 102104, 2020.
http://www.sciencedirect.com/science/article/pii/S2213158219304516 Bibtex-Entry
Menze B., Isensee F., Wiest R., Wiestler B., Maier-Hein K., Reyes M., and Bakas S..  Analyzing Magnetic Resonance Imaging Data from Glioma Patients using Deep Learning.  Computerized Medical Imaging and Graphics, 101828, 2020.
http://www.sciencedirect.com/science/article/pii/S0895611120301233 Bibtex-Entry
Rebsamen M., Suter Y., Wiest R., Reyes M., and Rummel C..  Brain Morphometry Estimation: From Hours to Seconds Using Deep Learning.  Frontiers in Neurology, 11, 244, 2020.
https://www.frontiersin.org/article/10.3389/fneur.2020.00244 Bibtex-Entry
Rebsamen M., Rummel C., Reyes M., Wiest R., and McKinley R..  Direct cortical thickness estimation using deep learning-based anatomy segmentation and cortex parcellation.  Human brain mapping, 41, 4804--4814, 2020.
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Reyes M., Meier R., Pereira S., Silva C., Dahlweid FM., von Teng-Kobligk H., Summers R., and Wiest R..  On the Interpretability of Artificial Intelligence in Radiology: Challenges and Opportunities.  Radiology: Artificial Intelligence, 2, e190043, 2020.
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Meier R., Lux P., Jung S., Fischer U., Gralla J., Reyes M., Wiest R., McKinley R., and Kaesmacher J..  Neural Network--derived Perfusion Maps for the Assessment of Lesions in Patients with Acute Ischemic Stroke.  Radiology: Artificial Intelligence, 1, e190019, 2019.
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Behzad Bozorgtabar, Dwarikanath Mahapatra, Hendrik von Teng, Alexander Pollinger, Lukas Ebner, Jean-Phillipe Thiran, and Mauricio Reyes.  Informative sample generation using class aware generative adversarial networks for classification of chest Xrays.  Computer Vision and Image Understanding, 184, 57--65, 2019.
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Barros N., Meier R., Pletscher M., Stettler S., Knecht U., Reyes M., Gralla J., Wiest R., and Slotboom J..  Analysis of metabolic abnormalities in high-grade glioma using MRSI and convex NMF.  NMR in Biomedicine, 32, e4109, 2019.
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Chandran V., Maquer G., Gerig T., Zysset P., and Reyes M..  Supervised learning for bone shape and cortical thickness estimation from CT images for finite element analysis.  Medical Image Analysis, 52, 42 - 55, 2019.
http://www.sciencedirect.com/science/article/pii/S1361841518308612 Bibtex-Entry
Pinto A., Mckinley R., Alves V., Wiest R., Silva C., and Reyes M..  Stroke Lesion Outcome Prediction Based on MRI Imaging Combined With Clinical Information.  Frontiers in Neurology, 9, 1060, 2018.
https://www.frontiersin.org/article/10.3389/fneur.2018.01060 Bibtex-Entry
Balsiger F., Steindel C., Arn M., Wagner B., Grunder L., El-Koussy M., Valenzuela W., Reyes M., and Scheidegger O..  Segmentation of Peripheral Nerves From Magnetic Resonance Neurography: A Fully-Automatic, Deep Learning-Based Approach.  Frontiers in Neurology, 9, 777, 2018.
https://www.frontiersin.org/article/10.3389/fneur.2018.00777 Bibtex-Entry
Habegger S., Wiest R., Weder B., Mordasini P., Gralla J., Haeni L., Jung S., Reyes M., and McKinley R..  Relating Acute Lesion Loads to Chronic Outcome in Ischemic Stroke‚ÄìAn Exploratory Comparison of Mismatch Patterns and Predictive Modeling.  Frontiers in Neurology, 9, 737, 2018.
https://www.frontiersin.org/article/10.3389/fneur.2018.00737 Bibtex-Entry
Winzeck S., Hakim A., McKinley R., Pinto J., Alves V., Silva C., Pisov M., Krivov E., Belyaev M., Monteiro M., Oliveira A., Choi Y., Paik M., Kwon Y., Lee H., Kim B., Won J-H, Islam M., Ren H., Robben D., Suetens P., Gong E., Niu Y., Xu J., Pauly J., Lucas C., Heinrich M., Rivera L., Castillo L., Daza L., Beers A., Arbelaezs P., Maier O., Chang K., Brown J., Kalpathy-Cramer J., Zaharchuk G., Wiest R., and Reyes M..  ISLES 2016 and 2017-Benchmarking Ischemic Stroke Lesion Outcome Prediction Based on Multispectral MRI.  Frontiers in Neurology, 9, 679, 2018.
https://www.frontiersin.org/article/10.3389/fneur.2018.00679 Bibtex-Entry
Pereira S., Meier R., McKinley R., Wiest R., Alves V., Silva C., and Reyes M..  Enhancing interpretability of automatically extracted machine learning features: application to a RBM-Random Forest system on brain lesion segmentation..  Med Image Anal, 44, 228--244, 2018.
https://dx.doi.org/10.1016/j.media.2017.12.009 Bibtex-Entry
Barros N., Meier R., Pletscher M., Stettler S., Knecht U., Herrmann E., Schucht P., Reyes M., Gralla J., Wiest R., and Slotboom J..  On the relation between MR spectroscopy features and the distance to MRI-visible solid tumor in GBM patients..  Magn Reson Med, 2018.
https://doi.org/10.1002/mrm.27359 Bibtex-Entry
Vimal Chandran, Mauricio Reyes, and Philippe Zysset.  A novel registration-based methodology for prediction of trabecular bone fabric from clinical QCT: A comprehensive analysis.  PLOS ONE, 12, 1-23, 2017.
https://doi.org/10.1371/journal.pone.0187874 Bibtex-Entry
Kellner-Weldon F., Stippich C., Wiest R., Lehmann V., Meier R., Beck J., Schucht P., Raabe A., Reyes M., and Bink A..  Comparison of perioperative automated versus manual two-dimensional tumor analysis in glioblastoma patients..  Eur J Radiol, 95, 75--81, 2017.
http://dx.doi.org/10.1016/j.ejrad.2017.07.028 Bibtex-Entry
Gerber N., Reyes M., Barazzetti L., Kjer H., Vera S., Stauber M., Mistrik P., Ceresa M., Mangado N., Wimmer W., Stark T., Paulsen R., Weber S., Caversaccio M., and Ballester-Gonzalez M..  A multiscale imaging and modelling dataset of the human inner ear.  Nature Scientific Data, 4, 170132 EP -, 2017.
http://dx.doi.org/10.1038/sdata.2017.132 Bibtex-Entry
McKinley R., Haeni L., Gralla J., El-Koussy M., Bauer S., Arnold M., Fischer U., Jung S., Mattmann K., Reyes M., and Wiest R..  Fully automated stroke tissue estimation using random forest classifiers (FASTER).  Journal of Cerebral Blood Flow and Metabolism, 37, 2728-2741, 2017.
http://jcb.sagepub.com/content/early/2016/10/18/0271678X16674221.abstract Bibtex-Entry
Lu P., Barazzetti L., Chandran V., Gavaghan K., Weber S., Gerber N., and Reyes M..  Highly accurate Facial Nerve Segmentation Refinement from CBCT/CT Imaging using a Super Resolution Classification Approach.  IEEE Transactions on Biomedical Engineering, PPs, 1-1, 2017.
http://dx.doi.org/10.1109/TBME.2017.2697916 Bibtex-Entry
Meier R., Porz N., Knecht U., Loosli T., Schucht P., Beck J., Slotboom J., Wiest R., and Reyes M..  Automatic estimation of extent of resection and residual tumor volume of patients with glioblastoma.  Journal of Neurosurgery, 1--9, 2017.
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Porz N., Habegger S., Meier R., Verma R.K., Jilch A., Fichtner J., Knecht U., Radina C., Schucht P., Jürgen B., Raabe A., Slotboom J., Reyes M., and Wiest R..  Fully Automated Enhanced Tumor Compartmentalization: Man vs. Machine Reloaded.  PLoS ONE, 11, 1-16, 2016.
http://dx.doi.org/10.1371%2Fjournal.pone.0165302 Bibtex-Entry
Meier R., Knecht U., Loosli T., Bauer S., Slotboom J., Wiest R., and Reyes M..  Clinical Evaluation of a Fully-automatic Segmentation Method for Longitudinal Brain Tumor Volumetry.  Nature Scientific Reports, 6, 2016.
http://dx.doi.org/10.1038/srep23376 Bibtex-Entry
Oskar Maier, Bjoern H Menze, Janina von der Gablentz, Levin H\"ani, Mattias P Heinrich, Matthias Liebrand, Stefan Winzeck, Abdul Basit, Paul Bentley, Liang Chen, Daan Christiaens, Francis Dutil, Karl Egger, Chaolu Feng, Ben Glocker, Michael G\"otz, Tom Haeck, Hanna-Leena Halme, Mohammad Havaei, Khan M Iftekharuddin, Pierre-Marc Jodoin, Konstantinos Kamnitsas, Elias Kellner, Antti Korvenoja, Hugo Larochelle, Christian Ledig, Jia-Hong Lee, Frederik Maes, Qaiser Mahmood, Klaus H Maier-Hein, Richard McKinley, John Muschelli, Chris Pal, Linmin Pei, Janaki Raman Rangarajan, Syed M S Reza, David Robben, Daniel Rueckert, Eero Salli, Paul Suetens, Ching-Wei Wang, Matthias Wilms, Jan S Kirschke, Ulrike M Kr\"amer, Thomas F M\"unte, Peter Schramm, Roland Wiest, Heinz Handels, and Mauricio Reyes.  ISLES 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral MRI.  Medical Image Analysis, 35, 250--269, 2016.
http://dx.doi.org/10.1016/j.media.2016.07.009 Bibtex-Entry
McKinley R., Haeni L., Gralla J., El-Koussy M., Bauer S., Arnold M., Fischer U., Jung S., Mattmann K., Reyes M., and Wiest R..  Fully automated stroke tissue estimation using random forest classifiers (FASTER).  Journal of Cerebral Blood Flow & Metabolism, 2016.
http://jcb.sagepub.com/content/early/2016/10/18/0271678X16674221.abstract Bibtex-Entry
Valenzuela W., Ferguson S., Ignasiak D., Diserens G., Haeni L., Wiest R., Vermathen P., Boesch C., and Reyes M..  FISICO: Fast Image SegmentatIon COrrection.  PLoS ONE, 11, 1-17, 2016.
http://dx.doi.org/10.1371%2Fjournal.pone.0156035 Bibtex-Entry
Seif M., Mani L., Lu H., Boesch C., Reyes M., Vogt B., and Vermathen P..  Diffusion tensor imaging of the human kidney: Does image registration permit scanning without respiratory triggering?.  J Magn Reson Imaging, 2016.
http://dx.doi.org/10.1002/jmri.25176 Bibtex-Entry
Taghizadeh E., Reyes M., Zysset P., Latypova A., Terrier A., and Buchler P..  Biomechanical Role of Bone Anisotropy Estimated on Clinical CT Scans by Image Registration..  Ann Biomed Eng, 2016.
http://dx.doi.org/10.1007/s10439-016-1551-4 Bibtex-Entry
Rios-Velazquez E., Meier R., Dunn W., Alexander B., Wiest R., Bauer S., Gutmann D., Reyes M., and Aerts H..  Fully automatic GBM segmentation in the TCGA-GBM dataset: Prognosis and correlation with VASARI features.  Nature Scientific Reports, 5, 2015.
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Menze B., Reyes M., and Van Leemput K..  The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)..  IEEE Trans Med Imaging, 34, 2015.
http://dx.doi.org/10.1109/TMI.2014.2377694 Bibtex-Entry
Cerrolaza J.J., Reyes M., Summers R.M., González-Ballester M.A., and Linguraru M.G..  Automatic multi-resolution shape modeling of multi-organ structures.  Medical Image Analysis, 25, 11-21, 2015.
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V. Chappuis, O. Engel, K. Shahim, M. Reyes, C. Katsaros, and D. Buser.  Soft Tissue Alterations in Esthetic Postextraction Sites: A 3-Dimensional Analysis.  Journal of Dental Research, 94, 187S-193S, 2015.
http://dx.doi.org/10.1177/0022034515592869 Bibtex-Entry
Seif M., Lu H., Boesch C., Reyes M., and Vermathen P..  Image registration for triggered and non-triggered DTI of the human kidney: Reduced variability of diffusion parameter estimation..  J Magn Reson Imaging, 41, 1228-1235, 2014.
http://dx.doi.org/10.1002/jmri.24671 Bibtex-Entry
Porz N., Bauer S., Pica A., Schucht P., Beck J., Verma R.K., Slotboom J., Reyes M., and Wiest R..  Multi-Modal Glioblastoma Segmentation: Man versus Machine.  PLoS ONE, 9, e96873, 2014.
http://dx.doi.org/10.1371%2Fjournal.pone.0096873 Bibtex-Entry
Bonaretti S., Seiler C., Boichon C., Reyes M., and Buechler P..  Image-based vs. mesh-based statistical appearance models of the human femur: Implications for finite element simulations.  Medical Engineering \& Physics, 36, 1626 - 1635, 2014.
http://dx.doi.org/10.1016/j.medengphy.2014.09.006 Bibtex-Entry
Bou-Sleiman H., Paul L., Nolte L.P., and Reyes M..  Comparative Evaluation of Pelvic Allograft Selection Methods..  Annals of Biomedical Engineering, 41, 931-938, 2013.
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Oliveira-Santos T., Baumberger C., Constantinescu M., Olariu R., Nolte L.P., Alaraibi S., and Reyes M..  3D Face Reconstruction from 2D Pictures: First Results of a Web-Based Computer Aided System for Aesthetic Procedures..  Annals of Biomedical Engineering, 41, 952--966, 2013.
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Lu H., Beisteiner R., Nolte L.P., and Reyes M..  Hierarchical segmentation-assisted multimodal registration for MR brain images.  Computerized Medical Imaging and Graphics, 37, 234--244, 2013.
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Bauer S., Lu H., May C., Nolte L.P., Buechler P., and Reyes M..  Integrated Segmentation of Brain Tumor Images for Radiotherapy and Neurosurgery.  International Journal of Imaging Systems and Technology, 23, 59--63, 2013.
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Bou Sleiman H., Iizuka T., Nolte L.P., and Reyes M..  Population-Based Design of Mandibular Fixation Plates with Bone Quality and Morphology Considerations.  Annals of Biomedical Engineering, 41, 377--384, 2013.
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Bauer S., Wiest R., Nolte L.P., and Reyes M..  A survey of MRI-based medical image analysis for brain tumor studies.  Physics in Medicine and Biology, 58, R97, 2013.
http://stacks.iop.org/0031-9155/58/i=13/a=R97 Bibtex-Entry
Chappuis V., Engel O., Reyes. M., Shahim K., Nolte L.P., and Buser D..  Ridge Alterations Post-extraction in the Esthetic Zone A 3D Analysis with CBCT.  Journal of Dental Research, 92, 195S--201S, 2013.
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Kim B.R., Oh K.M., Cevidanes L.H.S., Park J.E., Sim H.S., Seo S.K., Reyes M., Kim Y.J., and Park Y.H..  Analysis of 3D Soft Tissue Changes After 1-and 2-Jaw Orthognathic Surgery in Mandibular Prognathism Patients.  Journal of Oral and Maxillofacial Surgery, 71, 151--161, 2013.
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Seiler C., Pennec X., Nolte L.P., and Reyes M..  Capturing the Multiscale Anatomical Shape Variability with Polyaffine Transformation Trees.  Medical Image Analysis, 16, 1371-1384, 2012.
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Bauer S., Ritacco L.E., Boesch C., Nolte L.P., and Reyes M..  Automatic Scan Planning for Magnetic Resonance Imaging of the Knee Joint.  Annals of Biomedical Engineering, 40, 2033-2042, 2012.
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Blanc R., Seiler C., Székely G., Nolte L.P., and Reyes M..  Statistical Model Based Shape Prediction from a Combination of Direct Observations and Various Surrogates. Application to Orthopaedic Research.  Medical Image Analysis, 16, 1156-1166, 2012.
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Seiler C., Gazdhar A., Reyes M., Benneker L.M., Geiser T., Siebenrock K.A., and Gantenbein-Ritter B..  Time-Lapse Microscopy and Classification of 2D Human Mesenchymal Stem Cells Based on Cell Shape Picks Up Myogenic from Osteogenic and Adipogenic Differentiation.  Journal of Tissue Engineering and Regenerative Medicine, In Press, 2012.
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Ritacco L.E., Seiler C., Farfalli G.L., Nolte L., Reyes M., Muscolo D.L., and Tinao L.A..  Validity of an automatic measure protocol in distal femur for allograft selection from a three-dimensional virtual bone bank system..  Cell Tissue Bank, 1, 1--8, 2012.
http://dx.doi.org/10.1007/s10561-012-9307-3 Bibtex-Entry
de Heras Ciechomski P., Constantinescu M., Garcia J., Olariu R., Dindoyal I., Le Huu S., and Reyes M..  Development and Implementation of a Web-Enabled 3D Consultation Tool for Breast Augmentation Surgery Based on 3D-Image Reconstruction of 2D Pictures.  Journal of Medical Internet Research, 14, e21, 2012.
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Lu H., Nolte L.P., and Reyes M..  Interest points localization for brain image using landmark-annotated atlas.  International Journal of Imaging Systems and Technology, 22, 145--152, 2012.
http://dx.doi.org/10.1002/ima.22015 Bibtex-Entry
Schulz A.P, Reimers N. Nils, Wipf F., Vallotton M., Bonaretti S., Kozic N., Reyes M., and Kienast B.J..  Evidence Based Development of a Novel Lateral Fibula Plate (VariAx Fibula) Using a Real CT Bone Data Based Optimization Process During Device Development..  Open Orthop J, 6, 1--7, 2012.
http://dx.doi.org/10.2174/1874325001206010001 Bibtex-Entry
Kim Y.J., Oh K.M., Hong J.S., Lee J.H., Kim H.M., Reyes M., Cevidanes L.H.S., and Park Y.H..  Do Patients Treated With Bimaxillary Surgery Have More Stable Condylar Positions Than Those Who Have Undergone Single-Jaw Surgery?.  Journal of Oral and Maxillofacial Surgery, 70, 2143--52, 2011.
http://dx.doi.org/10.1016/j.joms.2011.08.028 Bibtex-Entry
Bauer S., May C., Dionysiou D., Stamatakos G., Buechler P., and Reyes M..  Multi-Scale Modeling for Image Analysis of Brain Tumor Studies..  IEEE Trans Biomed Eng, 59, 25--29, 2011.
http://dx.doi.org/10.1109/TBME.2011.2163406 Bibtex-Entry
Jürgens P., Klug C., Krol Z., Beinemann J., Kim H., Reyes M., Guevara-Rojas G., Zeilhofer H. F, Ewers R., and Schicho K..  Navigation-Guided Harvesting of Autologous Iliac Crest Graft for Mandibular Reconstruction.  J Oral Maxillofac Surg, 69, 2915--2923, 2011.
http://dx.doi.org/10.1016/j.joms.2010.12.045 Bibtex-Entry
Bou Sleiman H., Ritacco L.E., Aponte-Tinao L., Muscolo D.L., Nolte L.P., and Reyes M..  Allograft Selection for Transepiphyseal Tumor Resection Around the Knee Using Three-Dimensional Surface Registration.  Annals of Biomedical Engineering, 39, 1720--7, 2011.
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Marias K., Dionysiou D., Sakkalis V., Graf N., Bohle RM, Coveney PV, Wan S., Folarin A., Büchler P., Reyes M., and others.  Clinically driven design of multi-scale cancer models: the ContraCancrum project paradigm.  Interface Focus, 1, 450--461, 2011.
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Kim H., Jürgens P., Weber S., Nolte L.P., and Reyes M.  A New Soft-Tissue Simulation Strategy for Cranio-Maxillofacial Surgery Using Facial Muscle Template Model.  Progress in Biophysics and Molecular Biology. Special Issue on Soft Tissue Modelling, 103, 284--291, 2010.
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Tucker S., Cevidanes L., Styner M., Kim H., Reyes M., Proffit W., and Turvey T..  Comparison of actual surgical outcomes and 3-dimensional surgical simulations..  J Oral Maxillofac Surg, 68, 2412--2421, 2010.
http://dx.doi.org/10.1016/j.joms.2009.09.058 Bibtex-Entry
Kozic N., Weber S., Büchler P., Lutz C., Reimers N., González Ballester MA., and Reyes M..  Optimisation of orthopaedic implant design using statistical shape space analysis based on level sets.  Medical Image Analysis, 14, 265--275, 2010.
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Cevidanes L., Tucker S., Styner M., Kim H., Chapuis J., Reyes M., Proffit W., Turvey T., and Jaskolka M..  Three-dimensional surgical simulation.  American Journal of Orthodontics and Dentofacial Orthopedics, 138, 361 - 371, 2010.
http://dx.doi.org/10.1016/j.ajodo.2009.08.026 Bibtex-Entry
Kozic N., Weber S., González-Ballester M.A., Abdo G., Rufenacht D.A., Ferguson S., and Reyes M..  Automated cement segmentation in vertebroplasty..  Comput Aided Surg, 15, 49--55, 2010.
http://dx.doi.org/10.3109/10929088.2010.496176 Bibtex-Entry
Reyes M., Malandain G., Koulibaly P.M., González-Ballester M.A., and Darcourt J..  Model-based respiratory motion compensation for emission tomography image reconstruction.  Physics in Medicine and Biology, 52, 3579-3600, 2007.
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Linguraru M.G., Vercauteren T., Reyes M., González-Ballester M.A., and Ayache N..  Segmentation propagation from deformable atlases for brain mapping and analysis.  Brain Research Journal, 1, 269-287, 2007.
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Reyes M., González-Ballester M.A., and Linguraru M.G..  Statistical Bone Shape Analysis for Image Free Surgery.  Acta Universitatis Cibiniensis, Technical Series, Vol, LV, 121-129, 2007.
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Malandain G. and Reyes M..  La tomographie en mouvement.  Pour la science, 338, 132-137, 2005.
http://www.pourlascience.fr/ewb_pages/f/fiche-article-la-tomographie-en-mouvement-20411.php Bibtex-Entry
Reyes M. and Pereda J..  Reconstrucción Virtual de la Mano de un Embrión Humano, Evaluación Experimental.  Teoría y Metodologías. Clínica y Ciencia magazine, 1, 2001.
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Peer-reviewed Conference Articles

 

Amith Kamath, Zahira Mercado Auf der Maur, Robert Poel, Jonas Willmann, Ekin Ermis, Elena Riggenbach, Nicolaus Andratschke, and Mauricio Reyes.  Comparing the Performance of Radiation Oncologists versus a Deep Learning Dose Predictor to Estimate Dosimetric Impact of Segmentation Variations for Radiotherapy.  Medical Imaging with Deep Learning, 2024.
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Dwarikanath Mahapatra, Behzad Bozorgtabar, Zongyuan Ge, Mauricio Reyes, and Jean-Philippe Thiran.  Combining Graph Transformers Based Multi-Label Active Learning and Informative Data Augmentation for Chest Xray Classification.  Proceedings of the AAAI Conference on Artificial Intelligence, 38, 21378--21386, 2024.
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Haozhe Luo, Aurlie Pahud de Mortanges, Oana Inel, and Mauricio Reyes.  Dwarf: Disease-weighted network for attention map refinement.  iMIMIC , 311, 2024.
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Zahira Mercado, Amith Kamath, Robert Poel, Jonas Willmann, Ekin Ermis, Elena Riggenbach, Lucas Mose, Nicolaus Andratschke, and Mauricio Reyes.  AutoDoseRank: Automated Dosimetry-Informed Segmentation Ranking for Radiotherapy.  MICCAI Workshop on Cancer Prevention through Early Detection, 221--230, 2024.
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Shelley Zixin Shu, Aurlie Pahud de Mortanges, Alexander Poellinger, Dwarikanath Mahapatra, and Mauricio Reyes.  INFORMER-Interpretability Founded Monitoring of Medical Image Deep Learning Models.  International Workshop on Uncertainty for Safe Utilization of Machine Learning in Medical Imaging, 215--224, 2024.
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Amith Kamath, Jonas Willmann, Nicolaus Andratschke, and Mauricio Reyes.  Do We Really Need that Skip-Connection? Understanding Its Interplay with Task Complexity.  International Conference on Medical Image Computing and Computer-Assisted Intervention, 302--311, 2023.
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Elias Rüfenacht, Robert Poel, Amith Kamath, Ekin Ermis, Stefan Scheib, Michael K Fix, and Mauricio Reyes.  Dose Guidance for Radiotherapy-oriented Deep Learning Segmentation.  International Conference on Medical Image Computing and Computer-Assisted Intervention, 525--534, 2023.
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Dwarikanath Mahapatra, Antonio Jose Jimeno Yepes, Shiba Kuanar, Sudipta Roy, Behzad Bozorgtabar, Mauricio Reyes, and Zongyuan Ge.  Class Specific Feature Disentanglement and Text Embeddings for Multi-label Generalized Zero Shot CXR Classification.  International Conference on Medical Image Computing and Computer-Assisted Intervention, 276--286, 2023.
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Dwarikanath Mahapatra, Behzad Bozorgtabar, and Mauricio Reyes.  Medical Image Super Resolution by Preserving Interpretable and Disentangled Features.  Computer Vision--ECCV 2022 Workshops: Tel Aviv, Israel, October 23--27, 2022, Proceedings, Part VII, 709--721, 2023.
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Amith Kamath, Robert Poel, Jonas Willmann, Nicolaus Andratschke, and Mauricio Reyes.  How Sensitive Are Deep Learning Based Radiotherapy Dose Prediction Models To Variability In Organs At Risk Segmentation?.  2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), 1--4, 2023.
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Amith Kamath, Robert Poel, Jonas Willmann, Ekin Ermis, Nicolaus Andratschke, and Mauricio Reyes.  ASTRA: Atomic Surface Transformations for Radiotherapy Quality Assurance.  Proceedings of the International Conference of the IEEE Engineering in Medicine and Biology Society, Sydney, Australia, 24--27, 2023.
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Suhang You, Devavrat Tomar, Behzad Bozorgtabar, and Mauricio Reyes.  Sagtta: saliency guided test time augmentation for medical image segmentation across vendor domain shift.  2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), 1--4, 2023.
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Rudy Rizzo, Martyna Dziadosz, Sreenath P Kyathanahally, Mauricio Reyes, and Roland Kreis.  Reliability of Quantification Estimates in MR Spectroscopy: CNNs vs Traditional Model Fitting.  International Conference on Medical Image Computing and Computer-Assisted Intervention, 715--724, 2022.
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Annika Reinke, Lena Maier-Hein, Evangelia Christodoulou, Ben Glocker, Patrick Scholz, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael Alexander Riegler, and others.  Metrics Reloaded-A new recommendation framework for biomedical image analysis validation.  Medical Imaging with Deep Learning, 2022.
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Daniel Abler, Vincent Andrearczyk, Valentin Oreiller, Javier Barranco Garcia, Diem Vuong, Stephanie Tanadini-Lang, Matthias Guckenberger, Mauricio Reyes, and Adrien Depeursinge.  Comparison of MR Preprocessing Strategies and Sequences for Radiomics-Based MGMT Prediction.  International MICCAI Brainlesion Workshop, 367--380, 2022.
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Jean Pablo Vieira de Mello, Thiago M. Paixão, Rodrigo Berriel, Mauricio Reyes, Claudine Badue, Alberto F. De Souza, and Thiago Oliveira-Santos.  Deep Learning-based Type Identification of Volumetric MRI Sequences.  2020 25th International Conference on Pattern Recognition (ICPR), 1-8, 2021.
https://doi.org/10.1109/ICPR48806.2021.9413120 Bibtex-Entry
Annika Reinke, Matthias Eisenmann, Minu D Tizabi, Carole H Sudre, Tim Rädsch, Michela Antonelli, Tal Arbel, Spyridon Bakas, M Jorge Cardoso, Veronika Cheplygina, and others.  Common limitations of image processing metrics: A picture story.  Medical Imaging with Deep Learning (MIDL), 2021.
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Silva W., Cardoso J., and Reyes M..  Interpretability-guided Content-based Medical Image Retrieval.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2020, In Press, 2020.
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Fabian Balsiger, Yannick Soom, Olivier Scheidegger, and Mauricio Reyes.  Learning Shape Representation on Sparse Point Clouds for Volumetric Image Segmentation.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2019, In Press, 2019.
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Fabian Balsiger, Olivier Scheidegger, Pierre G Carlier, Benjamin Marty, and Mauricio Reyes.  On the Spatial and Temporal Influence for the Reconstruction of Magnetic Resonance Fingerprinting.  International Conference on Medical Imaging with Deep Learning, 27--38, 2019.
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Jungo A. and Reyes M..  Assessing Reliability and Challenges of Uncertainty Estimations for Medical Image Segmentation.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2019, Lecture Notes in Computer Science, In Press, 2019.
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Hu X., Kang M., Huang W., Wiest R., Scott M., and Reyes M..  Dual-Stream Pyramid Registration Network.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2019, In Press, 2019.
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Jungo A., Meier R., Ermis E., Blatti-Moreno M., Herrmann E., Wiest R., and Reyes M..  On the Effect of Inter-observer Variability for a Reliable Estimation of Uncertainty of Medical Image Segmentation.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2018, Lecture Notes in Computer Science, In Press, 2018.
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Dwarikanath M., Bozorgtabar S., Thiran J.P., and Reyes M..  Efficient Active Learning for Image Classification and Segmentation using a Sample Selection and Conditional Generative Adversarial Network.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2018, Lecture Notes in Computer Science, In Press, 2018.
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Pinto A., Pereira S., Meier R., Alves V., Wiest R., Silva C., and Reyes M..  Enhancing clinical MRI Perfusion maps with data-driven maps of complementary nature for lesion outcome prediction.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2018, Lecture Notes in Computer Science, In Press, 2018.
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Suter Y., Rummel C., Wiest R., and Reyes M..  Fast and Uncertainty-Aware Cerebral Cortex Morphometry Estimation Using Random Forest Regression.  ISBI 2018: Proceedings of the 2018 IEEE international conference on Biomedical imaging, In Press, 2018.
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Jungo A., Meier R., Ermis E., Herrmann E., and Reyes M..  Uncertainty-driven Sanity Check: Application to Postoperative Brain Tumor Cavity Segmentation.  1st Conference on Medical Imaging with Deep Learning (MIDL 2018), In Press, 2018.
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Shokiche C., Baumann P., Ruslan H., Djonov V., and Reyes M..  High-Throughput Glomeruli Analysis of micro-CT Kidney Images Using Tree Priors and Scalable Sparse Computation.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2016: 19th International Conference, Athens, Greece, October 17-21, 2016, Proceedings, Part II, 370--378, 2016.
http://dx.doi.org/10.1007/978-3-319-46723-8_43 Bibtex-Entry
Chandran V., Zysset P., and Reyes M..  Prediction of Trabecular Bone Anisotropy from Quantitative Computed Tomography using Supervised Learning and a Novel Morphometric Feature Descriptor.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015, Lecture Notes in Computer Science, In Press, 2015.
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Cerrolaza J.J., Villanueva A., M.A. Reyes M. Cabeza R. Gonzalez Ballester, and Linguraru M.G..  Generalized Multiresolution Hierarchical Shape Models via Automatic Landmark Clusterization.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2014, Lecture Notes in Computer Science, 17, 1-8, 2014.
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Guerig T., Shahim K., Reyes M., Vetter T., and Lüthi M..  Spatially Varying Registration using Gaussian Processes..  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2014, Lecture Notes in Computer Science, 17, 413-20, 2014.
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Meier R., Bauer S., Slotboom J., Wiest R., and Reyes M..  Patient-Specific Semi-Supervised Learning for Postoperative Brain Tumor Segmentation.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2014, Lecture Notes in Computer Science, 17, 714-21, 2014.
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Bauer S., Gratz P., Gralla J., Reyes M., and Wiest R..  Towards Automatic MRI Volumetry for Treatment Selection in Acute Ischemic Stroke Patients.  Proceedings of the 36th Annual International Conference of the IEEE EMBS Chicago, USA, Aug. 26-30, 1521 - 1524, 2014.
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Bauer S., Porz N., Meier R., Pica A., Slotboom J., Wiest R., and Reyes M..  Interactive Segmentation of MR Images from Brain Tumor Patients.  ISBI 2014: Proceedings of the 2014 IEEE international conference on Biomedical imaging, 862 -- 865, 2014.
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Shahim K., Cattin P., Jürgens P., Nolte L.P., and Reyes M.  Prediction of Cranio-Maxilofacial Surgical Planning using an Inverse Soft Tissue Modelling Approach.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2013, Lecture Notes in Computer Science, 8149, 18--25, 2013.
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Bauer S., Tessier J., Krieter O., Nolte L.P., and Reyes M..  Integrated Spatio-Temporal Segmentation of Longitudinal Brain Tumor Imaging Studies.  Medical Computer Vision. Large Data in Medical Imaging, Lecture Notes in Computer Science, 74-83, 2013.
http://dx.doi.org/10.1007/978-3-319-05530-5_8 Bibtex-Entry
Shahim K., Goksel O., Jürgens P., and Reyes M..  Accuracy Improvement In Cranio-Maxillofacial Soft Tissue Simulation Using A Muscle Embedded Meshing Approach.  Proceedings of the 35th Annual International Conference of the IEEE EMBS Osaka, Japan, July 3-7, 7156-9, 2013.
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Bou Sleiman H., Iizuka T., Nolte L.P., and Reyes M..  Population-Based Design of Mandibular Plates Based on Bone Quality and Morphology.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2012, Lecture Notes in Computer Science, 66--73, 2012.
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Seiler C., Pennec X., and Reyes M..  Simultaneous Multiscale Polyaffine Registration by Incorporating Deformation Statistics.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2012, Lecture Notes in Computer Science, 130--137, 2012.
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Bauer S., Nolte L.P., and Reyes M..  Fully Automatic Segmentation of Brain Tumor Images using Support Vector Machine Classiffication in Combination with Hierarchical Conditional Random Field Regularization..  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2011, 354--361, 2011.
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Bou Sleiman H., Ritacco L.E., Nolte L.P., and Reyes M..  Minimization of Intra-Operative Shaping of Orthopaedic Fixation Plates: A Population-Based Design.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2011, 409--416, 2011.
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Seiler C., Pennec X., and Reyes M..  Geometry-Aware Multiscale Image Registration Via OBBTree-Based Polyaffine Log-Demons.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2011, 631--638, 2011.
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Bauer S., Nolte L.P., and Reyes M..  Segmentation of brain tumor images based on atlas-registration combined with a Markov-Random-Field lesion growth model.  ISBI 2011: Proceedings of the 2011 IEEE international conference on Biomedical imaging, 2018-2021, 2011.
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Lu H., Cattin P., Nolte L.P., and Reyes M..  Diffusion weighted imaging distortion correction using hybrid multimodal image registration.  ISBI 2011: Proceedings of the 2011 IEEE international conference on Biomedical imaging, 594-597, 2011.
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Seiler C., Pennec X., Ritacco L.E., and Reyes M..  Femur Specific Polyaffine Model to Regularize the Log-Domain Demons Registration.  10th SPIE Medical Imaging 2011, 7962, 2011.
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Kim H., Jürgens P., Nolte L.P., and Reyes M.  Anatomically-Driven Soft-Tissue Simulation Strategy for Cranio-Maxillofacial Surgery Using Facial Muscle Template Model.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2010, Lecture Notes in Computer Science, 6361, 61-68, 2010.
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Lu H., Reyes M., Serifovic A., Weber S., Sakurai Y., Yamagata H., and Cattin P..  Multi-modal diffeomorphic demons registration based on point-wise mutual information.  ISBI 2010: Proceedings of the 2010 IEEE international conference on Biomedical imaging, 372--375, 2010.
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Seiler C., Pennec X., and Reyes M..  Parametric regression of 3D medical images through the exploration of non-parametric regression models.  ISBI 2010: Proceedings of the 2010 IEEE international conference on Biomedical imaging, 452--455, 2010.
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Bauer S., Seiler C., Bardyn T., Büchler P., and Reyes M..  Atlas-Based Segmentation of Brain Tumor Images Using a Markov Random Field-Based Tumor Growth Model and Non-Rigid Registration.  Proceedings of the 32nd Annual International Conference of the IEEE EMBS Buenos Aires, Argentina, August 31 - September 4, 4080--4083, 2010.
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Lu H., Cattin P. C., and Reyes M..  A Hybrid Multimodal Non-Rigid Registration of MR Images Based on Diffeomorphic Demons.  Proceedings of the 32nd Annual International Conference of the IEEE EMBS Buenos Aires, Argentina, August 31 - September 4, 5951--5954, 2010.
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Oliveira-Santos T., Peterhans M., Roth B., Reyes M., Nolte L.P., Thalmann G.N., and Weber S..  Computer Aided Surgery for Percutaneous Nephrolithotomy: Clinical Requirement Analysis and System Design.  Proceedings of the 32nd Annual International Conference of the IEEE EMBS Buenos Aires, Argentina, August 31 - September 4, 1, 442--445, 2010.
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Oliveira-Santos T., Weitzel T., Klaeser B., Krause T., Nolte L.P., Weber S., and Reyes M..  Multimodal Target Correction by Local Bone Registration: A PET/CT Evaluation.  Proceedings of the 32nd Annual International Conference of the IEEE EMBS Buenos Aires, Argentina, August 31 - September 4, 5616--5619, 2010.
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Reyes M., González Ballester M.A., Kozic N., Sandberg J.K., Summers R.M., and Linguraru M.G..  Hierarchical Patch Generation for Multi-level Statistical Shape Analysis by Principal Factor Analysis Decomposition.  9th SPIE Medical Imaging 2010, Biomedical Applications in Molecular, Structural, and Functional Imaging, 7626, 762617-762617-8, 2010.
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Blanc R., Reyes M., Seiler C., and Székely G..  Conditional variability of statistical shape models based on surrogate variables.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2009, 5762, 84--91, 2009.
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Kozic N., Buechler P., González-Ballester M.A., Reimers N., Nolte L.P., and Reyes M..  Population-Specific Evaluation of Implant Bone Fitting Using PCA Shape Space and Level Sets..  ISBI 2009: Proceedings of the Sixth IEEE international conference on Symposium on Biomedical Imaging, 883-886, 2009.
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Reyes M., González-Ballester M.A., Li Z., Kozic N., Chin S., Summers R.M., and Linguraru M.G..  Anatomical Variability of Organs Via Principal Factor Analysis from the Construction of an Abdominal Probabilistic Atlas..  ISBI 2009: Proceedings of the Sixth IEEE international conference on Symposium on Biomedical Imaging, 682--685, 2009.
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Kozic N. Reyes M., Tannast M., Nolte L.P., and González-Ballester M.A..  Statistical Shape Space Analysis Based on Level Sets.  4th International Workshop on Medical Imaging and Augmented Reality, Tokyo, Japan, 160--167, 2008.
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Reyes M., Linguraru M.G., Nolte L.P., and González-Ballester M.A..  Clusterization of deformation modes for quantitative evaluation on factor analysis techniques on statistical shape modeling.  4th International Workshop on Medical Imaging and Augmented Reality, Tokyo, Japan, 2008.
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Bonaretti S., Reimers N., Reyes M., Nikitsin A., Joensson A., Nolte L.P., and Buechler P..  Assessment of Peri-Articular Implant Fitting Based on Statistical Finite Element Modeling.  Computational Biomechanics for Medicine III (Miccai 2008 Workshop), 2008.
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Reyes M., González-Ballester M.A., Li Z., Kozic N., Summers R.M., and Linguraru G.M..  Interpretability of Anatomical Variability Analysis of Abdominal Organs via Clusterization of Decomposition Modes..  30th Annual International IEEE EMBS Conference, Vancouver, British Columbia, Canada, 2008, 355--358, 2008.
http://dx.doi.org/10.1109/IEMBS.2008.4649163 Bibtex-Entry
Reyes M., Linguraru M.G., Marias K., Ayache N., Nolte L.P., and González-Ballester M.A.  Statistical shape analysis via principal factor analysis.  ISBI 2007: Proceedings of the Fourth IEEE international conference on Symposium on Biomedical Imaging, 1216-1219, 2007.
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Reyes M., Malandain G., Darcourt J., and Koulibaly P.M..  Respiratory motion correction in emission tomography imaging.  Fully Three-Dimensional Image Reconstruction Meeting in Radiology and Nuclear Medicine, Salt Lake City, Utah, USA, 2005.
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González-Ballester M.A., Linguraru M.G., Reyes M., and Ayache N..  On the adequacy of principal factor analysis for the study of shape variability.  SPIE Medical Imaging 2005, 5747, 1392-1399, 2005.
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Reyes M., Malandain G., Koulibaly P.M., González-Ballester M.A., and Darcourt J..  Respiratory motion correction in emission tomography image reconstruction.  Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2005, Lecture Notes in Computer Science, Palm Springs, California, 3750, 369-376, 2005.
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Book Chapters

 

Crimi A., Menze B., Maier O., Reyes M., and Handels H..  Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries: First International Workshop, Brainles 2015, Held in Conjunction with MICCAI 2015, Munich, Germany, October 5, 2015, Revised Selected Papers.  9556, 2016.
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Reyes M., Shahim K., and Jürgens P..  Computer-Assisted Musculoskeletal Surgery: Thinking and Executing in 3D.  43--56, 2016.
http://dx.doi.org/10.1007/978-3-319-12943-3_5 Bibtex-Entry
Bauer S., Wiest R., Slotboom J., and Reyes M..  Atlas-based Segmentation of Tumor-bearing Brain Images.  12, 159-169, 2014.
http://www.springer.com/series/8812 Bibtex-Entry
Kim H., Jürgens P., and Reyes M..  Patient-Specific Modeling in Tomorrow's Medicine.  9, 413--440, 2012.
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Bardyn T., Reyes M., Larrea X., and Buechler P..  Influence of Smoothing on Voxel-Based Mesh Accuracy in Micro-Finite Element.  78--86, 2009.
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Seiler C., Büchler P., Nolte L.P., Paulsen R., and Reyes M..  Hierarchical Markov Random Fields Applied to Model Soft Tissue Deformations on Graphics Hardware.  133--148, 2008.
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Conference Abstracts

 

Pereira S., Meier R., Alves V., Reyes M., and Silva C..  Automatic brain tumor grading from MRI data using convolutional neural networks and quality assessment.  Understanding and Interpreting Machine Learning in Medical Image Computing Applications, 106--114, 2018.
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Balsiger F., Konar A., Chikop S., Chandran V., Scheidegger O., Geethanath S., and Reyes M..  Magnetic Resonance Fingerprinting Reconstruction via Spatiotemporal Convolutional Neural Networks.  International Workshop on Machine Learning for Medical Image Reconstruction, 11074, 39--46, 2018.
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Chikop S., Chandran V., Shaik I., Reyes M., and Geethanath S..  Application of Random Forest Regression for Fast and Robust MRF Dictionary Matching.  Annual Meeting of International Society for Magnetic Resonance in Medicine, 63, 2017.
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Taghizadeh E., Kistler M., Büchler P., and Reyes M..  Fast Prediction of Femoral Biomechanics Using Supervised Machine Learning and Statistical Shape Modeling.  Computational Biomechanics for Medicine X / MICCAI 2015, 115--127, 2015.
http://dx.doi.org/10.13140/RG.2.1.3290.1840 Bibtex-Entry
Lu P., Barazzetti L., Chandran V., Gavaghan K., Weber S., Gerber N., and Reyes M..  Facial Nerve Image Enhancement from CBCT using Supervised Learning Technique.  Proceedings of the 37th Annual International Conference of the IEEE EMBS Milan, Italy August 25-29, In Press, 2015.
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Meier R., Karamitsou V., Habegger S., Wiest R., and Reyes M..  Parameter Learning for CRF-based Tissue Segmentation of Brain Tumors.  Brain Tumor Segmentation Challenge - BRATS / MICCAI 2015, In Press, 2015.
http://dx.doi.org/10.13140/RG.2.1.3290.1840 Bibtex-Entry
Valenzuela W., Ferguson S., Ignasiak D., Diserens G., Vermathen P., Boesch C., and Reyes M..  Correction Tool for Active Shape Model Based Lumbar Muscle Segmentation.  Proceedings of the 37th Annual International Conference of the IEEE EMBS Milan, Italy August 25-29, In Press, 2015.
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Waldo Valenzuela, Juan Cerrolaza, Ronald M. Summers, Marius {George Linguraru}, and Mauricio Reyes.  Fast Correction Method for Abdominal Multi-Organ Segmentation Using 2D / 3D Free Form Deformation and Posterior Shape Models.  Interactive Medical Image Computing - IMIC / MICCAI 2015, In Press, 2015.
http://dx.doi.org/10.13140/RG.2.1.3290.1840 Bibtex-Entry
Valenzuela W., Vermathen P., Boesch C., Nolte L.P., and Reyes M..  iSix - Image Segmentation in Osirix.  30th Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology, 2013.
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Jürgens P., Shahim K., Cattin P., Zeilhofer H.F., and Reyes M..  Backward-planning for orthognatic surgery---a new inverse modelling algorithm to define the hard-tissue position from a desired soft-tissue surface.  42, 1331--1331, 2013.
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Lu H., Van der Zwaag W., Nolte L.P., and Reyes M..  Geometric and Intensity EPI Distortion Correction for 7T fMRI Using Simultaneous Classification and Registration.  Proceedings of ESMRMB 2012, Lisbon, Portugal, 2012.
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Seif M., Lu H., Boesch C., Reyes M., and Vermathen P..  Image co-registration for triggered and non-triggered DTI of the human kidney: Reduced variability of diffusion parameter estimation.  Proceedings of ESMRMB 2012, Lisbon, Portugal, 2012.
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Bonaretti S., Seiler C., Boichon C., Buechler P., and Reyes M..  Mesh-based vs. Image-based Statistical Appearance Model of the Human Femur: a Preliminary Comparison Study for the Creation of Finite Element Meshes.  Mesh Processing in Medical Image Analysis, Lecture Notes in Computer Science, 2011.
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Jürgens P., Kim H., Forter S., Beinemann J., Zeilhofer H.F., Reyes M., and Schwenzer K..  Three-dimensional control of maxillary position--validation of a 3-d real time navigational prototype system for routine application in orthognathic surgery.  Abstracts of the 20th International Conference on Oral and Maxillofacial Surgery, 40, 1064, 2011.
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Jürgens P., Kim H., and Reyes M..  Application of a new soft-tissue simulation strategy based on a mimic muscle template model to predict the outcome in orthognatic surgery.  Abstracts of the 20th International Conference on Oral and Maxillofacial Surgery, 40, 1064, 2011.
http://dx.doi.org/10.1016/j.ijom.2011.07.130%22 Bibtex-Entry
Bonaretti S., Helgason B., Seiler C., Kistler M., Reyes M., and Buechler P..  A Statistical Shape Model of Bone Anatomical Variability for Finite Element Assessment of Bone Mechanics.  17th Congress of the European Society of Biomechanics, Edinburgh, U.K., 2010.
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Kim H., Jürgens P., Cattin P., Weber S. Nolte L.P., and Reyes M..  Patient-specific, Fast Soft-Tissue Simulation for Cranio-Maxillofacial Surgery.  17th Congress of the European Society of Biomechanics, Edinburgh, U.K. -Accepted for podium presentation, 2010.
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Seiler C., Gazdhar A., Geiser T., Reyes M., and Gantenbein-Ritter B..  Mesenchymal Stem Cell Classification during Differentiation Based on Shape Information.  TERMIS -- Tissue Engineering and Regenerative Medicine International Society -- EU Meeting, Galway, Ireland, 2010.
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Stefan Bauer and Mauricio Reyes.  A Markov-Random-Field-Based Biomechanical Tumor Growth Model for Atlas-Based Segmentation of Brain Tumor Images.  Proceedings of the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation Athens, Greece September 8-9, 2010.
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Bonaretti S., Kistler M., Seiler C., Reyes M., and Buechler P..  Combined statistical model of bone shape and mechanical properties for bone and implant modeling.  9th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering, Valencia/Spain, Feb 24-27, 2010.
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Bou-Sleiman H., Ritacco L.E., and Reyes M..  Computer-assisted allograft selection for transepiphyseal tumor resection at the knee.  10th Annual Meeting of the International Society for Computer Assisted Surgery, Paris, France, June 16-19, 2010.
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X. Dong, H. Lu, Y. Sakurai, H. Yamagata, G. Zheng, and M. Reyes.  Automated Intervertebral Disc Detection from Low Resolution, Sparse MRI Images for the Planning of Scan Geometries.  Machine Learning in Medical Imaging, Lecture Notes in Computer Science, 6357, 10-17, 2010.
http://dx.doi.org/10.1007/978-3-642-15948-0_2 Bibtex-Entry
Kim H., Jürgens P., Cattin P., Weber S., Nolte L.P, and Reyes M..  Fast soft-tissue simulation method for cranio-maxillofacial surgery using facial muscle template models.  14th Annual Conference of the International Society for Computer Aided Surgery, Geneva, Switzerland, June, 2010.
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K. Marias, V. Sakkalis, A. Roniotis, I. Karatzanis, G. Stamatakos, D. Dionysiou, S. Giatili, N. Uzunoglou, N. Graf, R. Bohle, E. Meese, H. Stenzhorn, Y.-J. Kim, P. Coveney, S. Zasada, S. Wan, A. Folarin, P. Büchler, T. Bardyn, S. Bauer, M. Reyes, G. Clapworthy, E. Liu, T. Bily, V. Bednar, Karasek. M., A. Franz, R. Grewer, and J. Sabczynski.  CONTRACANCRUM AT THE PROJECT LEVEL: Clinically Oriented Translational Cancer Multilevel Modelling.  Proceedings of the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation Athens, Greece September 8-9, 2010.
K. Marias, V. Sakkalis, A. Roniotis, I. Karatzanis, G. Stamatakos, D. Dionysiou, S. Giatili, N. Uzunoglou, N. Graf, R. Bohle, E. Meese, H. Stenzhorn, Y.-J. Kim, P. Coveney, S. Zasada, S. Wan, A. Folarin, P. Büchler, T. Bardyn, S. Bauer, M. Reyes, G. Clapworthy, E. Liu, T. Bily, V. Bednar, Karasek. M., A. Franz, R. Grewer, and J. Sabczynski.  Clinically Oriented Translational Cancer Multilevel Modelling: The ContraCancrum project.  Proceedings of the Virtual Physiological Human Conference 2010 Brussels, Belgium September 30 - October 1, 2010.
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G. Stamatakos, D. Dionysiou, E. Kolokotroni, E. Georgiadi, A. Roniotis, V. Sakkalis, P. Coveney, S. Wan, S. Manos, S. Zasada, A. Folarin, P. Büchler, T. Bardyn, S. Bauer, M. Reyes, T. Bily, V. Bednar, M. Karasek., N. Graf, R.M. Bohle, E. Meese, Y.-J. Kim, H. Stenzhorn, G. Clapworthy, E. Liu, J. Sabczynski, and K. Marias.  CONTRA CANCRUM AT THE PROJECT LEVEL: The ContraCancrum Oncosimulator: Integrating Biomechanisms Across Scales in the Clinical Context.  Proceedings of the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation Athens, Greece September 8-9, 2010.
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Kim H., Jürgens P., Nolte L.P., Weber S., Zeilhofer H.F., and Reyes M..  Anatomically considered, fast soft-tissue simulation for cranio-maxillofacial surgery.  In Proceedings of Computer Aided Surgery around the Head, Paris, France, 2009.
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Schmidt W., Reyes M., Fischer F., Geesink R., Nolte L.P., Racanelli J., and Reimers N..  Quantifying human knee anthropometric differences between ethnic groups and gender using shape analysis.  Annual Meeting of the American Society of Biomechanics, Penn State University, 26-29, 2009.
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Bonaretti S., Buechler P., Reimers N., Schmidt W., Seiler C., Weber S., and Reyes M..  Automatic bone density evaluation from CT images.  9th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery, Boston, U.S.A, June 17-20, 625-627, 2009.
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Oliveira-Santos T., Weitzel T., Klaeser B., Reyes M., and Weber S..  Introducing Computer-Assisted Surgery into combined PET/CT image based Biopsy.  9th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery, Boston, U.S.A, June 17-20, 308-311, 2009.
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Seiler C., Weber S., Schmidt W., Fischer F., Reimers N., and Reyes M..  Automatic Landmark Propagation for Left and Right Symmetry Assessment of Tibia and Femur: A Computational Anatomy Based Approach.  9th Annual Meeting of the International Society for Computer Assisted Surgery, Boston, U.S.A, June 17-20, 195-198, 2009.
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Kozic N., Reyes M., Tannast M., Nolte L.P., and González Ballester M.A..  Assesment of anatomical criteria across populations using statistical shape models and level sets.  8th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery, Hong-Kong, China, 46-49, 2008.
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Kozic N. Reyes M., Nolte L.P., and González-Ballester M.A..  Global optimisation in PCA shape space using level sets.  12th Annual Conference of the International Society for Computer Aided Surgery, Barcelona, Spain, S109--S110, 2008.
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Reyes M., Bonaretti S., Reimers N., Lutz C., and González-Ballester M.A..  Evidence-based implant design using a statistical bone model and automated implant fitting.  8th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery, Hong-Kong, China, 2008.
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Bonaretti S., Reimers N., Rueckert D., Reyes M., González-Ballester M.A., and Buechler P..  Statistical Finite Element Analysis for Bone Modeling.  16th Congress of the European Society of Biomechanics, Lucerne, Switzerland, S369-S369, 2008.
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Larrea X., Reyes M., Boyd S., Buechler P., and González-Ballester M.A..  Automatic mesh smoothing for finite element modelling from 3D image data..  16th Congress of the European Society of Biomechanics, Lucerne, Switzerland, 2008.
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Reyes M., Larrea X., Boyd S., Buechler P., and González-Ballester M.A..  Constrained hexahedral mesh smoothing for finite element modelling from 3D image data.  Computer Methods in Biomechanics and Biomedical Engineering,Porto, Portugal, 2008.
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Reyes M., Nolte L.P., and González-Ballester M.A..  Clustering of deformation modes for quantitative evaluation of statistical shape models.  7th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery, Heidelberg, Germany, 271-273, 2007.
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Reyes M., Malandain G., Ayache N., Darcourt J., and Koulibaly P.M..  Respiratory motion compensation within emission tomographic reconstruction.  52nd Annual Meeting of the Society of Nuclear Medicine, Toronto, Canada, 2005.
Pereda J. and Reyes M..  Virtual Reconstruction: a new approach to the study of human embryology.  XVIII Congress of Brazilian Microscopy and Microanalysis Society. Sao Paulo, Brazil, 2001.
Pereda J. and Reyes M..  The Use of Computational Tools for the Design, and Elaboration of a Teaching Program on Fetal Anatomy.  XVII International Symposium on Morphological Sciences, Timisoara, Rumania, 11-15, 2001.
Pereda J. and Reyes M..  Nuevas Tendencias Educacionales: Reconstrucción Tridimensional. Una Nueva Alternativa en la Enseñanza de la Embriología Humana.  I Seminar of Universitary Teaching. Universidad de Santiago de Chile, Santiago, Chile, 26-28, 2001.
Reyes M. and Salinas R..  Visualización Tridimensional en BioIngeniería a partir de Cortes Seriados.  International Conference of Engineering Systems, Communications and Information Technologies (ICSECIT), Punta Arenas, Chile, 16-19, 2001.
Reyes M. and Moisan M..  Controlador Difuso Experimental para Sistema ball and beam, usando Visión Artificial como Realimentación.  XIV Congress of Chilean Automatic Control Association (ACCA), Concepcion, Chile, 23-27, 2000.