Results

Journal publications

2023
Andrey Zhylka, Nico Sollmann, Florian Kofler, Ahmed Radwan, Alberto De Luca, Jens Gempt, Benedikt Wiestler, Bjoern Menze, Axel Schroeder, Claus Zimmer, Jan S. Kirschke, Stefan Sunaert, Alexander Leemans, Sandro M. Krieg and Josien Pluim. Reconstruction of the Corticospinal Tract in Patients with Motor-Eloquent High-Grade Gliomas Using Multilevel Fiber Tractography Combined with Functional Motor Cortex Mapping. American Journal of Neuroradiology, 2023

2022
Lucas Fidon, Michael Aertsen, Thomas Deprest, Doaa Emam, Frédéric Guffens, Nada Mufti, Esther Van Elslander, Ernst Schwartz, Michael Ebner, Daniela Prayer, Gregor Kasprian, Anna L. David, Andrew Melbourne, Sébastien Ourselin, Jan Deprest, Georg Langs, Tom Vercauteren. Distributionally Robust Deep Learning using Hardness Weighted Sampling. Machine Learning for Biomedical Imaging, 2022
Luca Canalini, Jan Klein, Diana Waldmannstetter, Florian Kofler, Stefano Cerri, Alessa Hering, Stefan Heldmann, Sarah Schlaeger, Bjoern Menze, Benedikt Wiestler, Jan Kirschke, Horst Hahn. Quantitative evaluation of the influence of multiple MRI sequences and of pathological tissues on the registration of longitudinal data acquired in brain tumor treatment. Frontiers in Neuroimaging, 2022
Sveinn Pálsson, Stefano Cerri, Hans Skovgaard Poulsen, Thomas Urup, Ian Law, Koen Van Leemput. Predicting survival of glioblastoma from automatic whole-brain and tumor segmentation of MR images. Scientific Reports, 2022
Andrey Zhylka, Alexander Leemans, Josien P. W. Pluim, Alberto De Luca. Anatomically informed multi-level fiber tractography for targeted virtual dissection. Magnetic Resonance Materials in Physics, Biology and Medicine, 2022
Ezhov, Ivan, Mot, Tudor, Shit, Suprosanna, Lipkova, Jana, Paetzold, Johannes C., Kofler, Florian, Navarro, Fernando, Pellegrini, Chantal, Kollovieh, Marcel, Metz, Marie, Wiestler, Benedikt, Menze, Bjoern. Geometry-aware neural solver for fast Bayesian calibration of brain tumor models. IEEE Transactions on Medical Imaging, 2022
Ivan Ezhov, Kevin Scibilia, Katharina Franitza, Felix Steinbauer, Suprosanna Shit, Lucas Zimmer, Jana Lipkova, Florian Kofler, Johannes Paetzold, Luca Canalini, Diana Waldmannstetter, Martin Menten, Marie Metz, Benedikt Wiestler, Bjoern Menze. Learn-Morph-Infer: a new way of solving the inverse problem for brain tumor modeling . Medical Image Analysis, 2022
S. Shit, J. Zimmermann, I. Ezhov, J. Paetzold, A. F. Sanches, C. Pirkl, and B. H. Menze. SRflow: Deep learning based super-resolution of 4D-flow MRI data. Frontiers in Artificial Intelligence, 2022
Hélène Lajous, Christopher W. Roy, Tom Hilbert, Priscille de Dumast, Sébastien Tourbier, Yasser Alemán-Gómez, Jérôme Yerly, Thomas Yu, Hamza Kebiri, Kelly Payette, Jean-Baptiste Ledoux, Reto Meuli, Patric Hagmann, Andras Jakab, Vincent Dunet, Mériam Koob, Tobias Kober, Matthias Stuber, Meritxell Bach Cuadra. A Fetal Brain magnetic resonance Acquisition Numerical phantom (FaBiAN). Scientific Reports, 2022
Maffei, Chiara, Gabriel Girard, Kurt G. Schilling, Dogu Baran Aydogan, Nagesh Adluru, Andrey Zhylka, Ye Wu et al. Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset? NeuroImage, 2022

2021
Luis C. Garcia-Peraza-Herrera, Lucas Fidon, Claudia D'Ettorre, Danail Stoyanov, Tom Vercauteren, Sebastien Ourselin. Image Compositing for Segmentation of Surgical Tools without Manual Annotations. IEEE Transactions on Medical Imaging, 2021
Lucas Fidon, Elizabeth Viola, Nada Mufti, Nada Mufti, Anna L. David, Anna L. David, Andrew Melbourne, Philippe Demaerel, Sebastien Ourselin, Tom Vercauteren, Jan Deprest, Jan Deprest, Michael Aertsen. A spatio-temporal atlas of the developing fetal brain with spina bifida aperta. Open Research Europe, 2021
Nada Mufti, Michael Aertsen, Michael Ebner, Lucas Fidon, Premal Patel, Muhamad Bin Abdul Rahman, Yannick Brackenier, Gregor Ekart, Virginia Fernandez, Tom Vercauteren, Sebastien Ourselin, Dominic Thomson, Luc De Catte, Philippe Demaerel, Jan Deprest, Anna L. David, Andrew Melbourne. Cortical spectral matching and shape and volume analysis of the fetal brain pre- and post-fetal surgery for spina bifida: a retrospective study. Neuroradiology, 2021
Florian Kofler, Ivan Ezhov, Lucas Fidon, Carolin M. Pirkl, Johannes C. Paetzold, Egon Burian, Sarthak Pati, Malek El Husseini, Fernando Navarro, Suprosanna Shit, Jan Kirschke, Spyridon Bakas, Claus Zimmer, Benedikt Wiestler, Bjoern H. Menze. Robust, Primitive, and Unsupervised Quality Estimation for Segmentation Ensembles. Frontiers in Neuroscience, 2021
Ezequiel de la Rosa, Diana M. Sima, Bjoern H. Menze, Jan S. Kirschke, David Robben. AIFNet: Automatic vascular function estimation for perfusion analysis using deep learning. Medical Image Analysis, 2021
Rakić M, Vercruyssen S, Van Eyndhoven S, de la Rosa E, Jain S, Van Huffel S, Maes F, Smeets D, Sima DM. icobrain ms 5.1: Combining unsupervised and supervised approaches for improving the detection of multiple sclerosis lesions. NeuroImage: Clinical, 2021
Wittens, M., Sima, D. M., Houbrechts, R., Ribbens, A., Niemantsverdriet, E., Fransen, E., Bastin, C., Benoit, F., Bergmans, B., Bier, J. C., De Deyn, P. P., Deryck, O., Hanseeuw, B., Ivanoiu, A., Lemper, J. C., Mormont, E., Picard, G., de la Rosa, E., Salmon, E., Segers, K., ... Engelborghs, S.. Diagnostic Performance of Automated MRI Volumetry by icobrain dm for Alzheimer’s Disease in a Clinical Setting: A REMEMBER Study. Journal of Alzheimer's Disease, 2021
Maria Ines Meyer, Maria Ines Meyer, Ezequiel de la Rosa, Ezequiel de la Rosa, Nuno Pedrosa de Barros, Roberto Paolella, Roberto Paolella, Koen Van Leemput, Koen Van Leemput, Diana M. Sima. A Contrast Augmentation Approach to Improve Multi-Scanner Generalization in MRI. Frontiers in Neuroscience, 2021
Stefano Cerri, Oula Puonti, Dominik S.Meier, Jens Wuerfel, Mark Mühlau, Hartwig R.Siebner, Koen Van Leemput. A contrast-adaptive method for simultaneous whole-brain and lesion segmentation in multiple sclerosis. NeuroImage, 2021
Amnah Mahroo, Mareike Alicja Buck, Jörn Huber, Nora-Josefin Breutigam, Henk J. M. M. Mutsaerts, Martin Craig, Michael Chappell, Matthias Günther. Robust Multi-TE ASL-Based Blood–Brain Barrier Integrity Measurements. Frontiers in Neuroscience, 2021
Lisa Bartha-Doering, Ernst Schwartz, Kathrin Kollndorfer, Florian Ph. S. Fischmeister, Astrid Novak, Georg Langs, Harald Werneck, Daniela Prayer, Rainer Seidl, Gregor Kasprian. Effect of corpus callosum agenesis on the language network in children and adolescents. Brain structure & function, 2021
Matthias Perkonigg, Johannes Hofmanninger, Christian J. Herold, James A. Brink, Oleg S. Pianykh, Helmut Prosch, Georg Langs. Dynamic memory to alleviate catastrophic forgetting in continual learning with medical imaging. Nature Communications, 2021
Marie Khawam, Priscille de Dumast, Priscille de Dumast, Pierre Deman, Pierre Deman, Hamza Kebiri, Hamza Kebiri, Thomas Yu, Thomas Yu, Sébastien Tourbier, Hélène Lajous, Hélène Lajous, Patric Hagmann, Philippe Maeder, Jean-Philippe Thiran, Jean-Philippe Thiran, Jean-Philippe Thiran, Reto Meuli, Vincent Dunet, Meritxell Bach Cuadra, Meritxell Bach Cuadra, Mériam Koob. Fetal Brain Biometric Measurements on 3D Super-Resolution Reconstructed T2-Weighted MRI: An Intra- and Inter-observer Agreement Study. Frontiers in Pediatrics, 2021
Erick J. Canales-Rodríguez, Marco Pizzolato, Marco Pizzolato, Thomas Yu, Thomas Yu, Gian Franco Piredda, Gian Franco Piredda, Gian Franco Piredda, Tom Hilbert, Tom Hilbert, Tom Hilbert, Joaquim Radua, Joaquim Radua, Tobias Kober, Tobias Kober, Tobias Kober, Jean-Philippe Thiran, Jean-Philippe Thiran. Revisiting the T2 spectrum imaging inverse problem: Bayesian regularized non-negative least squares. NeuroImage, 2021
Thomas Yu, Erick J. Canales-Rodríguez, Erick J. Canales-Rodríguez, Marco Pizzolato, Gian Franco Piredda, Tom Hilbert, Elda Fischi-Gomez, Matthias Weigel, Muhamed Barakovic, Meritxell Bach Cuadra, Cristina Granziera, Tobias Kober, Jean-Philippe Thiran. Model-informed machine learning for multi-component T2 relaxometry. Medical Image Analysis, 2021
Erick Jorge Canales-Rodríguez, Marco Pizzolato, Gian Franco Piredda, Tom Hilbert, Nicolas Kunz, Caroline Pot, Thomas Yu, Raymond Salvador, Edith Pomarol-Clotet, Tobias Kober, Jean-Philippe Thiran, Alessandro Daducci. Comparison of non-parametric T2 relaxometry methods for myelin water quantification. Medical Image Analysis, 2021
La Rosa, Francesco, Thomas Yu, Germán Barquero, Jean-Philippe Thiran, Cristina Granziera, and Meritxell Bach Cuadra. MPRAGE to MP2RAGE UNI translation via generative adversarial network improves the automatic tissue and lesion segmentation in multiple sclerosis patients. Computers in Biology and Medicine, 2021

2020
Francesco La Rosa, Francesco La Rosa, Ahmed Abdulkadir, Mário João Fartaria, Reza Rahmanzadeh, Po-Jui Lu, Riccardo Galbusera, Muhamed Barakovic, Jean-Philippe Thiran, Cristina Granziera, Merixtell Bach Cuadra. Multiple sclerosis cortical and WM lesion segmentation at 3T MRI: a deep learning method based on FLAIR and MP2RAGE. NeuroImage: Clinical, 2020
Germán Barquero, Francesco La Rosa, Hamza Kebiri, Po-Jui Lu, Reza Rahmanzadeh, Matthias Weigel, Mário João Fartaria, Tobias Kober, Marie Théaudin, Renaud Du Pasquier, Pascal Sati, Daniel S. Reich, Martina Absinta, Cristina Granziera, Pietro Maggi, Meritxell Bach Cuadra. RimNet: A deep 3D multimodal MRI architecture for paramagnetic rim lesion assessment in multiple sclerosis. Neuroimage Clinical, 2020
Luca Canalini, Jan Klein, Dorothea Miller, Ron Kikinis. Enhanced registration of ultrasound volumes by segmentation of resection cavity in neurosurgical procedures. International Journal of Computer Assisted Radiology and Surgery, 2020
Hanne Struyfs, Diana M. Sima, Melissa Wittens, Annemie Ribbens, Nuno Pedrosa de Barros, Thanh Vân Phan, Maria Ines Meyer, Lene Claes, Ellis Niemantsverdriet, Sebastiaan Engelborghs, Wim Van Hecke, Dirk Smeets. Automated MRI volumetry as a diagnostic tool for Alzheimer's disease: Validation of icobrain dm. NeuroImage: Clinical, 2020
Karl-Heinz Nenning, Julia Furtner, Barbara Kiesel, Ernst Schwartz, Thomas Roetzer, Nikolaus Fortelny, Christoph Bock, Christoph Bock, Anna Grisold, Martha Marko, Fritz Leutmezer, Hesheng Liu, Polina Golland, Sophia Stoecklein, Johannes A. Hainfellner, Gregor Kasprian, Daniela Prayer, Christine Marosi, Georg Widhalm, Adelheid Woehrer, Georg Langs, Georg Langs. Distributed changes of the functional connectome in patients with glioblastoma. Scientific Reports, 2020
Karl-Heinz Nenning, Ting Xu, Ernst Schwartz, Jesús Arroyo, Adelheid Woehrer, Alexandre Rosa Franco, Joshua T. Vogelstein, Daniel S. Margulies, Hesheng Liu, Jonathan Smallwood, Michael P. Milham, Georg Langs. Joint embedding: A scalable alignment to compare individuals in a connectivity space. NeuroImage, 2020

2019
Luca Canalini, Jan Klein, Dorothea Miller, Ron Kikinis. Segmentation-based registration of ultrasound volumes for glioma resection in image-guided neurosurgery. International Journal of Computer Assisted Radiology and Surgery, 2019
Mikael Agn, Per Munck af Rosenschöld, Oula Puonti, Michael J. Lundemann, Laura Mancini, Anastasia Papadaki, Steffi Thust, John Ashburner, Ian Law, Koen Van Leemput. A modality-adaptive method for segmenting brain tumors and organs-at-risk in radiation therapy planning. Medical Image Analysis, 2019
Jonathan Scharff Nielsen, Jens Edmund, Koen Van Leemput. Magnetic resonance-based computed tomography metal artifact reduction using Bayesian modelling. Physics in Medicine & Biology, 2019
Jonathan Scharff Nielsen, Jonathan Scharff Nielsen, Koen Van Leemput, Koen Van Leemput, Jens Edmund. MR-based CT metal artifact reduction for head-and-neck photon, electron, and proton radiotherapy. Medical Physics, 2019
Amod Jog, Andrew Hoopes, Douglas N. Greve, Koen Van Leemput, Bruce Fischl. PSACNN: Pulse sequence adaptive fast whole brain segmentation. NeuroImage, 2019

Conference and other publications

2021
Maria Ines Meyer, Ezequiel de la Rosa, Nuno Barros, Roberto Paolella, Koen Van Leemput, Diana M. Sima An augmentation strategy to mimic multi-scanner variability in MRI. International Symposium on Biomedical Imaging (ISBI 2021). April 2021

2020
Viana JS, de la Rosa E, Vyvere TV, Robben D, Sima DM. Unsupervised 3D Brain Anomaly Detection. MICCAI Brain Lesion Workshop (BrainLes 2020), Lima, Peru, October 2020.
de la Rosa, E., Robben, D., Sima, D.M., Kirschke, J.S. and Menze, B., 2020, October. Differentiable Deconvolution for Improved Stroke Perfusion Analysis. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 593-602). Springer, Cham.
Amnah Mahroo, Josepha F. Hilmer, Nora-Josefin Breutigam, Michael Chappell, Matthias Günther Exchange time as a proxy measure of blood brain barrier integrity – A two-stage estimation ESMRMB 2020.
Amnah Mahroo, Nora-Josefin Breutigam, Matthias Günther Assessing Repeatability of Blood Brain Barrier Permeability Measure Using Contrast-free MRI ISMRM 2020.
Nora-Josefin Breutigam, Daniel Christopher Hoinkiss, Mareike Alicja Buck, Amnah Mahroo, Federico von Samson-Himmelstjerna, Matthias Günther Optimal subject-specific pCASL settings by automated inner-scan timing adaption ISMRM 2020.
Francesco La Rosa, Erin S Beck, Ahmed Abdulkadir, Jean-Philippe Thiran, Daniel S Reich, Pascal Sati, Meritxell Bach Cuadra Automated Detection of Cortical Lesions in Multiple Sclerosis Patients with 7T MRI International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2020.
Andrey Zhylka, Alexander Leemans, Josien Pluim, Alberto De Luca Anatomically informed multi-level fiber tractography for improved sensitivity of white matter bundle reconstruction in diffusion MRI ISMRM 2020.
Andrey Zhylka, Nico Sollmann, Alberto De Luca, Daniel Krahulec, Marcel Breeuwer, Alexander Leemans, Josien Pluim Multi-level fiber tracking: evaluation on clinical data ISMRM 2020.

2019
Billast M., Meyer M.I., Sima D.M., Robben D. Improved inter-scanner MS lesion segmentation by adversarial training on longitudinal data MICCAI Brain Lesion Workshop (BrainLes 2019), Shenzhen, China, October 2019.
S. Shit, A. Ravi Venkatakrishnan, I. Ezhov, J. Lipkova, M. Piraud, B. Menze Implicit Neural Solver for Time-dependent Linear PDEs with Convergence Guarantee Machine Learning with Guarantees NeurIPS 2019 (Workshop), Vancouver, Canada, December 2019.
J. Paetzold, S. Shit, I. Ezhov, G. Tetteh, A. Ertürk, B. Menze clDice-a Novel Connectivity-Preserving Loss Function for Vessel Segmentation Medical Imaging Meets NeurIPS 2019 (Workshop), Vancouver, Canada, December 2019. * Joint first author
Meyer M.I., de la Rosa E., Van Leemput K., Sima D.M. Relevance Vector Machines for Harmonization of MRI Brain Volumes Using Image Descriptors Proceedings of the 2nd Workshop on Machine Learning in Clinical Neuroimaging (MLCN 2019), Shenzhen, China, October 2019.
A. Zhylka, A. Leemans, J. Pluim, A. De Luca On fiber orientation distribution peak selection for diffusion MRI fiber tractography Magnetic Resonance Materials in Physics (2019) 32(Supplement 1): 1
F. Navarro, S. Shit, I. Ezhov, J. Paetzold, A. Gafita, J. Peeken, S. Combs, B. Menze Shape-Aware Complementary-Task Learning for Multi-Organ Segmentation Proceedings of the 10th International Workshop on Machine Learning in Medical Imaging (MLMI 2019), Shenzhen, China, October 2019. * Joint first author
I. Ezhov, J. Lipkova, S. Shit, F. Kofler, N. Collomb, B. Lemasson, E. Barbier, B. Menze Neural parameters estimation for brain tumor growth modeling Proceedings of the 22th International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI), Shenzhen, China, October 2019.
L. Fidon, M. Ebner, L. C. Garcia-Peraza-Herrera, M. Modat, S. Ourselin, T. Vercauteren Incompressible image registration using divergence-conforming B-splines MICCAI 2019.
Canalini, L., Klein, J., Miller, D., Kikinis, R. Registration of ultrasound volumes based on Euclidean distance transform, CuRIOUS Challenge, MICCAI 2019.
L. Ning, E. Bonet-Carne, F. Grussu, F. Sepehrband, E. Kaden, J. Veraart, S. Blumberg, C. S. Khoo, M. Palombo, J. Coll-Font, B. Scherrer, S. Warfield, S. Karayumak, Y. Rathi, S. Koppers, L. W., J. Ebert, D. Merhof, D. Moyer, M. Pietsch, D. Christiaens, R. Teixeira, J.-D. Tournier, A. Zhylka, J. Pluim, G. Parker, U. Rudrapatna, J. Evans, C. Charron, D. Jones, C.Tax Cross-scanner and cross-protocol harmonisation of multi-shell diffusion MRI data: open challenge and evaluation results ISMRM 2019
L. Ning, E. Bonet-Carne, F. Grussu, F. Sepehrband,E. Kaden, J. Veraart, S. B. Blumberg, C. S. Khoo, M. Palombo, J. Coll-Font, B. Scherrer, S. K. Warfield, Su C. Karayumak, Y. Rathi, S. Koppers, L. Weninger, J. Ebert, D. Merhof, D. Moyer, M. Pietsch, D. Christiaens, R. Teixeira, J.-D. Tournier, A. Zhylka, J. Pluim, G. Parker, U. Rudrapatna, J. Evans, C. Charron, D. K. Jones and C. W. M. Tax Muti-shell Diffusion MRI Harmonisationand Enhancement Challenge(MUSHAC): Progress and Results Computational Diffusion MRI: International MICCAI Workshop, Granada, Spain, September 2018. Springer, p. 217-224
de la Rosa, E., Sima, D. M., Vyvere, T. V., Kirschke, J. S., & Menze, B. (2018). A Radiomics Approach to Traumatic Brain Injury Prediction in CT Scans. International Symposium on Biomedical Imaging (ISBI), Venice, Italy (2019).
T. Yu; M. Pizzolato; E. J. Canales-Rodrı́guez; J.-P. Thiran Robust T2 Relaxometry with Hamiltonian MCMC for Myelin Water Fraction Estimation. IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), Venice, Italy, April 8-11, 2019.
T. Yu; M. Pizzolato; G. Girard; J. R. Patino Lopez; E. Jorge Canales-Rodriguez et al. Robust Biophysical Parameter Estimation with a Neural Network Enhanced Hamiltonian Markov Chain Monte Carlo Sampler. Information Processing in Medical Imaging (IPMI 2019), Hong Kong, June 2-7 2019.

2018

La Rosa, Francesco, Mário João Fartaria, Tobias Kober, Jonas Richiardi, Cristina Granziera, Jean-Philippe Thiran, Meritxell Bach Cuadra Shallow vs deep learning architectures for white matter lesion segmentation in the early stages of multiple sclerosis. International MICCAI Brainlesion Workshop. Springer, Cham, 2018.

Talks

2022
Andrey Zhylka, Alexander Leemans, Josien Pluim, Alberto De Luca Walking in the dark: spherical deconvolution methods in cortical gray matter ISMRM Diffusion MRI Workshop (2022)

2020
Amnah Mahroo, Josepha F. Hilmer, Nora-Josefin Breutigam, Michael Chappell, Matthias Günther Exchange time as a proxy measure of blood brain barrier integrity – A two-stage estimation ESMRMB Congress (2020)
Amnah Mahroo, Nora-Josefin Breutigam, Matthias Günther Assessing Repeatability of Blood Brain Barrier Permeability Measure Using Contrast-free MRI ISMRM Congress (2020)

2019
Zhylka A., Leemans A., Pluim J., De Luca A. On fiber orientation distribution peak selection for diffusion MRI fiber tractography ESMRMB Congress, Rotterdam, Netherlands (2019)
Canalini, L., Klein, J., Miller, D., Kikinis, R. Segmentation-based registration of ultrasound volumes Computer Assisted Radiology and Surgery (CARS), Rennes, France (2019)

MeVisLab demonstration networks

A number of ESRs have made available a small demo in MeVisLab to illustrate their methods. You can download these demos here.

MeVisLab is available for Windows, Linux, and macOS. You can download it from the official webpage (you don't need a license for running these networks). Each network is identified by the file extension .mlab. You can open the network from MeVisLab by clicking on File->Open and select the .mlab file you want to open. For each network, there is an accompanying document that gives a general overview of the functionality of the network. For some networks, example data is also provided.

If you have any questions regarding a specific MeVisLab network, please contact the corresponding ESR.