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Translational Brain Imaging Training Network

Deliverables

Transferable skills courses 3-4

Transferable skills courses 3-4

Scientific courses 1-4

Scientific courses 1-4

Scientific courses 5-8

Scientific courses 5-8

Transferable skills courses 1-2

Transferable skills courses 1-2

Report on deformable registration from pre-operative MRI to intra-operative US

Report on deformable registration from preoperative MRI to intraoperative US

Report on patient-adaptive tumor growth models

Report on patientadaptive tumor growth models

Report on imaging sequence independent spatio-temporal maps of blood flow

Report on imaging sequence independent spatiotemporal maps of blood flow

Report on estimation and visualization of uncertainty in fiber tracking

Report on estimation and visualization of uncertainty in fiber tracking

Report on robust segmentation for cortical and white matter MS lesions

Report on robust segmentation for cortical and white matter MS lesions

Publications

Prediction of MGMT Methylation Status of Glioblastoma using Radiomics and Latent Space Shape Features

Author(s): Pálsson, Sveinn; Cerri, Stefano; Van Leemput, Koen
Published in: International MICCAI Brainlesion Workshop, 2021
Publisher: Springer
DOI: 10.1007/978-3-031-09002-8_20

Distributionally Robust Segmentation of Abnormal Fetal Brain 3D MRI

Author(s): Fidon, Lucas; Aertsen, Michael; Mufti, Nada; Deprest, Thomas; Emam, Doaa; Guffens, Frédéric; Schwartz, Ernst; Ebner, Michael; Prayer, Daniela; Kasprian, Gregor; David, Anna L.; Melbourne, Andrew; Ourselin, Sébastien; Deprest, Jan; Langs, Georg; Vercauteren, Tom
Published in: Uncertainty for Safe Utilization of Machine Learning in Medical Imaging, and Perinatal Imaging, Placental and Preterm Image Analysis. UNSURE PIPPI 2021, 2021, Page(s) 263–273, ISBN 978-3-030-87735-4
Publisher: Springer
DOI: 10.1007/978-3-030-87735-4_25

Unsupervised 3D Brain Anomaly Detection

Author(s): Simarro Viana, J., de la Rosa, E., Vande Vyvere, T., Robben, D., Sima, D.M., Investigators, CENTER-TBI Participants and Investigators
Published in: Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2020. Lecture Notes in Computer Science, 2021
Publisher: Springer
DOI: 10.1007/978-3-030-72084-1_13

clDice - a Novel Topology-Preserving Loss Function for Tubular Structure Segmentation

Author(s): Suprosanna Shit; Johannes C. Paetzold; Anjany Sekuboyina; Ivan Ezhov; Alexander Unger; Andrey Zhylka; Josien P. W. Pluim; Ulrich Bauer; Bjoern H. Menze
Published in: CVPR, 2021
Publisher: Computer Vision Foundation
DOI: 10.48550/arxiv.2003.07311

Joint inference on structural and diffusion MRI for sequence-adaptive Bayesian segmentation of thalamic nuclei with probabilistic atlases.

Author(s): Juan Eugenio Iglesias; Koen Van Leemput; Polina Golland; Anastasia Yendiki
Published in: IPMI, 2019
Publisher: Springer
DOI: 10.1007/978-3-030-20351-1_60

Generalized Wasserstein Dice Score, Distributionally Robust Deep Learning, and Ranger for brain tumor segmentation: BraTS 2020 challenge

Author(s): Fidon, Lucas; Ourselin, Sebastien; Vercauteren, Tom
Published in: Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2020, 2021, Page(s) 200-214, ISBN 978-3-030-72087-2
Publisher: Springer
DOI: 10.1007/978-3-030-72087-2_18

Relationformer: A Unified Framework for Image-to-Graph Generation

Author(s): Suprosanna Shit, Rajat Koner, Bastian Wittmann, Johannes Paetzold, Ivan Ezhov, Hongwei Li, Jiazhen Pan, Sahand Sharifzadeh, Georgios Kaissis, Volker Tresp, Bjoern Menze
Published in: 2022
Publisher: Springer
DOI: 10.1007/978-3-031-19836-6_24

Semi-Supervised Variational Autoencoder for Survival Prediction

Author(s): Pálsson, Sveinn; Cerri, Stefano; Dittadi, Andrea; Van Leemput, Koen
Published in: International MICCAI Brainlesion Workshop, 2020
Publisher: Springer
DOI: 10.1007/978-3-030-46643-5_12

Cranial Implant Prediction using Low-Resolution 3D Shape Completion and High-Resolution 2D Refinement

Author(s): Bayat, Amirhossein; Shit, Suprosanna; Kilian, Adrian; Liechtenstein, J��rgen T.; Kirschke, Jan S.; Menze, Bjoern H.
Published in: Lecture Notes in Computer Science, 2020
Publisher: Springer
DOI: 10.48550/arxiv.2009.10769

A Longitudinal Method for Simultaneous Whole-Brain and Lesion Segmentation in Multiple Sclerosis

Author(s): Cerri, Stefano; Hoopes, Andrew; Greve, Douglas N.; M��hlau, Mark; Van Leemput, Koen
Published in: Machine Learning in Clinical Neuroimaging and Radiogenomics in Neuro-oncology., 2020
Publisher: Springer
DOI: 10.48550/arxiv.2008.05117

Label-set Loss Functions for Partial Supervision: Application to Fetal Brain 3D MRI Parcellation

Author(s): Fidon, Lucas; Aertsen, Michael; Emam, Doaa; Mufti, Nada; Guffens, Fr��d��ric; Deprest, Thomas; Demaerel, Philippe; David, Anna L.; Melbourne, Andrew; Ourselin, S��bastien; Deprest, Jan; Vercauteren, Tom
Published in: Medical Image Computing and Computer Assisted Intervention – MICCAI 2021, 2021, Page(s) 647–657, ISBN 978-3-030-87196-3
Publisher: Springer
DOI: 10.1007/978-3-030-87196-3_60

Spatio-temporal motion correction and iterative reconstruction of in-utero fetal fMRI

Author(s): Taymourtash, A., Kebiri, H., Schwartz, E., Nenning, K.H., Tourbier, S., Kasprian, G., Prayer, D., Bach Cuadra, M. and Langs, G
Published in: International Conference on Medical Image Computing and Computer-Assisted Intervention 2022, 2022
Publisher: Springer
DOI: 10.1007/978-3-031-16446-0_57

Red-GAN: Attacking class imbalance via conditioned generation. Yet another perspective on medical image synthesis for skin lesion dermoscopy and brain tumor MRI

Author(s): Qasim, Ahmad B; Ezhov, Ivan; Shit, Suprosanna; Schoppe, Oliver; Paetzold, Johannes C; Sekuboyina, Anjany; Kofler, Florian; Lipkova, Jana; Li, Hongwei; Menze, Bjoern
Published in: Proceedings of Machine Learning Research, 2020
Publisher: 2640-3498
DOI: 10.48550/arxiv.2004.10734

Generalized Wasserstein Dice Loss, Test-Time Augmentation, and Transformers for the BraTS 2021 Challenge

Author(s): Lucas Fidon, Suprosanna Shit, Ivan Ezhov, Johannes C. Paetzold, Sébastien Ourselin, Tom Vercauteren
Published in: Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2021, 2022, Page(s) 187-196, ISBN 978-3-031-09002-8
Publisher: Springer
DOI: 10.1007/978-3-031-09002-8_17

Automated Detection of Cortical Lesions in Multiple Sclerosis Patients with 7T MRI

Author(s): Francesco La Rosa; Erin S Beck; Ahmed Abdulkadir; Jean-Philippe Thiran; Daniel S. Reich; Pascal Sati; Meritxell Bach Cuadra
Published in: Medical Image Computing and Computer Assisted Intervention – MICCAI 2020, 2020, ISBN 978-3-030-59719-1
Publisher: Springer, Cham
DOI: 10.1007/978-3-030-59719-1_57

Muti-shell Diffusion MRI Harmonisation and Enhancement Challenge (MUSHAC): Progress and Results

Author(s): Lipeng Ning, Elisenda Bonet-Carne, Francesco Grussu, Farshid Sepehrband, Enrico Kaden, Jelle Veraart, Stefano B. Blumberg, Can Son Khoo, Marco Palombo, Jaume Coll-Font, Benoit Scherrer, Simon K. Warfield, Suheyla Cetin Karayumak, Yogesh Rathi, Simon Koppers, Leon Weninger, Julia Ebert, Dorit Merhof, Daniel Moyer, Maximilian Pietsch, Daan Christiaens, Rui Teixeira, Jacques-Donald Tournier, Andrey Z
Published in: Computational Diffusion MRI - International MICCAI Workshop, Granada, Spain, September 2018, 2019, Page(s) 217-224, ISBN 978-3-030-05830-2
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-05831-9_18

Neural Parameters Estimation for Brain Tumor Growth Modeling

Author(s): Ivan Ezhov, Jana Lipkova, Suprosanna Shit, Florian Kofler, Nore Collomb, Benjamin Lemasson, Emmanuel Barbier, Bjoern Menze
Published in: Medical Image Computing and Computer Assisted Intervention – MICCAI 2019 - 22nd International Conference, Shenzhen, China, October 13–17, 2019, Proceedings, Part II, Issue 11765, 2019, Page(s) 787-795, ISBN 978-3-030-32244-1
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-32245-8_87

Robust Biophysical Parameter Estimation with a Neural Network Enhanced Hamiltonian Markov Chain Monte Carlo Sampler

Author(s): Thomas Yu, Marco Pizzolato, Gabriel Girard, Jonathan Rafael-Patino, Erick Jorge Canales-Rodríguez, Jean-Philippe Thiran
Published in: Information Processing in Medical Imaging - 26th International Conference, IPMI 2019, Hong Kong, China, June 2–7, 2019, Proceedings, Issue 11492, 2019, Page(s) 818-829, ISBN 978-3-030-20350-4
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-20351-1_64

Shape-Aware Complementary-Task Learning for Multi-organ Segmentation

Author(s): Fernando Navarro, Suprosanna Shit, Ivan Ezhov, Johannes Paetzold, Andrei Gafita, Jan C. Peeken, Stephanie E. Combs, Bjoern H. Menze
Published in: Machine Learning in Medical Imaging - 10th International Workshop, MLMI 2019, Held in Conjunction with MICCAI 2019, Shenzhen, China, October 13, 2019, Proceedings, Issue 11861, 2019, Page(s) 620-627, ISBN 978-3-030-32691-3
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-32692-0_71

A novel segmentation framework for uveal melanoma in magnetic resonance imaging based on class activation maps

Author(s): Huu-Giao Nguyen, Alessia Pica, Jan Hrbacek, Damien C. Weber, Francesco La Rosa, Ann Schalenbourg, Raphael Sznitman, Meritxell Bach Cuadra
Published in: MIDL2019, 2019
Publisher: Proceedings of Machine Learning Research

Quantifying Residual Motion Artifacts in Fetal fMRI Data

Author(s): Athena Taymourtash, Ernst Schwartz, Karl-Heinz Nenning, Daniel Sobotka, Mariana Diogo, Gregor Kasprian, Daniela Prayer, Georg Langs
Published in: Smart Ultrasound Imaging and Perinatal, Preterm and Paediatric Image Analysis - First International Workshop, SUSI 2019, and 4th International Workshop, PIPPI 2019, Held in Conjunction with MICCAI 2019, Shenzhen, China, October 13 and 17, 2019, Proceedings, Issue 11798, 2019, Page(s) 171-180, ISBN 978-3-030-32874-0
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-32875-7_19

Relevance Vector Machines for Harmonization of MRI Brain Volumes Using Image Descriptors

Author(s): Maria Ines Meyer, Ezequiel de la Rosa, Koen Van Leemput, Diana M. Sima
Published in: OR 2.0 Context-Aware Operating Theaters and Machine Learning in Clinical Neuroimaging - Second International Workshop, OR 2.0 2019, and Second International Workshop, MLCN 2019, Held in Conjunction with MICCAI 2019, Shenzhen, China, October 13 and 17, 2019, Proceedings, Issue 11796, 2019, Page(s) 77-85, ISBN 978-3-030-32694-4
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-32695-1_9

Implicit Neural Solver for Time-dependent Linear PDEs with Convergence Guarantee

Author(s): Suprosanna Shit, Abinav Ravi Venkatakrishnan, Ivan Ezhov, Jana Lipkova, Marie Piraud, Bjoern Menze
Published in: NeurIPS 2019, 2019
Publisher: NIPS proceedings

Incompressible Image Registration Using Divergence-Conforming B-Splines

Author(s): Lucas Fidon, Michael Ebner, Luis C. Garcia-Peraza-Herrera, Marc Modat, Sébastien Ourselin, Tom Vercauteren
Published in: Medical Image Computing and Computer Assisted Intervention – MICCAI 2019 - 22nd International Conference, Shenzhen, China, October 13–17, 2019, Proceedings, Part II, Issue 11765, 2019, Page(s) 438-446, ISBN 978-3-030-32244-1
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-32245-8_49

Robust T 2 Relaxometry With Hamiltonian MCMC for Myelin Water Fraction Estimation

Author(s): Thomas Yu, Marco Pizzolato, Erick Jorge Canales-Rodriguez, Jean-Philippe Thiran
Published in: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), 2019, Page(s) 1813-1817, ISBN 978-1-5386-3641-1
Publisher: IEEE
DOI: 10.1109/isbi.2019.8759446

Shallow vs Deep Learning Architectures for White Matter Lesion Segmentation in the Early Stages of Multiple Sclerosis

Author(s): Francesco La Rosa, Mário João Fartaria, Tobias Kober, Jonas Richiardi, Cristina Granziera, Jean-Philippe Thiran, Meritxell Bach Cuadra
Published in: Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries - 4th International Workshop, BrainLes 2018, Held in Conjunction with MICCAI 2018, Granada, Spain, September 16, 2018, Revised Selected Papers, Part I, Issue 11383, 2019, Page(s) 142-151, ISBN 978-3-030-11722-1
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-11723-8_14

clDice - a Novel Connectivity-Preserving Loss Function for Vessel Segmentation

Author(s): Johannes Paetzold, Suprosanna Shit, Ivan Ezhov, Giles Tetteh, Ali Ertuerk, Bjoern Menze
Published in: NeurIPS 2019, 2019
Publisher: NIPS proceedings

A Radiomics Approach to Traumatic Brain Injury Prediction in CT Scans

Author(s): Ezequiel de la Rosa, Diana M. Sima, Thijs Vande Vyvere, Jan S. Kirschke, Bjoern Menze
Published in: Proceedings IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019). Apr. 2019, IEEE., 2019, Page(s) pp. 732-735, ISBN 978-1-5386-3641-1
Publisher: IEEE
DOI: 0.1109/isbi.2019.8759229

Improved inter-scanner MS lesion segmentation by adversarial training on longitudinal data

Author(s): Billast, Mattias; Meyer, Maria Ines; Sima, Diana M.; Robben, David
Published in: BrainLes 2019: Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries, 2020
Publisher: Springer
DOI: 10.48550/arxiv.2002.00952

Differentiable Deconvolution for Improved Stroke Perfusion Analysis

Author(s): de la Rosa, E., Robben, D., Sima, D.M., Kirschke, J.S., Menze, B.
Published in: Medical Image Computing and Computer Assisted Intervention – MICCAI 2020. MICCAI 2020. Lecture Notes in Computer Science, 2020
Publisher: Springer
DOI: 10.1007/978-3-030-59728-3_58

Knowledge-Guided Segmentation of Isointense Infant Brain

Author(s): Vujadinovic, J., Viana, J.S., de la Rosa, E., Ortibus, E., Sima, D.M
Published in: Perinatal, Preterm and Paediatric Image Analysis. PIPPI 2022. Lecture Notes in Computer Science, 2022
Publisher: Springer
DOI: 10.1007/978-3-031-17117-8_10

3D Reconstruction and Segmentation of Dissection Photographs for MRI-free Neuropathology

Author(s): Tregidgo, Henry; Casamitjana, Adria; Latimer, Caitlin; Kilgore, Mitchell; Robinson, Eleanor; Blackburn, Emily; Van Leemput, Koen; Fischl, Bruce; Dalca, Adrian; Mac Donald, Christine; Keene, Dirk; Iglesias, Juan Eugenio
Published in: Medical Image Computing and Computer Assisted Intervention – MICCAI 2020, 2020
Publisher: Springer
DOI: 10.48550/arxiv.2009.05596

A clinical research software prototype with diffusion MRI tractography for glioma surgery planning

Author(s): Daniel Krahulec, Frank Thiele, Ahmed Radwan, Fabian Wenzel, Stephan Sunaert, Maarten Versluis, Kim van de Ven, and Marcel Breeuwer
Published in: Proceedings OHBM 26th Annual Virtual Meeting, 2020
Publisher: OHBM

An Augmentation Strategy to Mimic Multi-Scanner Variability in MRI

Author(s): Maria Ines Meyer; Ezequiel de la Rosa; Nuno Pedrosa de Barros; Roberto Paolella; Koen Van Leemput; Diana M. Sima
Published in: IEEE 18th International Symposium on Biomedical Imaging (ISBI), 2021, Page(s) 1196-1200
Publisher: IEEE
DOI: 10.1109/isbi48211.2021.9433833

Robust, Primitive, and Unsupervised Quality Estimation for Segmentation Ensembles

Author(s): 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
Published in: Frontiers in Neuroscience, Issue 1662453X, 2021, Page(s) 752780, ISSN 1662-453X
Publisher: Frontiers
DOI: 10.3389/fnins.2021.752780

Geometry-aware neural solver for fast Bayesian calibration of brain tumor models

Author(s): 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
Published in: IEEE Transactions on Medical Imaging, Issue 1558254X, 2022, ISSN 1558-254X
Publisher: IEEE
DOI: 10.1109/tmi.2021.3136582

A spatio-temporal atlas of the developing fetal brain with spina bifida aperta

Author(s): 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
Published in: Open Research Europe, Issue 27325121, 2022, ISSN 2732-5121
Publisher: F1000 Research Limited
DOI: 10.12688/openreseurope.13914.2

Robust Multi-TE ASL-Based Blood–Brain Barrier Integrity Measurements

Author(s): Amnah Mahroo, Mareike Alicja Buck, Jörn Huber, Nora-Josefin Breutigam, Henk J. M. M. Mutsaerts, Martin Craig, Michael Chappell, Matthias Günther
Published in: Frontiers in Neuroscience, Issue 15, 2021, ISSN 1662-453X
Publisher: Frontiers Media SA
DOI: 10.3389/fnins.2021.719676

Learn-Morph-Infer: a new way of solving the inverse problem for brain tumor modeling

Author(s): 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
Published in: Medical Image Analysis, Issue 13618415, 2023, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2022.102672

icobrain ms 5.1: Combining unsupervised and supervised approaches for improving the detection of multiple sclerosis lesions

Author(s): Rakić M, Vercruyssen S, Van Eyndhoven S, de la Rosa E, Jain S, Van Huffel S, Maes F, Smeets D, Sima DM
Published in: NeuroImage: Clinical, Issue 22131582, 2021, ISSN 2213-1582
Publisher: Elsevier BV
DOI: 10.1016/j.nicl.2021.102707

Joint embedding: A scalable alignment to compare individuals in a connectivity space.

Author(s): 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; Georg Langs
Published in: NeuroImage, Issue 10538119, 2020, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2020.117232

Dynamic memory to alleviate catastrophic forgetting in continual learning with medical imaging.

Author(s): Matthias Perkonigg; Johannes Hofmanninger; Christian J. Herold; James A. Brink; Oleg S. Pianykh; Helmut Prosch; Georg Langs
Published in: Nature Communications, Issue 20411723, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-25858-z

AIFNet: Automatic vascular function estimation for perfusion analysis using deep learning.

Author(s): Ezequiel de la Rosa; Diana M. Sima; Bjoern H. Menze; Jan S. Kirschke; David Robben
Published in: Medical Image Analysis, Issue 13618415, 2021, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2021.102211

Distributionally Robust Deep Learning using Hardness Weighted Sampling

Author(s): 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
Published in: Machine Learning for Biomedical Imaging, Issue 2766905X, 2022, ISSN 2766-905X
Publisher: MELBA
DOI: 10.48550/arxiv.2001.02658

Revisiting the T2 spectrum imaging inverse problem: Bayesian regularized non-negative least squares.

Author(s): 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
Published in: NeuroImage, Issue 10538119, 2021, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2021.118582

Anatomically informed multi-level fiber tractography for targeted virtual dissection

Author(s): Andrey Zhylka; Alexander Leemans; Josien P. W. Pluim; Alberto De Luca
Published in: Magnetic Resonance Materials in Physics, Biology and Medicine, Issue 13528661, 2022, ISSN 1352-8661
Publisher: Springer
DOI: 10.1007/s10334-022-01033-3

PSACNN: Pulse sequence adaptive fast whole brain segmentation

Author(s): Amod Jog; Andrew Hoopes; Douglas N. Greve; Koen Van Leemput; Bruce Fischl
Published in: Jog , A , Hoopes , A , Greve , D N , Van Leemput , K & Fischl , B 2019 , ' PSACNN: Pulse sequence adaptive fast whole brain segmentation ' , NeuroImage , vol. 199 , pp. 553-569 . https://doi.org/10.1016/j.neuroimage.2019.05.033, Issue 19, 2019, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2019.05.033

Enhanced registration of ultrasound volumes by segmentation of resection cavity in neurosurgical procedures.

Author(s): Luca Canalini; Jan Klein; Dorothea Miller; Ron Kikinis
Published in: International Journal of Computer Assisted Radiology and Surgery, Issue 18616429, 2020, ISSN 1861-6429
Publisher: Springer VErlag
DOI: 10.1007/s11548-020-02273-1

Fetal Brain Biometric Measurements on 3D Super-Resolution Reconstructed T2-Weighted MRI: An Intra- and Inter-observer Agreement Study.

Author(s): 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
Published in: Frontiers in Pediatrics, Issue 22962360, 2021, ISSN 2296-2360
Publisher: Frontiers
DOI: 10.3389/fped.2021.639746

Automated MRI volumetry as a diagnostic tool for Alzheimer's disease: Validation of icobrain dm.

Author(s): 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
Published in: NeuroImage: Clinical, Issue Vol 26, 2020, Page(s) 102243, ISSN 2213-1582
Publisher: Elsevier BV
DOI: 10.1016/j.nicl.2020.102243

A Fetal Brain magnetic resonance Acquisition Numerical phantom (FaBiAN)

Author(s): 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
Published in: Scientific Reports, Issue 20452322, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-10335-4

Segmentation-based registration of ultrasound volumes for glioma resection in image-guided neurosurgery

Author(s): Luca Canalini, Jan Klein, Dorothea Miller, Ron Kikinis
Published in: International Journal of Computer Assisted Radiology and Surgery, Issue 14/10, 2019, Page(s) 1697-1713, ISSN 1861-6410
Publisher: Springer Verlag
DOI: 10.1007/s11548-019-02045-6

A modality-adaptive method for segmenting brain tumors and organs-at-risk in radiation therapy planning

Author(s): Mikael Agn, Per Munck af Rosenschöld, Oula Puonti, Michael J. Lundemann, Laura Mancini, Anastasia Papadaki, Steffi Thust, John Ashburner, Ian Law, Koen Van Leemput
Published in: Medical Image Analysis, Issue 54, 2019, Page(s) 220-237, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2019.03.005

Image Compositing for Segmentation of Surgical Tools without Manual Annotations.

Author(s): Luis C. Garcia-Peraza-Herrera; Lucas Fidon; Claudia D'Ettorre; Danail Stoyanov; Tom Vercauteren; Sebastien Ourselin
Published in: IEEE Transactions on Medical Imaging, Issue 02780062, 2021, Page(s) 1450-1460, ISSN 0278-0062
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.48550/arxiv.2102.09528

Quantitative evaluation of the influence of multiple MRI sequences and of pathological tissues on the registration of longitudinal data acquired in brain tumor treatment

Author(s): Luca Canalini, Jan Klein, Diana Waldmannstetter, Florian Kofler, Stefano Cerri, Alessa Hering, Stefan Heldmann, Sarah Schlaeger, Bjoern Menze, Benedikt Wiestler, Jan Kirschke, Horst Hahn
Published in: Frontiers in Neuroimaging, section Brain Imaging Methods, Issue 28131193, 2022, ISSN 2813-1193
Publisher: Frontiers
DOI: 10.3389/fnimg.2022.977491

SRflow: Deep learning based super-resolution of 4D-flow MRI data

Author(s): S. Shit, J. Zimmermann, I. Ezhov, J. Paetzold, A. F. Sanches, C. Pirkl, and B. H. Menze
Published in: Frontiers in Artificial Intelligence, Issue 26248212, 2022, ISSN 2624-8212
Publisher: Frontier
DOI: 10.3389/frai.2022.928181

Comparison of non-parametric T2 relaxometry methods for myelin water quantification

Author(s): 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
Published in: Medical Image Analysis, Issue 13618415, 2021, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2021.101959

Cortical spectral matching and shape and volume analysis of the fetal brain pre- and post-fetal surgery for spina bifida: a retrospective study

Author(s): 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
Published in: Neuroradiology, Issue 00283940, 2021, Page(s) 1721–1734, ISSN 0028-3940
Publisher: Springer Verlag
DOI: 10.1007/s00234-021-02725-8

Diagnostic Performance of Automated MRI Volumetry by icobrain dm for Alzheimer’s Disease in a Clinical Setting: A REMEMBER Study

Author(s): 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.
Published in: Journal of Alzheimer's Disease, Issue 13872877, 2021, Page(s) 623-639, ISSN 1387-2877
Publisher: IOS Press
DOI: 10.3233/jad-210450

MPRAGE to MP2RAGE UNI translation via generative adversarial network improves the automatic tissue and lesion segmentation in multiple sclerosis patients

Author(s): La Rosa, Francesco, Thomas Yu, Germán Barquero, Jean-Philippe Thiran, Cristina Granziera, and Meritxell Bach Cuadra.
Published in: Computers in Biology and Medicine, Issue 00104825, 2021, ISSN 0010-4825
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.compbiomed.2021.104297

Model-informed machine learning for multi-component T2 relaxometry.

Author(s): 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
Published in: Medical Image Analysis, Issue 13618415, 2021, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.48550/arxiv.2007.10225

Magnetic resonance-based computed tomography metal artifact reduction using Bayesian modelling.

Author(s): Jonathan Scharff Nielsen; Jens Edmund; Koen Van Leemput
Published in: Physics in Medicine & Biology, 2019, ISSN 0031-9155
Publisher: Institute of Physics Publishing
DOI: 10.1088/1361-6560/ab5b70

RimNet: A deep 3D multimodal MRI architecture for paramagnetic rim lesion assessment in multiple sclerosis

Author(s): 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
Published in: Neuroimage Clinical, Issue 22131582, 2020, ISSN 2213-1582
Publisher: Elsevier BV
DOI: 10.1016/j.nicl.2020.102412

Predicting survival of glioblastoma from automatic whole-brain and tumor segmentation of MR images

Author(s): Sveinn Pálsson, Stefano Cerri, Hans Skovgaard Poulsen, Thomas Urup, Ian Law, Koen Van Leemput
Published in: Scientific Reports, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-19223-3

Distributed changes of the functional connectome in patients with glioblastoma.

Author(s): 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
Published in: Scientific Reports, Issue 20452322, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-74726-1

A contrast-adaptive method for simultaneous whole-brain and lesion segmentation in multiple sclerosis

Author(s): Stefano Cerri, Oula Puonti. Dominik S.Meier, Jens Wuerfel, Mark Mühlau, Hartwig R.Siebner, KoenVan Leemput
Published in: NeuroImage, Issue 10538119, 2021, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2020.117471

Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?

Author(s): Maffei, Chiara, Gabriel Girard, Kurt G. Schilling, Dogu Baran Aydogan, Nagesh Adluru, Andrey Zhylka, Ye Wu et al
Published in: NeuroImage, Issue 10538119, 2021, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2022.119327

MR-based CT metal artifact reduction for head-and-neck photon, electron, and proton radiotherapy.

Author(s): Jonathan Scharff Nielsen; Jonathan Scharff Nielsen; Koen Van Leemput; Koen Van Leemput; Jens Edmund
Published in: Medical Physics, 2019, ISSN 2473-4209
Publisher: Wiley
DOI: 10.1002/mp.13729

A Contrast Augmentation Approach to Improve Multi-Scanner Generalization in MRI.

Author(s): 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
Published in: Frontiers in Neuroscience, Issue 16624548, 2021, Page(s) 708196, ISSN 1662-4548
Publisher: Frontiers Research Foundation
DOI: 10.3389/fnins.2021.708196

Multiple sclerosis cortical and WM lesion segmentation at 3T MRI: a deep learning method based on FLAIR and MP2RAGE

Author(s): 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
Published in: NeuroImage. Clinical, vol. 27, pp. 102335, Issue 22131582, 2020, ISSN 2213-1582
Publisher: Elsevier BV
DOI: 10.1016/j.nicl.2020.102335

Effect of corpus callosum agenesis on the language network in children and adolescents

Author(s): Lisa Bartha-Doering; Ernst Schwartz; Kathrin Kollndorfer; Florian Ph. S. Fischmeister; Astrid Novak; Georg Langs; Harald Werneck; Daniela Prayer; Rainer Seidl; Gregor Kasprian
Published in: Brain structure & function, Issue 18632661, 2021, ISSN 1863-2661
Publisher: Springer
DOI: 10.1007/s00429-020-02203-6

An Open-Source Tool for Longitudinal Whole-Brain and White Matter Lesion Segmentation

Author(s): Stefano Cerri, Douglas N. Greve, Andrew Hoopes, Henrik Lundell, Hartwig R. Siebner, Mark Mühlau, Koen Van Leemput
Published in: arXiv, 2022
Publisher: arXiv

MONAIfbs: MONAI-based fetal brain MRI deep learning segmentation

Author(s): Ranzini, Marta B. M.; Fidon, Lucas; Ourselin, Sébastien; Modat, Marc; Vercauteren, Tom
Published in: IEEE International Symposium on Biomedical Imaging (ISBI) 2021 - Short Extended Abstract, 2021
Publisher: arXiv
DOI: 10.48550/arxiv.2103.13314

Comparative study of deep learning methods for the automatic segmentation of lung, lesion and lesion type in CT scans of COVID-19 patients

Author(s): Sofie Tilborghs; Ine Dirks; Lucas Fidon; Siri Willems; Tom Eelbode; Jeroen Bertels; Bart Ilsen; Arne Brys; Adriana Dubbeldam; Nico Buls; Panagiotis Gonidakis; Sebastian Amador; Annemiek Snoeckx; Parizel, Paul M.; Johan de Mey; Dirk Vandermeulen; Tom Vercauteren; David Robben; Dirk Smeets; Frederik Maes; Jef Vandemeulebroucke; Paul Suetens
Published in: arXiv, 2020
Publisher: arXiv
DOI: 10.5281/zenodo.5847470

Microstructural Imaging in Stroke Patients

Author(s): Carmen Genis, Hanne Krarup Christensen, Tim B. Dyrby
Published in: 2019
Publisher: ClinicalTrails.gov

ESMRMB 2019, 36th Annual Scientific Meeting, Rotterdam, NL, October 3–October 5: Abstracts, Thursday

Author(s): A. Zhylka, A. Leemans, J. Pluim, A. De Luca
Published in: Magnetic Resonance Materials in Physics, Biology and Medicine, Issue 32/S1, 2019, Page(s) 1-105, ISSN 0968-5243
Publisher: Springer Verlag
DOI: 10.1007/s10334-019-00753-3

Harmonization of Brain Volumes from Magnetic Resonance Images of Multiple Sclerosis Patients Using Image Descriptors

Author(s): Maria Ines Meyer, Ezequiel de la Rosa, Greg Dudra, Eline Van Vlierberghe, Koen Van Leemput, Diana M. Sima
Published in: International Journal of MS case, 2019, Page(s) Pp 51
Publisher: Consortium of Multiple Sclerosis Centers

Deep learning-based detection of cortical lesions in multiple sclerosis patients with FLAIR, DIR, and MP2RAGE MRI sequences.

Author(s): F. La Rosa, M.J. Fartaria, A. Abdulkadir, R. Rahmanzadeh,, P.-J. Lu, R. Galbusera, C. Granziera, J.-P. Thiran, M. Bach Cuadra
Published in: ECTRIMS proceedings in Multiple Sclerosis Journal, 2019
Publisher: SAGE PUBLICATIONS LTD

Registration of Ultrasound Volumes Based on Euclidean Distance Transform

Author(s): Luca Canalini, Jan Klein, Dorothea Miller, Ron Kikinis
Published in: Large-Scale Annotation of Biomedical Data and Expert Label Synthesis and Hardware Aware Learning for Medical Imaging and Computer Assisted Intervention - International Workshops, LABELS 2019, HAL-MICCAI 2019, and CuRIOUS 2019, Held in Conjunction with MICCAI 2019, Shenzhen, China, October 13 and 17, 2019, Proceedings, Issue 11851, 2019, Page(s) 127-135, ISBN 978-3-030-33641-7
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-33642-4_14

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