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598 results on '"Cuadra, Meritxell"'

54. Shallow vs deep learning architectures for white matter lesion segmentation in the early stages of multiple sclerosis

Author

La Rosa, Francesco, Fartaria, Mário João, Kober, Tobias, Richiardi, Jonas, Granziera, Cristina, Thiran, Jean-Philippe, and Cuadra, Meritxell Bach

Subjects
Computer Science - Machine Learning, Computer Science - Computer Vision and Pattern Recognition, Statistics - Machine Learning
Abstract

In this work, we present a comparison of a shallow and a deep learning architecture for the automated segmentation of white matter lesions in MR images of multiple sclerosis patients. In particular, we train and test both methods on early stage disease patients, to verify their performance in challenging conditions, more similar to a clinical setting than what is typically provided in multiple sclerosis segmentation challenges. Furthermore, we evaluate a prototype naive combination of the two methods, which refines the final segmentation. All methods were trained on 32 patients, and the evaluation was performed on a pure test set of 73 cases. Results show low lesion-wise false positives (30%) for the deep learning architecture, whereas the shallow architecture yields the best Dice coefficient (63%) and volume difference (19%). Combining both shallow and deep architectures further improves the lesion-wise metrics (69% and 26% lesion-wise true and false positive rate, respectively)., Comment: Accepted to the MICCAI 2018 Brain Lesion (BrainLes) workshop

Published
2018

56. A Fetal Brain magnetic resonance Acquisition Numerical phantom (FaBiAN)

Author

Lajous, Hélène, Roy, Christopher W., Hilbert, Tom, de Dumast, Priscille, Tourbier, Sébastien, Alemán-Gómez, Yasser, Yerly, Jérôme, Yu, Thomas, Kebiri, Hamza, Payette, Kelly, Ledoux, Jean-Baptiste, Meuli, Reto, Hagmann, Patric, Jakab, Andras, Dunet, Vincent, Koob, Mériam, Kober, Tobias, Stuber, Matthias, and Bach Cuadra, Meritxell

Published
2022
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57. Diagnostic Surveillance of High-Grade Gliomas: Towards Automated Change Detection Using Radiology Report Classification

Author

Di Noto, Tommaso, Atat, Chirine, Teiga, Eduardo Gamito, Hegi, Monika, Hottinger, Andreas, Cuadra, Meritxell Bach, Hagmann, Patric, Richiardi, Jonas, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Kamp, Michael, editor, Koprinska, Irena, editor, Bibal, Adrien, editor, Bouadi, Tassadit, editor, Frénay, Benoît, editor, Galárraga, Luis, editor, Oramas, José, editor, Adilova, Linara, editor, Krishnamurthy, Yamuna, editor, Kang, Bo, editor, Largeron, Christine, editor, Lijffijt, Jefrey, editor, Viard, Tiphaine, editor, Welke, Pascal, editor, Ruocco, Massimiliano, editor, Aune, Erlend, editor, Gallicchio, Claudio, editor, Schiele, Gregor, editor, Pernkopf, Franz, editor, Blott, Michaela, editor, Fröning, Holger, editor, Schindler, Günther, editor, Guidotti, Riccardo, editor, Monreale, Anna, editor, Rinzivillo, Salvatore, editor, Biecek, Przemyslaw, editor, Ntoutsi, Eirini, editor, Pechenizkiy, Mykola, editor, Rosenhahn, Bodo, editor, Buckley, Christopher, editor, Cialfi, Daniela, editor, Lanillos, Pablo, editor, Ramstead, Maxwell, editor, Verbelen, Tim, editor, Ferreira, Pedro M., editor, Andresini, Giuseppina, editor, Malerba, Donato, editor, Medeiros, Ibéria, editor, Fournier-Viger, Philippe, editor, Nawaz, M. Saqib, editor, Ventura, Sebastian, editor, Sun, Meng, editor, Zhou, Min, editor, Bitetta, Valerio, editor, Bordino, Ilaria, editor, Ferretti, Andrea, editor, Gullo, Francesco, editor, Ponti, Giovanni, editor, Severini, Lorenzo, editor, Ribeiro, Rita, editor, Gama, João, editor, Gavaldà, Ricard, editor, Cooper, Lee, editor, Ghazaleh, Naghmeh, editor, Richiardi, Jonas, editor, Roqueiro, Damian, editor, Saldana Miranda, Diego, editor, Sechidis, Konstantinos, editor, and Graça, Guilherme, editor

Published
2021
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58. Segmentation of the Cortical Plate in Fetal Brain MRI with a Topological Loss

Author

de Dumast, Priscille, Kebiri, Hamza, Atat, Chirine, Dunet, Vincent, Koob, Mériam, Cuadra, Meritxell Bach, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Sudre, Carole H., editor, Licandro, Roxane, editor, Baumgartner, Christian, editor, Melbourne, Andrew, editor, Dalca, Adrian, editor, Hutter, Jana, editor, Tanno, Ryutaro, editor, Abaci Turk, Esra, editor, Van Leemput, Koen, editor, Torrents Barrena, Jordina, editor, Wells, William M., editor, and Macgowan, Christopher, editor

Published
2021
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59. Simulated Half-Fourier Acquisitions Single-shot Turbo Spin Echo (HASTE) of the Fetal Brain: Application to Super-Resolution Reconstruction

Author

Lajous, Hélène, Hilbert, Tom, Roy, Christopher W., Tourbier, Sébastien, de Dumast, Priscille, Alemán-Gómez, Yasser, Yu, Thomas, Kebiri, Hamza, Ledoux, Jean-Baptiste, Hagmann, Patric, Meuli, Reto, Dunet, Vincent, Koob, Mériam, Stuber, Matthias, Kober, Tobias, Bach Cuadra, Meritxell, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Sudre, Carole H., editor, Licandro, Roxane, editor, Baumgartner, Christian, editor, Melbourne, Andrew, editor, Dalca, Adrian, editor, Hutter, Jana, editor, Tanno, Ryutaro, editor, Abaci Turk, Esra, editor, Van Leemput, Koen, editor, Torrents Barrena, Jordina, editor, Wells, William M., editor, and Macgowan, Christopher, editor

Published
2021
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60. Quantitative Evaluation of Enhanced Multi-plane Clinical Fetal Diffusion MRI with a Crossing-Fiber Phantom

Author

Kebiri, Hamza, Lajous, Hélène, Alemán-Gómez, Yasser, Girard, Gabriel, Rodríguez, Erick Canales, Tourbier, Sébastien, Pizzolato, Marco, Ledoux, Jean-Baptiste, Fornari, Eleonora, Jakab, András, Cuadra, Meritxell Bach, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Cetin-Karayumak, Suheyla, editor, Christiaens, Daan, editor, Figini, Matteo, editor, Guevara, Pamela, editor, Gyori, Noemi, editor, Nath, Vishwesh, editor, and Pieciak, Tomasz, editor

Published
2021
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70. Shallow vs Deep Learning Architectures for White Matter Lesion Segmentation in the Early Stages of Multiple Sclerosis

Author

La Rosa, Francesco, Fartaria, Mário João, Kober, Tobias, Richiardi, Jonas, Granziera, Cristina, Thiran, Jean-Philippe, Cuadra, Meritxell Bach, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Crimi, Alessandro, editor, Bakas, Spyridon, editor, Kuijf, Hugo, editor, Keyvan, Farahani, editor, Reyes, Mauricio, editor, and van Walsum, Theo, editor

Published
2019
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72. MBIS: Multivariate Bayesian Image Segmentation Tool

Author

Esteban, Oscar, Wollny, Gert, Gorthi, Subrahmanyam, Ledesma-Carbayo, Maria-J., Thiran, Jean-Philippe, Santos, Andres, and Bach-Cuadra, Meritxell

Subjects
Computer Science - Computer Vision and Pattern Recognition, 62P10, 62F15
Abstract

We present MBIS (Multivariate Bayesian Image Segmentation tool), a clustering tool based on the mixture of multivariate normal distributions model. MBIS supports multi-channel bias field correction based on a B-spline model. A second methodological novelty is the inclusion of graph-cuts optimization for the stationary anisotropic hidden Markov random field model. Along with MBIS, we release an evaluation framework that contains three different experiments on multi-site data. We first validate the accuracy of segmentation and the estimated bias field for each channel. MBIS outperforms a widely used segmentation tool in a cross-comparison evaluation. The second experiment demonstrates the robustness of results on atlas-free segmentation of two image sets from scan-rescan protocols on 21 healthy subjects. Multivariate segmentation is more replicable than the monospectral counterpart on T1-weighted images. Finally, we provide a third experiment to illustrate how MBIS can be used in a large-scale study of tissue volume change with increasing age in 584 healthy subjects. This last result is meaningful as multivariate segmentation performs robustly without the need for prior knowledge

Published
2014
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73. An automatic multi-tissue human fetal brain segmentation benchmark using the Fetal Tissue Annotation Dataset

Author

Payette, Kelly, de Dumast, Priscille, Kebiri, Hamza, Ezhov, Ivan, Paetzold, Johannes C., Shit, Suprosanna, Iqbal, Asim, Khan, Romesa, Kottke, Raimund, Grehten, Patrice, Ji, Hui, Lanczi, Levente, Nagy, Marianna, Beresova, Monika, Nguyen, Thi Dao, Natalucci, Giancarlo, Karayannis, Theofanis, Menze, Bjoern, Bach Cuadra, Meritxell, and Jakab, Andras

Published
2021
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74. Ocular Structures Segmentation from Multi-sequences MRI Using 3D Unet with Fully Connected CRFs

Author

Nguyen, Huu-Giao, Pica, Alessia, Maeder, Philippe, Schalenbourg, Ann, Peroni, Marta, Hrbacek, Jan, Weber, Damien C., Cuadra, Meritxell Bach, Sznitman, Raphael, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Stoyanov, Danail, editor, Taylor, Zeike, editor, Ciompi, Francesco, editor, Xu, Yanwu, editor, Martel, Anne, editor, Maier-Hein, Lena, editor, Rajpoot, Nasir, editor, van der Laak, Jeroen, editor, Veta, Mitko, editor, McKenna, Stephen, editor, Snead, David, editor, Trucco, Emanuele, editor, Garvin, Mona K., editor, Chen, Xin Jan, editor, and Bogunovic, Hrvoje, editor

Published
2018
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75. Quantitative Evaluation of Enhanced Multi-plane Clinical Fetal Diffusion MRI with a Crossing-Fiber Phantom

Author

Kebiri, Hamza, primary, Lajous, Hélène, additional, Alemán-Gómez, Yasser, additional, Girard, Gabriel, additional, Rodríguez, Erick Canales, additional, Tourbier, Sébastien, additional, Pizzolato, Marco, additional, Ledoux, Jean-Baptiste, additional, Fornari, Eleonora, additional, Jakab, András, additional, and Cuadra, Meritxell Bach, additional

Published
2021
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76. Simulated Half-Fourier Acquisitions Single-shot Turbo Spin Echo (HASTE) of the Fetal Brain: Application to Super-Resolution Reconstruction

Author

Lajous, Hélène, primary, Hilbert, Tom, additional, Roy, Christopher W., additional, Tourbier, Sébastien, additional, de Dumast, Priscille, additional, Alemán-Gómez, Yasser, additional, Yu, Thomas, additional, Kebiri, Hamza, additional, Ledoux, Jean-Baptiste, additional, Hagmann, Patric, additional, Meuli, Reto, additional, Dunet, Vincent, additional, Koob, Mériam, additional, Stuber, Matthias, additional, Kober, Tobias, additional, and Bach Cuadra, Meritxell, additional

Published
2021
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78. T2 Mapping from Super-Resolution-Reconstructed Clinical Fast Spin Echo Magnetic Resonance Acquisitions

Author

Lajous, Hélène, primary, Hilbert, Tom, additional, Roy, Christopher W., additional, Tourbier, Sébastien, additional, de Dumast, Priscille, additional, Yu, Thomas, additional, Thiran, Jean-Philippe, additional, Ledoux, Jean-Baptiste, additional, Piccini, Davide, additional, Hagmann, Patric, additional, Meuli, Reto, additional, Kober, Tobias, additional, Stuber, Matthias, additional, van Heeswijk, Ruud B., additional, and Bach Cuadra, Meritxell, additional

Published
2020
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81. Towards an Automated Segmentation of the Ventro-Intermediate Thalamic Nucleus

Author

Najdenovska, Elena, Tuleasca, Constantin, Jorge, João, Marques, José P., Maeder, Philippe, Thiran, Jean-Philippe, Levivier, Marc, Cuadra, Meritxell Bach, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Cardoso, M. Jorge, editor, Arbel, Tal, editor, Luo, Xiongbiao, editor, Wesarg, Stefan, editor, Reichl, Tobias, editor, González Ballester, Miguel Ángel, editor, McLeod, Jonathan, editor, Drechsler, Klaus, editor, Peters, Terry, editor, Erdt, Marius, editor, Mori, Kensaku, editor, Linguraru, Marius George, editor, Uhl, Andreas, editor, Oyarzun Laura, Cristina, editor, and Shekhar, Raj, editor

Published
2017
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82. Segmentation of Cortical and Subcortical Multiple Sclerosis Lesions Based on Constrained Partial Volume Modeling

Author

Fartaria, Mário João, Roche, Alexis, Meuli, Reto, Granziera, Cristina, Kober, Tobias, Bach Cuadra, Meritxell, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Descoteaux, Maxime, editor, Maier-Hein, Lena, editor, Franz, Alfred, editor, Jannin, Pierre, editor, Collins, D. Louis, editor, and Duchesne, Simon, editor

Published
2017
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97. FetMRQC: an open-source machine learning framework for multi-centric fetal brain MRI quality control

Author

Sanchez, Thomas, Esteban, Oscar, Gomez, Yvan, Pron, Alexandre, Koob, Mériam, Dunet, Vincent, Girard, Nadine, Jakab, Andras, Eixarch, Elisenda, Auzias, Guillaume, Cuadra, Meritxell Bach, Sanchez, Thomas, Esteban, Oscar, Gomez, Yvan, Pron, Alexandre, Koob, Mériam, Dunet, Vincent, Girard, Nadine, Jakab, Andras, Eixarch, Elisenda, Auzias, Guillaume, and Cuadra, Meritxell Bach

Abstract

Fetal brain MRI is becoming an increasingly relevant complement to neurosonography for perinatal diagnosis, allowing fundamental insights into fetal brain development throughout gestation. However, uncontrolled fetal motion and heterogeneity in acquisition protocols lead to data of variable quality, potentially biasing the outcome of subsequent studies. We present FetMRQC, an open-source machine-learning framework for automated image quality assessment and quality control that is robust to domain shifts induced by the heterogeneity of clinical data. FetMRQC extracts an ensemble of quality metrics from unprocessed anatomical MRI and combines them to predict experts' ratings using random forests. We validate our framework on a pioneeringly large and diverse dataset of more than 1600 manually rated fetal brain T2-weighted images from four clinical centers and 13 different scanners. Our study shows that FetMRQC's predictions generalize well to unseen data while being interpretable. FetMRQC is a step towards more robust fetal brain neuroimaging, which has the potential to shed new insights on the developing human brain., Comment: 22 pages, 10 Figures

Published
2023

98. Efficient Total Variation Algorithm for Fetal Brain MRI Reconstruction

Author

Tourbier, Sébastien, Bresson, Xavier, Hagmann, Patric, Thiran, Jean-Philippe, Meuli, Reto, Cuadra, Meritxell Bach, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Golland, Polina, editor, Hata, Nobuhiko, editor, Barillot, Christian, editor, Hornegger, Joachim, editor, and Howe, Robert, editor

Published
2014
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