no code implementations • 20 Mar 2024 • Xiaoling Hu, Annabel Sorby-Adams, Frederik Barkhof, W Taylor Kimberly, Oula Puonti, Juan Eugenio Iglesias
White matter hyperintensities (WMH) are a hallmark of cerebrovascular disease and multiple sclerosis.
no code implementations • 8 Dec 2023 • Pablo Laso, Stefano Cerri, Annabel Sorby-Adams, Jennifer Guo, Farrah Mateen, Philipp Goebl, Jiaming Wu, Peirong Liu, Hongwei Li, Sean I. Young, Benjamin Billot, Oula Puonti, Gordon Sze, Sam Payabavash, Adam DeHavenon, Kevin N. Sheth, Matthew S. Rosen, John Kirsch, Nicola Strisciuglio, Jelmer M. Wolterink, Arman Eshaghi, Frederik Barkhof, W. Taylor Kimberly, Juan Eugenio Iglesias
Brain atrophy and white matter hyperintensity (WMH) are critical neuroimaging features for ascertaining brain injury in cerebrovascular disease and multiple sclerosis.
no code implementations • 10 Aug 2023 • Tiantian He, Elinor Thompson, Anna Schroder, Neil P. Oxtoby, Ahmed Abdulaal, Frederik Barkhof, Daniel C. Alexander
We account for the heterogeneity of disease by fitting the model at the individual level, allowing the epicenters and rate of progression to vary among subjects.
1 code implementation • 18 Apr 2023 • Ragnhild Holden Helland, Alexandros Ferles, André Pedersen, Ivar Kommers, Hilko Ardon, Frederik Barkhof, Lorenzo Bello, Mitchel S. Berger, Tora Dunås, Marco Conti Nibali, Julia Furtner, Shawn Hervey-Jumper, Albert J. S. Idema, Barbara Kiesel, Rishi Nandoe Tewari, Emmanuel Mandonnet, Domenique M. J. Müller, Pierre A. Robe, Marco Rossi, Lisa M. Sagberg, Tommaso Sciortino, Tom Aalders, Michiel Wagemakers, Georg Widhalm, Marnix G. Witte, Aeilko H. Zwinderman, Paulina L. Majewska, Asgeir S. Jakola, Ole Solheim, Philip C. De Witt Hamer, Ingerid Reinertsen, Roelant S. Eijgelaar, David Bouget
The current standard method for estimating it is subject to high inter- and intra-rater variability, and an automated method for segmentation of residual tumor in early post-operative MRI could lead to a more accurate estimation of extent of resection.
no code implementations • 25 Feb 2023 • Lemuel Puglisi, Frederik Barkhof, Daniel C. Alexander, Geoffrey JM Parker, Arman Eshaghi, Daniele Ravì
Our framework is a semi-self-supervised contrastive deep learning approach with three main innovations.
no code implementations • 15 Aug 2022 • Carole H. Sudre, Kimberlin Van Wijnen, Florian Dubost, Hieab Adams, David Atkinson, Frederik Barkhof, Mahlet A. Birhanu, Esther E. Bron, Robin Camarasa, Nish Chaturvedi, Yuan Chen, Zihao Chen, Shuai Chen, Qi Dou, Tavia Evans, Ivan Ezhov, Haojun Gao, Marta Girones Sanguesa, Juan Domingo Gispert, Beatriz Gomez Anson, Alun D. Hughes, M. Arfan Ikram, Silvia Ingala, H. Rolf Jaeger, Florian Kofler, Hugo J. Kuijf, Denis Kutnar, Minho Lee, Bo Li, Luigi Lorenzini, Bjoern Menze, Jose Luis Molinuevo, Yiwei Pan, Elodie Puybareau, Rafael Rehwald, Ruisheng Su, Pengcheng Shi, Lorna Smith, Therese Tillin, Guillaume Tochon, Helene Urien, Bas H. M. van der Velden, Isabelle F. van der Velpen, Benedikt Wiestler, Frank J. Wolters, Pinar Yilmaz, Marius de Groot, Meike W. Vernooij, Marleen de Bruijne
This challenge aimed to promote the development of methods for automated detection and segmentation of small and sparse imaging markers of cerebral small vessel disease, namely enlarged perivascular spaces (EPVS) (Task 1), cerebral microbleeds (Task 2) and lacunes of presumed vascular origin (Task 3) while leveraging weak and noisy labels.
no code implementations • 29 Jun 2022 • Vikram Venkatraghavan, Sebastian R. van der Voort, Daniel Bos, Marion Smits, Frederik Barkhof, Wiro J. Niessen, Stefan Klein, Esther E. Bron
Regarding prediction, i. e. estimation of the future 'condition' of the patient, we will zoom in on use cases such as predicting the disease course in multiple sclerosis and predicting patient outcomes after treatment in brain cancer.
no code implementations • 7 Jun 2022 • Daniele Ravi, Frederik Barkhof, Daniel C. Alexander, Lemuel Puglisi, Geoffrey JM Parker, Arman Eshaghi
To tackle this problem, we propose a framework with four main components: 1) artefact generators inspired by magnetic resonance physics to corrupt brain MRI scans and augment a training dataset, 2) abstract and engineered features to represent images compactly, 3) a feature selection process depending on the artefact class to improve classification, and 4) SVM classifiers to identify artefacts.
1 code implementation • NeurIPS 2020 • Le Zhang, Ryutaro Tanno, MouCheng Xu, Chen Jin, Joseph Jacob, Olga Cicarrelli, Frederik Barkhof, Daniel Alexander
In all cases, our method outperforms competing methods and relevant baselines particularly in cases where the number of annotations is small and the amount of disagreement is large.
3 code implementations • 31 Jul 2020 • Le Zhang, Ryutaro Tanno, Mou-Cheng Xu, Chen Jin, Joseph Jacob, Olga Ciccarelli, Frederik Barkhof, Daniel C. Alexander
Recent years have seen increasing use of supervised learning methods for segmentation tasks.
4 code implementations • 9 Feb 2020 • Razvan V. Marinescu, Neil P. Oxtoby, Alexandra L. Young, Esther E. Bron, Arthur W. Toga, Michael W. Weiner, Frederik Barkhof, Nick C. Fox, Arman Eshaghi, Tina Toni, Marcin Salaterski, Veronika Lunina, Manon Ansart, Stanley Durrleman, Pascal Lu, Samuel Iddi, Dan Li, Wesley K. Thompson, Michael C. Donohue, Aviv Nahon, Yarden Levy, Dan Halbersberg, Mariya Cohen, Huiling Liao, Tengfei Li, Kaixian Yu, Hongtu Zhu, Jose G. Tamez-Pena, Aya Ismail, Timothy Wood, Hector Corrada Bravo, Minh Nguyen, Nanbo Sun, Jiashi Feng, B. T. Thomas Yeo, Gang Chen, Ke Qi, Shiyang Chen, Deqiang Qiu, Ionut Buciuman, Alex Kelner, Raluca Pop, Denisa Rimocea, Mostafa M. Ghazi, Mads Nielsen, Sebastien Ourselin, Lauge Sorensen, Vikram Venkatraghavan, Keli Liu, Christina Rabe, Paul Manser, Steven M. Hill, James Howlett, Zhiyue Huang, Steven Kiddle, Sach Mukherjee, Anais Rouanet, Bernd Taschler, Brian D. M. Tom, Simon R. White, Noel Faux, Suman Sedai, Javier de Velasco Oriol, Edgar E. V. Clemente, Karol Estrada, Leon Aksman, Andre Altmann, Cynthia M. Stonnington, Yalin Wang, Jianfeng Wu, Vivek Devadas, Clementine Fourrier, Lars Lau Raket, Aristeidis Sotiras, Guray Erus, Jimit Doshi, Christos Davatzikos, Jacob Vogel, Andrew Doyle, Angela Tam, Alex Diaz-Papkovich, Emmanuel Jammeh, Igor Koval, Paul Moore, Terry J. Lyons, John Gallacher, Jussi Tohka, Robert Ciszek, Bruno Jedynak, Kruti Pandya, Murat Bilgel, William Engels, Joseph Cole, Polina Golland, Stefan Klein, Daniel C. Alexander
TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease.
no code implementations • 3 Dec 2019 • Daniele Ravi, Stefano B. Blumberg, Silvia Ingala, Frederik Barkhof, Daniel C. Alexander, Neil P. Oxtoby
To evaluate our approach, we trained the framework on 9852 T1-weighted MRI scans from 876 participants in the Alzheimer's Disease Neuroimaging Initiative dataset and held out a separate test set of 1283 MRI scans from 170 participants for quantitative and qualitative assessment of the personalised time series of synthetic images.
1 code implementation • 1 Apr 2019 • Hugo J. Kuijf, J. Matthijs Biesbroek, Jeroen de Bresser, Rutger Heinen, Simon Andermatt, Mariana Bento, Matt Berseth, Mikhail Belyaev, M. Jorge Cardoso, Adrià Casamitjana, D. Louis Collins, Mahsa Dadar, Achilleas Georgiou, Mohsen Ghafoorian, Dakai Jin, April Khademi, Jesse Knight, Hongwei Li, Xavier Lladó, Miguel Luna, Qaiser Mahmood, Richard McKinley, Alireza Mehrtash, Sébastien Ourselin, Bo-yong Park, HyunJin Park, Sang Hyun Park, Simon Pezold, Elodie Puybareau, Leticia Rittner, Carole H. Sudre, Sergi Valverde, Verónica Vilaplana, Roland Wiest, Yongchao Xu, Ziyue Xu, Guodong Zeng, Jian-Guo Zhang, Guoyan Zheng, Christopher Chen, Wiesje van der Flier, Frederik Barkhof, Max A. Viergever, Geert Jan Biessels
Segmentation methods had to be containerized and submitted to the challenge organizers.