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BUNGEE-TOOLS SIGNED

Building Next-Generation Computational Tools for High Resolution Neuroimaging Studies

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

BUNGEE-TOOLS project word cloud

Explore the words cloud of the BUNGEE-TOOLS project. It provides you a very rough idea of what is the project "BUNGEE-TOOLS" about.

ex lies images ing nexus imaging structural superior core vivo resonance magnetic recent substructures modern relies combining organ inability health freesurfer tools economy neuroscience capitalize progress visible promise acquisition quest generation ultra day lower atlas decade designed brain tremendous improvement fsl human ultimately vision scientific community disease mr data resolution hold analyze medical histology resolutions statistics computational hampering bayesian segmentation spm probabilistic made completely multimodal advantage understand vast biomedical opening computer full neuroimaging scans public

Project "BUNGEE-TOOLS" data sheet

The following table provides information about the project.

Coordinator	UNIVERSITY COLLEGE LONDON Organization address address: GOWER STREET city: LONDON postcode: WC1E 6BT website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.
Coordinator Country	United Kingdom [UK]
Project website	https://sites.google.com/site/jeiglesias/bungee-tools
Total cost	1˙450˙075 €
EC max contribution	1˙450˙075 € (100%)
Programme	1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
Code Call	ERC-2015-STG
Funding Scheme	ERC-STG
Starting year	2016
Duration (year-month-day)	from 2016-09-01 to 2021-08-31

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	UNIVERSITY COLLEGE LONDON UNIVERSITY COLLEGE LONDON Organization address address: GOWER STREET city: LONDON postcode: WC1E 6BT website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	UK (LONDON)	coordinator	1˙450˙075.00

Map

Project objective

Recent advances in magnetic resonance (MR) acquisition technology are providing us with images of the human brain of increasing detail and resolution. While these images hold promise to greatly increase our understanding of such a complex organ, the neuroimaging community relies on tools (e.g. SPM, FSL, FreeSurfer) which, being over a decade old, were designed to work at much lower resolutions. These tools do not consider brain substructures that are visible in present-day scans, and this inability to capitalize on the vast improvement of MR is hampering progress in the neuroimaging field.

In this ambitious project, which lies at the nexus of medical histology, neuroscience, biomedical imaging, computer vision and statistics, we propose to build a set of next-generation computational tools that will enable neuroimaging studies to take full advantage of the increased resolution of modern MR technology. The core of the tools will be an ultra-high resolution probabilistic atlas of the human brain, built upon multimodal data combining from histology and ex vivo MR. The resulting atlas will be used to analyze in vivo brain MR scans, which will require the development of Bayesian segmentation methods beyond the state of the art.

The developed tools, which will be made freely available to the scientific community, will enable the analysis of MR data at a superior level of structural detail, opening completely new opportunities of research in neuroscience. Therefore, we expect the tools to have a tremendous impact on the quest to understand the human brain (in health and in disease), and ultimately on public health and the economy.

Publications

List of publications.
year	authors and title	journal	last update
2018	Juan Eugenio Iglesias, Shauna Crampsie, Catherine Strand, Mohamed Tachrount, David L Thomas, Janice L Holton Effect of Fluorinert on the Histological Properties of Formalin-Fixed Human Brain Tissue published pages: 1085-1090, ISSN: 0022-3069, DOI: 10.1093/jnen/nly098	Journal of Neuropathology & Experimental Neurology 77/12	2019-05-27
2019	Martina Bocchetta, Juan Eugenio Iglesias, David M. Cash, Jason D. Warren, Jonathan D. Rohrer Amygdala subnuclei are differentially affected in the different genetic and pathological forms of frontotemporal dementia published pages: 136-141, ISSN: 2352-8729, DOI: 10.1016/j.dadm.2018.12.006	Alzheimer\'s & Dementia: Diagnosis, Assessment & Disease Monitoring 11	2019-05-27
2018	Ignacio Arganda-Carreras, Tudor Manoliu, Nicolas Mazuras, Florian Schulze, Juan E. Iglesias, Katja BÃ¼hler, Arnim Jenett, FranÃ§ois Rouyer, Philippe Andrey A Statistically Representative Atlas for Mapping Neuronal Circuits in the Drosophila Adult Brain published pages: , ISSN: 1662-5196, DOI: 10.3389/fninf.2018.00013	Frontiers in Neuroinformatics 12	2019-05-27
2018	Sebastiano Ferraris, Johannes van der Merwe, Lennart Van Der Veeken, Ferran Prados, Juan-Eugenio Iglesias, Andrew Melbourne, Marco Lorenzi, Marc Modat, Willy Gsell, Jan Deprest, Tom Vercauteren A magnetic resonance multi-atlas for the neonatal rabbit brain published pages: 187-198, ISSN: 1053-8119, DOI: 10.1016/j.neuroimage.2018.06.029	NeuroImage 179	2019-05-27
2019	Martina Bocchetta, Juan Eugenio Iglesias, Lucy L. Russell, Caroline V. Greaves, Charles R. Marshall, Marzia A. Scelsi, David M. Cash, Sebastien Ourselin, Jason D. Warren, Jonathan D. Rohrer Segmentation of medial temporal subregions reveals early right-sided involvement in semantic variant PPA published pages: , ISSN: 1758-9193, DOI: 10.1186/s13195-019-0489-9	Alzheimer\'s Research & Therapy 11/1	2019-09-17
2019	William Stewart, Kieren Allinson, Safa Al-Sarraj, Corbin Bachmeier, Karen Barlow, Antonio Belli, Mark P Burns, Alan Carson, Fiona Crawford, Kristen Dams-O\'Connor, Ramon Diaz-Arrastia, C Edward Dixon, Brian L Edlow, Scott Ferguson, Bruce Fischl, Rebecca D Folkerth, Steve Gentleman, Christopher C Giza, M Sean Grady, Adel Helmy, Mark Herceg, Janice L Holton, David Howell, Peter J Hutchinson, Diego Iacono, Juan E Iglesias, Milos D Ikonomovic, Victoria E Johnson, C Dirk Keene, Julia K Kofler, Vassilis E Koliatsos, Edward B Lee, Harvey Levin, Jonathan Lifshitz, Helen Ling, David J Loane, Seth Love, Andrew IR Maas, Niklas Marklund, Christina L Master, Damien M McElvenny, David F Meaney, David K Menon, Thomas J Montine, Benoit Mouzon, Elliott J Mufson, Joseph O Ojo, Mayumi Prins, Tamas Revesz, Craig W Ritchie, Colin Smith, Richard Sylvester, Cheuk Y Tang, John Q Trojanowski, Kathryn Urankar, Robert Vink, Cheryl Wellington, Elisabeth A Wilde, Lindsay Wilson, Keith Yeates, Douglas H Smith Primum non nocere: a call for balance when reporting on CTE published pages: 231-233, ISSN: 1474-4422, DOI: 10.1016/s1474-4422(19)30020-1	The Lancet Neurology 18/3	2019-05-10
2018	Lyon W. Chen, Delin Sun, Sarah L. Davis, Courtney C. Haswell, Emily L. Dennis, Chelsea A. Swanson, Christopher D. Whelan, Boris Gutman, Neda Jahanshad, Juan Eugenio Iglesias, Paul Thompson, H. Ryan Wagner, Philipp Saemann, Kevin S. LaBar, Rajendra A. Morey Smaller hippocampal CA1 subfield volume in posttraumatic stress disorder published pages: 1018-1029, ISSN: 1091-4269, DOI: 10.1002/da.22833	Depression and Anxiety 35/11	2019-05-10
2018	Juan Eugenio Iglesias, Marc Modat, LoÃ¯c Peter, Allison Stevens, Roberto Annunziata, Tom Vercauteren, Ed Lein, Bruce Fischl, Sebastien Ourselin Joint registration and synthesis using a probabilistic model for alignment of MRI and histological sections published pages: 127-144, ISSN: 1361-8415, DOI: 10.1016/j.media.2018.09.002	Medical Image Analysis 50	2019-05-10
2018	Juan Eugenio Iglesias, Ricardo Insausti, Garikoitz Lerma-Usabiaga, Martina Bocchetta, Koen Van Leemput, Douglas N. Greve, Andre van der Kouwe, Bruce Fischl, CÃ©sar Caballero-Gaudes, Pedro M. Paz-Alonso A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology published pages: 314-326, ISSN: 1053-8119, DOI: 10.1016/j.neuroimage.2018.08.012	NeuroImage 183	2019-05-10
2018	Martina Bocchetta, Juan Eugenio Iglesias, Marzia A. Scelsi, David M. Cash, M. Jorge Cardoso, Marc Modat, Andre Altmann, Sebastien Ourselin, Jason D. Warren, Jonathan D. Rohrer Hippocampal Subfield Volumetry: Differential Pattern of Atrophy in Different Forms of Genetic Frontotemporal Dementia published pages: 497-504, ISSN: 1387-2877, DOI: 10.3233/JAD-180195	Journal of Alzheimer\'s Disease 64/2	2019-05-10
2017	New Fei Ho, Daphne J Holt, Mike Cheung, Juan Eugenio Iglesias, Alex Goh, Mingyuan Wang, Joseph KW Lim, Joshua de Souza, Joann S Poh, Yuen Mei See, Alison R Adcock, Stephen J Wood, Michael WL Chee, Jimmy Lee, Juan Zhou Progressive Decline in Hippocampal CA1 Volume in Individuals at Ultra-High-Risk for Psychosis Who Do Not Remit: Findings from the Longitudinal Youth at Risk Study published pages: 1361-1370, ISSN: 0893-133X, DOI: 10.1038/npp.2017.5	Neuropsychopharmacology 42/6	2019-06-19
2017	Z.M. Saygin, D. Kliemann, J.E. Iglesias, A.J.W. van der Kouwe, E. Boyd, M. Reuter, A. Stevens, K. Van Leemput, A. McKee, M.P. Frosch, B. Fischl, J.C. Augustinack High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas published pages: 370-382, ISSN: 1053-8119, DOI: 10.1016/j.neuroimage.2017.04.046	NeuroImage 155	2019-06-19
2017	Juan Eugenio Iglesias Globally Optimal Coupled Surfaces for Semi-automatic Segmentation of Medical Images published pages: 610-621, ISSN: , DOI: 10.1007/978-3-319-59050-9_48	International Conference on Information Processing in Medical Imaging	2019-06-19
2017	New Fei Ho, Daphne J Holt, Mike Cheung, Juan Eugenio Iglesias, Alex Goh, Mingyuan Wang, Joseph KW Lim, Joshua de Souza, Joann S Poh, Yuen Mei See, Alison R Adcock, Stephen J Wood, Michael WL Chee, Jimmy Lee, Juan Zhou Progressive Decline in Hippocampal CA1 Volume in Individuals at Ultra-High-Risk for Psychosis Who Do Not Remit: Findings from the Longitudinal Youth at Risk Study published pages: 1361-1370, ISSN: 0893-133X, DOI: 10.1038/npp.2017.5	Neuropsychopharmacology 42/6	2019-05-10
2018	Jonas Pichat, Juan Eugenio Iglesias, Tarek Yousry, SÃ©bastien Ourselin, Marc Modat A Survey of Methods for 3D Histology Reconstruction published pages: , ISSN: 1361-8415, DOI: 10.1016/j.media.2018.02.004	Medical Image Analysis	2019-06-19
2017	Iman Aganj, Juan Eugenio Iglesias, Martin Reuter, Mert Rory Sabuncu, Bruce Fischl Mid-space-independent deformable image registration published pages: 158-170, ISSN: 1053-8119, DOI: 10.1016/j.neuroimage.2017.02.055	NeuroImage 152	2019-06-19
2018	Marcel Tella-Amo, Loic Peter, Dzhoshkun I. Shakir, Jan Deprest, Danail Stoyanov, Juan Eugenio Iglesias, Tom Vercauteren, Sebastien Ourselin Probabilistic visual and electromagnetic data fusion for robust drift-free sequential mosaicking: application to fetoscopy published pages: 1, ISSN: 2329-4302, DOI: 10.1117/1.JMI.5.2.021217	Journal of Medical Imaging 5/02	2019-06-19

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