no code implementations • 22 Nov 2023 • Karoline Leiberg, Timo Blattner, Bethany Little, Victor B. B. Mello, Fernanda H. P. de Moraes, Christian Rummel, Peter N. Taylor, Bruno Mota, Yujiang Wang
Motivation: Characterising the changes in cortical morphology across the lifespan is fundamental for a range of research and clinical applications.
no code implementations • 21 Jul 2023 • Richard McKinley, Christian Rummel
Recent studies using a synthetic cortical thickness phantom have demonstrated that the combination of DiReCT and deep-learning-based segmentation is more sensitive to subvoxel cortical thinning than Freesurfer.
1 code implementation • Human Brain Mapping 2022 • Michael Rebsamen, Richard McKinley, Piotr Radojewski, Maximilian Pistor, Christoph Friedli, Robert Hoepner, Anke Salmen, Andrew Chan, Mauricio Reyes, Franca Wagner, Roland Wiest, Christian Rummel
The segmentations were derived with FreeSurfer from the non-enhanced image and used as ground truth for the coregistered CE image.
1 code implementation • 5 Nov 2020 • Michael Rebsamen, Christian Rummel, Mauricio Reyes, Roland Wiest, Richard McKinley
DL+DiReCT is a promising combination of a deep learning‐based method with a traditional registration technique to detect subtle changes in cortical thickness.
1 code implementation • 8 Apr 2020 • Michael Rebsamen, Yannick Suter, Roland Wiest, Mauricio Reyes, Christian Rummel
We propose a deep learning-based approach to predict the volumes of anatomically delineated subcortical regions of interest (ROI), and mean thicknesses and curvatures of cortical parcellations directly from T1-weighted MRI.
no code implementations • 5 Apr 2019 • Richard McKinley, Lorenz Grunder, Rik Wepfer, Fabian Aschwanden, Tim Fischer, Christoph Friedli, Raphaela Muri, Christian Rummel, Rajeev Verma, Christian Weisstanner, Mauricio Reyes, Anke Salmen, Andrew Chan, Roland Wiest, Franca Wagner
Instead, we propose a method for identifying lesion changes of high certainty, and establish on a dataset of longitudinal multiple sclerosis cases that this method is able to separate progressive from stable timepoints with a very high level of discrimination (AUC = 0. 99), while changes in lesion volume are much less able to perform this separation (AUC = 0. 71).
no code implementations • 4 Apr 2019 • Richard McKinley, Michael Rebsamen, Raphael Meier, Mauricio Reyes, Christian Rummel, Roland Wiest
In applications of supervised learning applied to medical image segmentation, the need for large amounts of labeled data typically goes unquestioned.
no code implementations • 22 Jan 2019 • Richard McKinley, Rik Wepfer, Fabian Aschwanden, Lorenz Grunder, Raphaela Muri, Christian Rummel, Rajeev Verma, Christian Weisstanner, Mauricio Reyes, Anke Salmen, Andrew Chan, Franca Wagner, Roland Wiest
We trained two state-of-the-art fully convolutional CNN architectures on the 2016 MSSEG training dataset, which was annotated by seven independent human raters: a reference implementation of a 3D Unet, and a more recently proposed 3D-to-2D architecture (DeepSCAN).