Reconstruction of neuronal pathways from diffusion imaging data

Diffusion imaging provides information about the course and location of white matter tracts. White matter tracts, i.e. motor or sensory pathways, are important structures within the human brain. For neurosurgery, diffusion imaging data is of high value since these fiber tracts must remain intact in order to avoid neurological deficits after brain surgery.

However, the reconstruction of neuronal structures from diffusion imaging data is a non-trivial task due to the complexity of the diffusion information that is captured per voxel. Our research in this field addresses the reconstruction of the diffusion signal based on compressed sensing, as well as tracking and clustering of white matter pathways.

BA/MA theses:
New theses in the field of diffusion imaging, fiber tracking and connectivity analysis are offered at irregular intervals. For current topics please contact Leon Weninger.

Partners:
Prof. Dr. med. Christopher Nimsky, Direktor der Klinik für Neurochirurgie, Universitätsklinikum Gießen und Marburg
Jun.Prof. Dr. Thomas Schultz, Arbeitsgruppe Visualisierung und Medizinische Bildanalyse, Universität Bonn
Prof. Dr. med. Wolfgang Grodd, Klinik für Psychiatrie, Psychotherapie und Psychosomatik, Uniklinik RWTH Aachen
Dr. med. Georg Neuloh, Klinik für Neurochirurgie, Uniklinik RWTH Aachen
Dr. rer. nat. Katrin Sakreida, Lehrstuhl Klinische Kognitionsforschung, Uniklinik RWTH Aachen

Contact:
Leon Weninger
Simon Koppers

Publications:

	2019 BibTeX	J. Christopher Edgar, Marissa Dipiero, Emma McBride, Heather L. Green, Jeffrey I. Berman, Matthew Ku, Song Liu, Lisa Blaskey, Emily Kuschner, Megan Airey, Judith L. Ross, Luke Bloy, Mina Kim, Simon Koppers, William Gaetz, Robert T. Schultz and Timothy P. L. Roberts Abnormal maturation of the resting-state peak alpha frequency in children with autism spectrum disorder In: Human Brain Mapping
	2019 BibTeX	Chantal MW Tax, Francesco Grussu, Enrico Kaden, Lipeng Ning, Umesh Rudrapatna, John Evans, Samuel St-Jean, Alexander Leemans, Simon Koppers, Dorit Merhof, others Cross-scanner and cross-protocol diffusion MRI data harmonisation: A benchmark database and evaluation of algorithms In: NeuroImage
	2019 BibTeX        PDF	Simon Koppers, Edouard Coussoux, Sandro Romanzetti, Kathrin Reetz, Dorit Merhof Sodium Image Denoising based on a Convolutional Denoising Autoencoder In: Bildverarbeitung für die Medizin (BVM)
	2018 BibTeX        PDF	Leon Weninger, Oliver Rippel, Simon Koppers and Dorit Merhof Segmentation of Brain Tumors in 3D-MRI Data and Patient Survival Prediction: Methods for the BraTS 2018 Challenge In: MICCAI Brainlesion Workshop (BrainLes)
	2018 BibTeX        PDF	Boaz Arad, Ohad Ben-Shahar, Radu Timofte, Luc Van Gool, Lei Zhang, Ming-Hsuan Yang, Zhiwei Xiong, Chang Chen, Zhan Shi, Dong Liu, Feng Wu, Charis Lanaras, Silvano Galliani, Konrad Schindler, Tarek Stiebel, Simon Koppers, Philipp Seltsam, Ruofan Zhou, Majed El Helou, Fayez Lahoud, Marjan Shahpaski, Ke Zheng, Lianru Gao, Bing Zhang, Ximin Cui, Haoyang Yu, Yigit Baran Can, Aitor Alvarez-Gila, Joost van de Weijer, Estibaliz Garrote, Adrian Galdran, Manoj Sharma, Sriharsha Koundinya, Avinash Upadhyay, Raunak Manekar, Rudrabha Mukhopadhyay, Himanshu Sharma, Santanu Chaudhury, Koushik Nagasubramanian, Sambuddha Ghosal, Asheesh K. Singh, Arti Singh, Baskar Ganapathysubramanian and Soumik Sarkar NTIRE 2018 Challenge on Spectral Reconstruction from RGB Images In: The IEEE Conference on Computer Vision and Pattern Recognition (CVPR) Workshops
	2018 BibTeX        PDF	Tarek Stiebel, Simon Koppers, Philipp Seltsam and Dorit Merhof Reconstructing Spectral Images from RGB-Images using a Convolutional Neural Network In: IEEE Conference on Computer Vision and Pattern Recognition (CVPR) Workshops
	2018 BibTeX        PDF	Simon Koppers, Luke Bloy, Jeffrey I. Berman, Chantal M.W. Tax, J. Christopher Edgar and Dorit Merhof Spherical Harmonic Residual Network for Diffusion Signal Harmonization In: MICCAI Workshop on Computational Diffusion MRI (CDMRI)
	2017 BibTeX        PDF	Simon Koppers, Matthias Friedrichs and Dorit Merhof Reconstruction of Diffusion Anisotropies using 3D Deep Convolutional Neural Networks in Diffusion Imaging In: Modeling, Analysis, and Visualization of Anisotropy
	2017 BibTeX        PDF	Simon Koppers, Christoph Haarburger, J. Christopher Edgar and Dorit Merhof Reliable Estimation of the Number of Compartments in Diffusion MRI In: Bildverarbeitung für die Medizin (BVM)
	2016 BibTeX        PDF	Simon Koppers, Christoph Haarburger and Dorit Merhof Diffusion MRI Signal Augmentation - From Single Shell to Multi Shell with Deep Learning In: MICCAI Workshop on Computational Diffusion MRI (CDMRI)
	2016 BibTeX        PDF	Simon Koppers and Dorit Merhof Direct Estimation of Fiber Orientations using Deep Learning in Diffusion Imaging In: MICCAI Workshop on Machine Learning in Medical Imaging (MLMI)
	2016 BibTeX        PDF	Simon Koppers and Dorit Merhof Qualitative Comparison of Reconstruction Algorithms for Diffusion Imaging In: Visualization of the Brain and its Pathologies – Technical and Neurosurgical Aspects
	2016 BibTeX        PDF	Simon Koppers, Christoph Hebisch and Dorit Merhof A Feature Selection Framework for White Matter Fiber Clustering Based on Normalized Cuts In: Bildverarbeitung für die Medizin (BVM)
	2015 BibTeX        PDF	Simon Koppers, Thomas Schultz and Dorit Merhof Spherical Ridgelets for Multi-Diffusion-Tensor Refinement - Concept and Evaluation In: Bildverarbeitung für die Medizin (BVM)