Outputs

Theses

Faezeh Moshfeghifar: Hip Joint Finite Element Modelling  

José D. Tascón-Vidarte: Real-time Deformable Image Registration - Applied to Tumor Tracking in 2D Cine-MRI (ku.dk)

 

Publications in postprint format:

Claus, Susanne; Kerfriden, Pierre; Moshfeghifar, Faezeh; Darkner, Sune; Erleben, Kenny; Wong, Christian: Contact modeling from images using cut finite element solvers. Published in Advanced Modeling and Simulation in Engineering Sciences by Springer Nature. Available at https://rdcu.be/cl7OF

Torkan Gholamalizadeh, Sune Darkner, Paolo Maria Cattaneo, Peter Søndergaard, Kenny Erleben: Mandibular Teeth Movement Variations in Tipping Scenario: A Finite Element Study on Several Patients. Conference paper published in Computational Biomechanics for Medicine. Solid and Fluid Mechanics Informing Therapy, Springer 2021; Compilation of contributions from the MICCAI 2020 Computational Biomechanics for Medicine XV Workshop. Available at https://link.springer.com/chapter/10.1007/978-3-030-70123-9_3  

Shayestehpour, Hamed; Rasmussen, John; Galibarov, Pavel; Wong, Christian: An articulated spine and ribcage kinematic model for simulation of scoliosis deformities. Journal article published in the journal Multibody System Dynamics, 53, pages115–134 (2021), by Springer Nature. Available at https://link.springer.com/article/10.1007/s11044-021-09787-9 

Patricia Alcañiz, Jesús Pérez, Alessandro Gutiérrez, Héctor Barreiro, Ángel Villalobos, David Miraut, Carlos Illana, Jorge Guiñales, Miguel A. Otaduy: Soft-Tissue Simulation for Computational Planning of Orthognathic Surgery. Journal article published in Journal of Personalized Medicine, vol 11, issue 10, 2021. Available at https://doi.org/10.3390/jpm11100982 

Mazier, Arnaud; Ribes, Sophie; Gilles, Benjamin; Bordas, Stéphane P.A.: A rigged model of the breast for preoperative surgical planning, in Journal of Biomechanics Volume 128, 9 November 2021, 110645 Elsevier. Available at https://doi.org/10.1016/j.jbiomech.2021.110645 

Torkan Gholamalizadeh, Sune Darkner, Peter Søndergaard, Kenny Erleben: A multi-patient analysis of the center of rotation trajectories using finite element models of the human mandible. Published in PLoS One 16(11), 2021. Available at https://doi.org/10.1371/journal.pone.0259794

Krokos, Vasilis; Xuan, Viet Bui; Bordas, Stéphane P. A.; Young, Philippe; Kerfriden, Pierre: A Bayesian multiscale CNN framework to predict local stress fields in structures with microscale features. Journal article published in the Computational Mechanics Journal, Springer. Available at https://doi.org/10.1007/s00466-021-02112-3 

Koutras, Christos; Pérez, Jesús; Kardash, Kateryna; Otaduy, Miguel A.: A Study of the Sensitivity of Biomechanical Models of the Spine for Scoliosis Brace Design. Journal article published in Journal of Computer Methods and Programs in Biomedicine, vol. 207 Aug. 2021 106125, Elsevier. Available at https://doi.org/10.1016/j.cmpb.2021.106125 

Mazier, Arnaud; Bilger, Alexandre; Forte, Antonio E.; Peterlik, Igor; Hale, Jack S.; Bordas, Stéphane P. A.: Inverse deformation analysis: an experimental and numerical assessment using the FEniCS Project. Journal article published in Engineering with Computers. An International Journal for Simulation-Based Engineering, (2022), Springer. Available at https://doi.org/10.1007/s00366-021-01597-z 

E. Mikaeili, S. Claus, P. Kerfriden: Concurrent multiscale analysis without meshing: Microscale representation with CutFEM and micro/macro model blending. Journal article published in Computer Methods in Applied Mechanics and Engineering, vol. 393, 1 April 2022, 114807. Available at https://doi.org/10.1016/j.cma.2022.114807 

José D Tascón-Vidarte, Isak Wahlstedt, Julien Jomier, Kenny Erleben, Ivan R Vogelius, Sune Darkner: Cine-MRI Simulation to Evaluate Tumor Tracking. Conference presentation printed in SASHIMI 2021: Simulation and Synthesis in Medical Imaging by Springer. Available at https://link.springer.com/chapter/10.1007/978-3-030-87592-3_13 

Rohmer, Damien; Tarini, Marco; Kalyanasundaram, Niranjan; Moshfeghifar, Faezeh; Cani, Marie-Paule; Zordan, Victor: Velocity Skinning for Real-time Stylized Skeletal Animation. Journal article published in EUROGRAPHICS 2021 no. 2, vol. 40. Available at https://doi.org/10.1111/cgf.142654  

Zeraatpisheh, Milad, Stéphane P.A. Bordas and Lars Beex: Bayesian model uncertainty quantification for hyperelastic soft tissue models. Journal article published in Data Centric Engineering 2021 (vol. 2) by Cambridge University Press, 2022. Available at https://doi.org/10.1017/dce.2021.9 

Torkan Gholamalizadeh, Faezeh Moshfeghifar, Zachary Ferguson, Teseo Schneider, Daniele Panozzo , Sune Darkner, Masrour Makaremi, François Chan, Peter Lampel Søndergaard, Kenny Erleben: Open-Full-Jaw: An open-access dataset and pipeline for finite element models of human jaw, peer-reviewed article in Journal of Computer Methods and Programs in Biomedicine (Elsevier). Available in UCPH's CURIS platform and at https://doi.org/10.1016/j.cmpb.2022.107009. “Dataset related to the article is shared at https://github.com/diku-dk/Open-Full-Jaw.
Result of a collaboration initiated with the New York University

Saurabh Deshpande, Jakub Lengiewicz, Stéphane P.A. Bordas: Probabilistic Deep Learning for Real-Time Large Deformation Simulations, peer-reviewed article in the Journal of Computer Methods in Applied Mechanics and Engineering. Available at https://doi.org/10.1016/j.cma.2022.115307 and at https://arxiv.org/abs/2111.01867v3 

Publications in preprint format:

  • Faezeh Moshfeghifar, Max Kragballe Nielsen, Jose D. Tascón-Vidarte, Sune Darkner, Kenny Erleben: A direct geometry processing cartilage generation method for datasets with poor cartilage visibility. Paper accepted in the MICCAI 2021 Computational Biomechanics for Medicine XVI-2021 Workshop. Peer-reviewed preprint available at https://github.com/diku-dk/CarGen, https://doi.org/10.5281/zenodo.6579629 and https://arxiv.org/abs/2203.10667. Submitted and accepted for print in paper proceedings by Springer and currently in publishing phase. 
    Result of a collaboration with other researchers at Dep. of Computer Science at UCPH.
  • Faezeh Moshfeghifar, Torkan Gholamalizadeh, Zachary Ferguson, Teseo Schneider, Michael Bachmann Nielsen, Daniele Panozzo, Sune Darkner, Kenny Erleben: LibHip: An Open-Access Hip Joint Model Repository suitable for Finite Element Method Simulation, preprint article under peer review for Journal of Computer Methods and Programs in Biomedicine (Elsevier). Dataset related to the article is shared at: https://diku-dk.github.io/libhip/  
    Result of a collaboration initiated with the New York University and a clinical collaboration with the Copenhagen University Hospital, Rigshospitalet.
  • Thomas Alscher, Sune Darkner, Kenny Erleben: {Collision-constrained Deformable Image Registration Framework for Discontinuity Management. Preprint conference paper to be submitted for peer review
  • José D Tascón-Vidarte, Isak Wahlstedt, Julien Jomier, Kenny Erleben, Ivan R Vogelius, Sune Darkner: Real-time algorithms for tracking tumor and organs in 2D Cine-MRI. Journal article submitted for peer review to be published in International Journal of Radiation and Oncology by Elsevier.
  •  José D Tascón-Vidarte, Line B Stick, Mirjana Josipovic, Signe Risum, Julien Jomier, Kenny Erleben, Ivan R Vogelius, Sune Darkner: Accuracy and consistency of deformable image registration in 4DCT for tumor motion estimation in liver radiotherapy planning. Journal article submitted for peer review to by published in PLoS One.
  • Hamed Shayestehpour, Mohammad Amin Shayestehpour, Christian Wong, John Rasmussen: Kinetic investigation of a thoracolumbar spine model including the ribcage. Journal article to be submitted for peer review and publication in Medical Engineering & Physics by Elsevier. 
  • Christos Koutras; Hamed Shayestehpour; Jesús Pérez Rodríguez; Christian Wong; John Rasmussen; Maxime Tournier; Matthieu Nesme; Miguel A. Otaduy: Simulation-Based Morphing of Personalized Models of the Torso for Scoliosis Brace Design. Journal article submitted for publication in Journal of Computer Methods and Programs in Biomedicine by Elsevier. Peer-reviewed preprint.
  • Zhongyun He, Jesus Perez, Miguel Otaduy: Numerical Coarsening under Topology Changes Using Local Factorizations. Preprint journal article to be submitted for peer review to Journal Computer Graphics Forum, published by Wiley
  • Antoine Perney, Stephane Bordas, Pierre Kerfriden: NURBS-Based surfaces generation from images: spectral construction and data-centric model selection. Preprint journal article to be submitted to peer review to Computer Graphics Forum published by John Wiley & Sons Ltd.
  • E. Mikaeili, S. Claus, P. Kerfriden: A novel hierarchical multiresolution framework using CutFEM. Journal article to be submitted for peer review to the journal Computer Methods in Applied Mechanics and Engineering published by Cornell. Preprint available at 2201.04698.pdf (arxiv.org)
  • Vasilis Krokos, Stéphane P. A. Bordas, Pierre Kerfriden: A Graph-based probabilistic geometric deep learning framework with online physics-based corrections to predict the criticality of defects in porous materials. Available at https://doi.org/10.48550/arXiv.2205.06562

Data sets

Gholamalizadeh, T.; Darkner, S.; Søndergaard, P.; Erleben, K.,:  OpenJaw Dataset. Publishhed in University of Copnehagen's Electronic Research Data Archive, 2021. Available at https://erda.ku.dk/archives/97cd65fe80e83356f618bb9fbc7d5980/published-archive.html 

Other

Mazier, Arnaud; Bilger, Alexandre; Forte, Antonio; Peterlik, Igor; Hale, Jack; Bordas, Stéphane: Inverse simulation for retrieving the undeformed position for hyperelastic materials: application to breast simulation. Peer reviewed unpublished paper accepted for the WCCM 2020 conference (not presented) available at http://orbilu.uni.lu/handle/10993/42678

Kerfriden, Pierre; Deshpande, Saurabh; Mikaeili, Ehsan: Efficient Meta-modelling for the simulation of soft tissue deformations. Project deliverable published in EU continuous reporting portal and zenodo repository, https://zenodo.org/record/4470106