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Tetrahedral Mesh Generation for Non-rigid Registration of Brain MRI: Analysis of the Requirements and Evaluation of Solutions [chapter]

Andriy Fedorov, Nikos Chrisochoides
Proceedings of the 17th International Meshing Roundtable  
This approach requires tetrahedral tessellation of the brain volume for biomechanical model construction.  ...  We focus on a validated, physics-based non-rigid registration approach, which has been used in clinical studies for the last three years.  ...  We thank Hang Si and Joachim Shöberl for the development and continuing support of extraordinary mesh generation software.  ... 
doi:10.1007/978-3-540-87921-3_4 dblp:conf/imr/FedorovC08 fatcat:5caou674o5dw5exm5jgazydeyi

Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery

Neculai Archip, Olivier Clatz, Stephen Whalen, Dan Kacher, Andriy Fedorov, Andriy Kot, Nikos Chrisochoides, Ferenc Jolesz, Alexandra Golby, Peter M. Black, Simon K. Warfield
2007 NeuroImage  
Our objectives were (i) to evaluate the feasibility of non-rigid registration that compensates for the brain deformations within the time constraints imposed by neurosurgery, and (ii) to create augmented  ...  ., Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery, NeuroImage (2007) ,  ...  The computational intensive part of this work was performed in computational facilities at the College of William and Mary which were enabled by grants from Sun Microsystems, the National Science Foundation  ... 
doi:10.1016/j.neuroimage.2006.11.060 pmid:17289403 pmcid:PMC3358788 fatcat:p3ks7grs7vfjten7qbr5lgqmiu

Real-time registration of volumetric brain MRI by biomechanical simulation of deformation during image guided neurosurgery

Simon K. Warfield, Florin Talos, Alida Tei, Aditya Bharatha, Arya Nabavi, Matthieu Ferrant, Peter McL. Black, Ferenc A. Jolesz, Ron Kikinis
2002 Computing and Visualization in Science  
The key challenge faced by a neurosurgeon is the removal from the brain of as much tumor tissue as possible while minimizing the removal of healthy tissue and avoiding the disruption of critical anatomical  ...  We developed an algorithm to create enhanced visualizations of tumor and critical brain structures by aligning preoperatively acquired image data with intraoperative images of the patient's brain during  ...  This investigation was supported by NIH grants P41 RR13218, P01 CA67165, R01 RR11747, R01 CA86879 and by a New Concept Award from the Center for Integration of Medicine and Innovative Technology (SKW).  ... 
doi:10.1007/s00791-002-0083-7 fatcat:itl7ynks2zabzochvusyjm4opm

Adaptive Physics-Based Non-Rigid Registration for Immersive Image-Guided Neuronavigation Systems

Fotis Drakopoulos, Christos Tsolakis, Angelos Angelopoulos, Yixun Liu, Chengjun Yao, Kyriaki Rafailia Kavazidi, Nikolaos Foroglou, Andrey Fedorov, Sarah Frisken, Ron Kikinis, Alexandra Golby, Nikos Chrisochoides
2021 Frontiers in Digital Health  
Using clinical data, this paper reports the results of a comparison of the accuracy and performance among several non-rigid registration methods for handling brain deformation.  ...  An Adaptive Physics-Based Non-Rigid Registration method (A-PBNRR) registers preoperative and intraoperative MRI for each patient.  ...  Mesh Generation The segmentation is used to generate a patient-specific finite element mesh for physics-based non-rigid registration methods.  ... 
doi:10.3389/fdgth.2020.613608 pmid:34713074 pmcid:PMC8521897 fatcat:5edxya6tovekncnq3wavu77y2q

Biomechanical modeling and computer simulation of the brain during neurosurgery [article]

K. Miller, G. R. Joldes, G. Bourantas, S. K. Warfield, D. E. Hyde, R. Kikinis, A. Wittek
2019 arXiv   pre-print
We present two examples to showcase these methods: brain shift estimation for image registration and brain deformation computation for neuronavigation in epilepsy treatment.  ...  for obtaining the numerical solutions.  ...  We thank the Raine Medical Research Foundation for funding G. R. Joldes through a Raine Priming Grant, and the Department of Health, Western Australia, for funding G. R. Joldes through a Merit Award.  ... 
arXiv:1904.01192v1 fatcat:w6l3a6mimjejdo4m5xjdw7lhw4

Patient-specific non-linear finite element modelling for predicting soft organ deformation in real-time; Application to non-rigid neuroimage registration

Adam Wittek, Grand Joldes, Mathieu Couton, Simon K. Warfield, Karol Miller
2010 Progress in Biophysics and Molecular Biology  
We used patientspecific finite element meshes consisting of hexahedral and non-locking tetrahedral elements, together with realistic material properties for the brain tissue and appropriate contact conditions  ...  Long computation times of non-linear (i.e. accounting for geometric and material non-linearity) biomechanical models have been regarded as one of the key factors preventing application of such models in  ...  Ron Kikinis of Brigham and Women's Hospital (Boston, MA) for very helpful suggestions.  ... 
doi:10.1016/j.pbiomolbio.2010.09.001 pmid:20868706 pmcid:PMC3107968 fatcat:ew6ziwlj5bhxrbldqv4rtfccli

Bayesian longitudinal segmentation of hippocampal substructures in brain MRI using subject-specific atlases

Juan Eugenio Iglesias, Koen Van Leemput, Jean Augustinack, Ricardo Insausti, Bruce Fischl, Martin Reuter
2016 NeuroImage  
ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following:  ...  "), and also from the Spanish Ministry of Economy and Competitiveness (MINECO, reference TEC2014-51882-P).  ...  Some approaches do not require non-linear registration to produce the segmentations -though rigid registrations are still used to bring the images into rough alignment.  ... 
doi:10.1016/j.neuroimage.2016.07.020 pmid:27426838 pmcid:PMC5026967 fatcat:47bvzll4yvg6jkupi2ub3dvsv4

Biomechanical Model as a Registration Tool for Image-Guided Neurosurgery: Evaluation Against BSpline Registration

Ahmed Mostayed, Revanth Reddy Garlapati, Grand Roman Joldes, Adam Wittek, Aditi Roy, Ron Kikinis, Simon K. Warfield, Karol Miller
2013 Annals of Biomedical Engineering  
We define an edge based Hausdorff distance metric to quantitatively evaluate the accuracy of registration for these two algorithms.  ...  In this paper we evaluate the accuracy of warping of neuro-images using brain deformation predicted by means of a patient-specific biomechanical model against registration using a BSpline-based free form  ...  of high quality pre-operative images onto the intra-operative position of the brain, as is now possible with intra-operative MRI and state-of-the-art non-rigid registration algorithm.  ... 
doi:10.1007/s10439-013-0838-y pmid:23771299 pmcid:PMC3939696 fatcat:jmdi2dix2je6xhww3w65taxw5e

Modelling brain deformations for computer-integrated neurosurgery

K. Miller, A. Wittek, G. Joldes, A. Horton, T. Dutta-Roy, J. Berger, L. Morriss
2010 International Journal for Numerical Methods in Biomedical Engineering  
We support our recommendations and conclusions with two examples: computation of the reaction force acting on a biopsy needle, and computation of the brain shift for image registration.  ...  We consider numerical problems such as the use of hexahedral and mixed hexahedral-tetrahedral meshes as well as meshless spatial discretization schemes.  ...  (Nagakute, Aichi, Japan) for providing the THUMS brain model.  ... 
doi:10.1002/cnm.1260 fatcat:2c734cv3q5g2jg3piz723t4ema

A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology

Juan Eugenio Iglesias, Ricardo Insausti, Garikoitz Lerma-Usabiaga, Martina Bocchetta, Koen Van Leemput, Douglas N. Greve, Andre van der Kouwe, Bruce Fischl, César Caballero-Gaudes, Pedro M. Paz-Alonso
2018 NeuroImage  
The atlas, which was encoded as an adaptive tetrahedral mesh, shows a good agreement with previous histological studies of the thalamus in terms of volumes of representative nuclei.  ...  In this study, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histological data, as well as the application of the atlas to in vivo MRI segmentation.  ...  Acknowledgements The authors would like to thank Professor Karla Miller (Oxford) for her help with the design of the ex vivo MRI acquisition; Ms. Mercedes Iñiguez de Onzoño and Mr.  ... 
doi:10.1016/j.neuroimage.2018.08.012 pmid:30121337 pmcid:PMC6215335 fatcat:55gjgh365ncmvpsjpxln7sr3pq

A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology [article]

Juan Eugenio Iglesias, Ricardo Insausti, Garikoitz Lerma-Usabiaga, Martina Bocchetta, Koen Van Leemput, Douglas N Greve, Andre van der Kouwe, Bruce Fischl, Cesar Caballero-Gaudes, Pedro M Paz-Alonso
2018 arXiv   pre-print
In this study, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histological data, as well as the application of the atlas to in vivo MRI segmentation.  ...  The atlas, which was encoded as an adaptive tetrahedral mesh, shows a good agreement with with previous histological studies of the thalamus in terms of volumes of representative nuclei.  ...  Acknowledgements The authors would like to thank Professor Karla Miller (Oxford) for her help with the design of the ex vivo MRI acquisition; Ms. MercedesÍñiguez de Onzoño and Mr.  ... 
arXiv:1806.08634v1 fatcat:tb2ljhd6o5h4vnli3njuezacse

Real-Time Non-rigid Registration of Medical Images on a Cooperative Parallel Architecture

Yixun Liu, Andriy Fedorov, Ron Kikinis, Nikos Chrisochoides
2009 2009 IEEE International Conference on Bioinformatics and Biomedicine  
The results of our evaluation on clinical brain MRI data show that the GPU-based Block Matching (regular part) can run at least 1.9 times faster than on a typical cluster of workstations with eight high-performance  ...  Unacceptable execution time of Non-rigid registration (NRR) often presents a major obstacle to its routine clinical use. Parallel computing is an effective way to accelerate NRR.  ...  Medical image registration falls into two categories: Rigid registration and Non-rigid registration (NRR).  ... 
doi:10.1109/bibm.2009.10 dblp:conf/bibm/LiuFKC09 fatcat:sazovmvywvcxjer47wrmrwewqu

Capturing intraoperative deformations: research experience at Brigham and Women's hospital

Simon K. Warfield, Steven J. Haker, Ion-Florin Talos, Corey A. Kemper, Neil Weisenfeld, Andrea U.J. Mewes, Daniel Goldberg-Zimring, Kelly H. Zou, Carl-Fredrik Westin, William M. Wells, Clare M.C. Tempany, Alexandra Golby (+3 others)
2005 Medical Image Analysis  
and the intraoperative configuration of the patientÕs brain.  ...  This paper reviews the experience at Brigham and WomenÕs Hospital through the process of developing and applying novel algorithms for capturing intraoperative deformations in support of image guided therapy  ...  Acknowledgements This investigation was supported in part by NIH Grants R21 MH67054, R01 LM007861, P41 RR13218, P01 CA67165, R01 AG19513 and R33 CA99015 and by a research grant from CIMIT.  ... 
doi:10.1016/j.media.2004.11.005 pmid:15721230 fatcat:mahu4a6za5gz5lpg3sr2crzkfq

Suite of finite element algorithms for accurate computation of soft tissue deformation for surgical simulation

Grand Roman Joldes, Adam Wittek, Karol Miller
2009 Medical Image Analysis  
Real time computation of soft tissue deformation is important for the use of augmented reality devices and for providing haptic feedback during operation or surgeon training.  ...  For a brain model having more than 7000 degrees of freedom, we computed the reaction forces due to indentation with frequency of around 1000 Hz using a standard dual core PC.  ...  Acknowledgements The first author was an IPRS scholar in Australia during the completion of this research. The financial support of the Australian Research Council (Grant Nos.  ... 
doi:10.1016/j.media.2008.12.001 pmid:19152791 pmcid:PMC2783832 fatcat:yekdsvcwm5a3hcatu7yokethnu

Tetrahedral Image-to-Mesh Conversion Software for Anatomic Modeling of Arteriovenous Malformations

Fotis Drakopoulos, Ricardo Ortiz, Andinet Enquobahrie, Deanna Sasaki-Adams, Nikos Chrisochoides
2015 Procedia Engineering  
It uses non-connectivity patterns to implicitly control the number of the extracted feature points needed for the registration, and thus, adjusts the trade-off between the achieved mesh fidelity and the  ...  We describe a new implementation of an adaptive multi-tissue tetrahedral mesh generator targeting anatomic modeling of Arteriovenous Malformation (AVM) for surgical simulations.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH and NSF.  ... 
doi:10.1016/j.proeng.2015.10.139 fatcat:juniiir4wndotownzwgrqa5wgi
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