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Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration

Arno Klein, Jesper Andersson, Babak A. Ardekani, John Ashburner, Brian Avants, Ming-Chang Chiang, Gary E. Christensen, D. Louis Collins, James Gee, Pierre Hellier, Joo Hyun Song, Mark Jenkinson (+7 others)
2009 NeuroImage  
A viscous fluid regularizer was applied to guarantee diffeomorphic (i.e., smooth, one-to-one) deformation mappings.  ...  The nonlinear deformation programs are listed in alphabetical order after the linear registration program FLIRT.  ... 
doi:10.1016/j.neuroimage.2008.12.037 pmid:19195496 pmcid:PMC2747506 fatcat:447owlbmybclzjafnkai35o6r4

MRI構造画像を用いたVoxel-based morphometry
Voxel-based Morphometry Using Structural MRI

2016 Medical Imaging Technology  
.: Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration.  ...  Neuroimage 14: 1454-1462, 2001 [ 4 ] Eckert MA, Tenforde A, Galaburda AM, et al.: To modulate or not to modulate: Differing results in uniquely shaped Williams syndrome brains.  ...  It has become a major analysis technique since it was firstly applied to psychological and neurological diseases accompanying cerebral atrophy, and is now also applied to cognitive sciences fields.  ... 
doi:10.11409/mit.34.3 fatcat:2cgyfexvgfhjzlxnhlx64cxmai

Performing label-fusion-based segmentation using multiple automatically generated templates

M. Mallar Chakravarty, Patrick Steadman, Matthijs C. van Eede, Rebecca D. Calcott, Victoria Gu, Philip Shaw, Armin Raznahan, D. Louis Collins, Jason P. Lerch
2012 Human Brain Mapping  
We demonstrate the efficacy of our method for the mouse and human using two different nonlinear registration algorithms (ANIMAL and ANTs).  ...  Classically, model-based segmentation procedures match magnetic resonance imaging (MRI) volumes to an expertly labeled atlas using nonlinear registration.  ...  MMC would also like to thank G. Clinton, E. Hazel, and B. Worrell for inspiring this work.  ... 
doi:10.1002/hbm.22092 pmid:22611030 pmcid:PMC4896505 fatcat:vrn5y7zndvhadklclm4j7xkpsy

Image Registration Methods for Patient-Specific Virtual Physiological Human Models [article]

Julia E. E. De Oliveira, Paul Giessler, Thomas M. Deserno
2015 Eurographics Workshop on Visual Computing for Biomedicine  
Virtual physiological human (VPH) model and magnetic resonance image (MRI) are used for patient-specific image registration.  ...  Results are presented in the form of image registration with respect to the skin of the models.  ...  [LSU * 12] developed a technique to automate landmark selection for nonlinear medical image registration using local curvature on anatomical contours applied to MRI and histological sections of brain images  ... 
doi:10.2312/vcbm.20151206 dblp:conf/vcbm/OliveiraGD15 fatcat:mclo3uclgrdvtdlkeumvecqhzy

Flexible Bayesian Modelling for Nonlinear Image Registration [article]

Mikael Brudfors, Yaël Balbastre, Guillaume Flandin, Parashkev Nachev, John Ashburner
2020 arXiv   pre-print
The model is evaluated at inter-subject registration of 3D human brain scans. Here, the main modeling assumption is that individual anatomies can be generated by deforming a latent 'average' brain.  ...  The method is agnostic to imaging modality and can be applied with no prior processing. We evaluate the algorithm using freely available, manually labelled datasets.  ...  Using the affine registrations as baseline, the results showed 6% to 17% greater accuracy improvements when compared to those achieved for the second most accurate nonlinear registration algorithm evaluated  ... 
arXiv:2006.02338v1 fatcat:vgqnm3zhvna4xpnmo64samvnwe

Nonlinear Registration and Template-Driven Segmentation [chapter]

Simon Warfield, Andre Robatino, Joachim Dengler, Ferenc Jolesz, Ron Kikinis
1999 Brain Warping  
Acknowledgements This investigation was supported by grants P01 CA67165-01A1 (FJ, RK), P01 AG4953-14 (RK) and BES 9631710 (RK).  ...  We applied an automated analysis to a series of 28 MR scans, from 14 schizophrenia patients and 14 normal controls.  ...  Deformations were applied to the atlas after artificially colouring the sections, and the elastic matching algorithm applied to recover the deformation.  ... 
doi:10.1016/b978-012692535-7/50080-x fatcat:yvg63jiblzgopdogu46evqtkqy

Non-linear cerebral registration with sulcal constraints [chapter]

D. Louis Collins, Georges Le Goualher, Alan C. Evans
1998 Lecture Notes in Computer Science  
the standard linear and nonlinear registration methods, respectively.  ...  Here, the technique is modified to incorporate sulcal ribbons in conjunction with a chamfer distance objective function to improve registration in real MRI data as well.  ...  This work forms part of a continuing project of the HBMP-funded International Consortium for Brain Mapping (ICBM) to develop a probabilistic atlas of human neuroanatomy.  ... 
doi:10.1007/bfb0056286 fatcat:kfirvpanvnfmdgt6rkztmswsgm

Slice-to-Volume Nonrigid Registration of Histological Sections to MR Images of the Human Brain

Sergey Osechinskiy, Frithjof Kruggel
2011 Anatomy Research International  
Algorithms are applied to cross-modality registration of histological and magnetic resonance images of the human brain.  ...  Registration performance is evaluated across a range of optimization algorithms and intensity-based cost functions.  ...  of Leipzig.  ... 
doi:10.1155/2011/287860 pmid:22567290 pmcid:PMC3335496 fatcat:qdwyg6fczzhsxnw4iiqdf7pjri

Optimization of the SNR-resolution tradeoff for registration of magnetic resonance images

Shoan C. Kale, Jason P. Lerch, R. Mark Henkelman, X. Josette Chen
2008 Human Brain Mapping  
The deformation fields were used to evaluate registration performance of each tradeoff relative to the gold standard.  ...  Image resolution should be adjusted to produce this target voxel SNR when registration is a central processing task. Hum Brain Mapp 29:1147-1158, 2008. V V C 2007 Wiley-Liss, Inc.  ...  The authors thank Victoria Bonn for specimen preparation, Nir Lifshitz and Jun Dazai for design/construction of the imaging probe, and Brian Nieman for pulse sequence development. Dr. R.  ... 
doi:10.1002/hbm.20453 pmid:17957707 fatcat:lqlicrsmpvcjznd35o4wboghbu

Mapping registration sensitivity in MR mouse brain images

Matthijs C. van Eede, Jan Scholz, M. Mallar Chakravarty, R. Mark Henkelman, Jason P. Lerch
2013 NeuroImage  
Here we develop a novel approach to simulate deformations on MR brain images to evaluate the ability of two registration algorithms to extract structural differences corresponding to biologically plausible  ...  Nonlinear registration algorithms provide a way to estimate structural (brain) differences based on magnetic resonance images.  ...  In excess of 125,000 CPU hours were used to create the simulated deformation fields and perform the registrations.  ... 
doi:10.1016/j.neuroimage.2013.06.004 pmid:23756204 fatcat:clypzaibj5aojhbs6j6xj2nxdq

Warping an atlas derived from serial histology to 5 high-resolution MRIs

Stephanie Tullo, Gabriel A. Devenyi, Raihaan Patel, Min Tae M. Park, D. Louis Collins, M. Mallar Chakravarty
2018 Scientific Data  
Dice's Kappa metric was used to demonstrate high quality registration and segmentation accuracy of the atlases.  ...  to facilitate atlas-to-template nonlinear transformation estimation.  ...  Nonlinear Registration Algorithms The ANIMAL algorithm 42, 43 was used for the nonlinear registration of the histologically-derived atlas to the five MRI templates, which deforms a source MRI volume,  ... 
doi:10.1038/sdata.2018.107 pmid:29917012 pmcid:PMC6007088 fatcat:vzn5il6irretzmjusi75jhmbfm

Multimodal Whole Brain Registration: MRI and High Resolution Histology

Maryana Alegro, Edson Amaro, Burlen Loring, Helmut Heinsen, Eduardo Alho, Lilla Zollei, Daniela Ushizima, Lea T. Grinberg
2016 2016 IEEE Conference on Computer Vision and Pattern Recognition Workshops (CVPRW)  
Integration on ultra-high field mri and histology Mann, and R. V. Parsey. Evaluation of 14 nonlinear defor- for connectome based research of brain disorders.  ...  Frontiers mation algorithms applied to human brain mri registration. in Neuroanatomy, 7, 2013. 2 NeuroImage, 1(46), 2009. 5 [36] P. A.  ... 
doi:10.1109/cvprw.2016.85 dblp:conf/cvpr/AlegroALHAZUG16 fatcat:izxuwskkybcx5i62badvy5z5ya

Validation of a nonrigid registration algorithm for multimodal data

Peter Rogelj, Stanislav Kovacic, James C. Gee, Milan Sonka, J. Michael Fitzpatrick
2002 Medical Imaging 2002: Image Processing  
We describe the evaluation of a non-rigid image registration method for multi-modal data.  ...  Each of these approaches are limited and in this paper, we illustrate some of the problems that arise based on their application to the evaluation of our multi-modal non-rigid registration method.  ...  Toga for providing the MRI dataset.  ... 
doi:10.1117/12.467170 dblp:conf/miip/RogeljKG02 fatcat:hcg36ttp6vfv7jl54uowj7j7rm

Synthesis of 3D MRI Brain Images With Shape and Texture Generative Adversarial Deep Neural Networks

Chee Keong Chong, Eric Tatt Wei Ho
2021 IEEE Access  
Brain registration algorithms in established brain processing pipelines [15] , [22] apply a twostep transformation process namely a global affine alignment and a local nonlinear registration.  ...  State-of-art nonlinear registration algorithms apply a topology-preserving diffeomorphic transform, which iteratively optimizes an energy function and are computationally demanding.  ... 
doi:10.1109/access.2021.3075608 fatcat:wkmezhv2ujdsddjv4zwabxx3j4

Statistically assisted fluid image registration algorithm - SAFIRA

Caroline C. Brun, Natasha Lepore, Xavier Pennec, Yi-Yu Chou, Agatha D. Lee, Marina Barysheva, Greig I. de Zubicaray, Katie L. McMahon, Margaret J. Wright, Paul M. Thompson
2010 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro  
Here we extend this algorithm to 3D: given 3D brain images from a population, vector fields and their corresponding deformation matrices are computed in a first round of registrations using the non-statistical  ...  We also compared the power of the different algorithms using tensor-based morphometry -a technique to analyze local volumetric differences in brain structure-applied to 46 3D brain scans from healthy monozygotic  ...  The use of empirical statistics has been advocated many times, but none of the 14 nonlinear registration methods evaluated in [10] uses empirical information on brain variation during the registration  ... 
doi:10.1109/isbi.2010.5490335 pmid:30555622 pmcid:PMC6291216 fatcat:7cwrewlsybdurpqofmpnoj7ohq
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