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Implicit reference-based group-wise image registration and its application to structural and functional MRI

Xiujuan Geng, Gary E. Christensen, Hong Gu, Thomas J. Ross, Yihong Yang
2009 NeuroImage  
The performance of pair-wise and group-wise registration algorithms was evaluated for spatial normalization of structural and functional MRI data.  ...  In contrast, implicit reference group-wise (IRG) registration estimates correspondences between a group of images by jointly registering the images to an implicit reference corresponding to the group average  ...  Acknowledgments This work was supported in part by the Intramural Research Program of the National Institute on Drug Abuse (NIDA), National Institute of Health (NIH) and NIH grant EB004126.  ... 
doi:10.1016/j.neuroimage.2009.04.024 pmid:19371788 pmcid:PMC2719682 fatcat:ke6atmthqndhdnnokv6bablpp4

Learning unbiased group-wise registration (LUGR) and joint segmentation: evaluation on longitudinal diffusion MRI [article]

Bo Li, Wiro J. Niessen, Stefan Klein, M. Arfan Ikram, Meike W. Vernooij, Esther E. Bron
2021 arXiv   pre-print
We here propose an analytical framework based on an unbiased learning strategy for group-wise registration that simultaneously registers images to the mean space of a group to obtain consistent segmentations  ...  The results confirm that the implicit reference image is an average of the input image.  ...  , CVON2018-28), and the Dutch Heart Foundation (PPP Allowance, 2018B011).  ... 
arXiv:2011.01869v2 fatcat:avlqepi5gnhuliqhrdw5k6o5iu

Unbiased Group-Wise Image Registration: Applications in Brain Fiber Tract Atlas Construction and Functional Connectivity Analysis

Xiujuan Geng, Hong Gu, Wanyong Shin, Thomas J. Ross, Yihong Yang
2010 Journal of medical systems  
We propose an unbiased implicit-reference group-wise (IRG) image registration method and demonstrate its applications in the construction of a brain white matter fiber tract atlas and the analysis of resting-state  ...  Compared to reference-based registration, the IRG registration improves the fiber track overlap within the group.  ...  The current work applies an unbiased implicit-reference group-wise (IRG) registration framework [9] to the study of brain white matter fiber tracts and resting-state functional connectivity.  ... 
doi:10.1007/s10916-010-9509-9 pmid:20703687 pmcid:PMC2987551 fatcat:fdlbvlwbozghfonythfslg6zxm

Particle-Guided Image Registration [chapter]

Joohwi Lee, Ilwoo Lyu, İpek Oğuz, Martin A. Styner
2013 Lecture Notes in Computer Science  
We demonstrate the results of our method in an application of rodent brain structure segmentation and show that our method provides better accuracy in two structures compared to other registration methods  ...  Moreover, the use of corresponding particles naturally extends our method to a group-wise registration by computing a mean of particles.  ...  Non-rigid registration is a crucial tool to process such MRIs providing structural segmentations and enabling the analysis of group differences.  ... 
doi:10.1007/978-3-642-40760-4_26 fatcat:3cglbw4bxjbhnaeaiuxgyxnati

Registration of challenging pre-clinical brain images

William R. Crum, Michel Modo, Anthony C. Vernon, Gareth J. Barker, Steven C.R. Williams
2013 Journal of Neuroscience Methods  
Existing systems for registration (the systematic alignment of scans into a consistent anatomical coordinate system), which assume image similarity to a reference scan, may fail when applied to these images  ...  We tested this technique systematically in a simulated human population of brain tumour images before applying it to pre-clinical models of Parkinson's disease and stroke.  ...  Group-wise registration can be computationally demanding; however, it is not clear that defining such a compromise reference is advantageous when there is large variation in image appearances.  ... 
doi:10.1016/j.jneumeth.2013.03.015 pmid:23558335 pmcid:PMC3683149 fatcat:jehsf4z5nbgbxk54vcti4pji7a

A comparison of automated anatomical–behavioural mapping methods in a rodent model of stroke

William R. Crum, Vincent P. Giampietro, Edward J. Smith, Natalia Gorenkova, R. Paul Stroemer, Michel Modo
2013 Journal of Neuroscience Methods  
Tensor-based morphometry (TBM) has been used to perform voxel-wise structural analyses over the entire brain; however, a combination of lesion hyper-intensities and subtle structural remodelling away from  ...  damage, due to conditions such as stroke, results in a complex pattern of structural changes and significant behavioural dysfunctions; the automated analysis of magnetic resonance imaging (MRI) and discovery  ...  The authors would like to thank the British Heart Foundation for providing supporting the 7T MRI scanner (Preclinical Imaging Unit, King's College London) used in this work.  ... 
doi:10.1016/j.jneumeth.2013.05.009 pmid:23727124 pmcid:PMC3759848 fatcat:r3xqgkzb7naybmyekbs22drk5a

DeepCSR: A 3D Deep Learning Approach for Cortical Surface Reconstruction [article]

Rodrigo Santa Cruz, Leo Lebrat, Pierrick Bourgeat, Clinton Fookes, Jurgen Fripp, Olivier Salvado
2020 arXiv   pre-print
The study of neurodegenerative diseases relies on the reconstruction and analysis of the brain cortex from magnetic resonance imaging (MRI).  ...  Traditional frameworks for this task like FreeSurfer demand lengthy runtimes, while its accelerated variant FastSurfer still relies on a voxel-wise segmentation which is limited by its resolution to capture  ...  This registration aims to unify the coordinate systems across different MR scans easing the learning and prediction of implicit surfaces.  ... 
arXiv:2010.11423v1 fatcat:yuiaqrjx75gexcl3vhghblhfi4

Computational neuroanatomy of baby brains: A review

Gang Li, Li Wang, Pew-Thian Yap, Fan Wang, Zhengwang Wu, Yu Meng, Pei Dong, Jaeil Kim, Feng Shi, Islem Rekik, Weili Lin, Dinggang Shen
2018 NeuroImage  
The first postnatal years are an exceptionally dynamic and critical period of structural, functional and connectivity development of the human brain.  ...  We also summarize publically available infant-dedicated resources, including MRI datasets, computational tools, grand challenges, and brain atlases.  ...  Acknowledgements This work was partially supported by NIH grants (MH100217, MH107815, MH108914, MH109773, MH110274 and NS093842).  ... 
doi:10.1016/j.neuroimage.2018.03.042 pmid:29574033 pmcid:PMC6150852 fatcat:w2o27wt5afhktd7zoophmhnmi4

Front Matter: Volume 10574

Proceedings of SPIE, Elsa D. Angelini, Bennett A. Landman
2018 Medical Imaging 2018: Image Processing  
using a Base 36 numbering system employing both numerals and letters.  ...  Utilization of CIDs allows articles to be fully citable as soon as they are published online, and connects the same identifier to all online and print versions of the publication.  ...  24] 10574 0Q Self-reference-based and during-registration detection of motion artifacts in spatio- temporal image data [10574-25] 10574 0R GPU-based stochastic-gradient optimization for non-rigid  ... 
doi:10.1117/12.2315755 fatcat:jdfbaent6vhu5dwlrqrqt66vce

Advances and challenges in deformable image registration: From image fusion to complex motion modelling

Julia A. Schnabel, Mattias P. Heinrich, Bartłomiej W. Papież, Sir J. Michael Brady
2016 Medical Image Analysis  
, the advent of dedicated longitudinal and cross-sectional brain studies soon necessitated the development of more sophisticated methods that are able to detect and measure local structural or functional  ...  , deformable image registration for a wide range of medical applications and imaging modalities, involving the compensation and analysis of physiological organ motion or of tissue changes due to growth  ...  Acknowledgments The authors wish to acknowledge funding 270 from CRUK and EPSRC, and the contributions of other researchers associated with their laboratories, including but not limited to: Amalia Cifor  ... 
doi:10.1016/ pmid:27364430 fatcat:ug7aw3jbhbb2xe5qrwhd3qbitu

From label fusion to correspondence fusion: A new approach to unbiased groupwise registration

P. A. Yushkevich, Hongzhi Wang, J. Pluta, B. B. Avants
2012 2012 IEEE Conference on Computer Vision and Pattern Recognition  
Instead of computing a consensus segmentation, weighted voting is used to estimate a consensus coordinate map between a target image and a reference space.  ...  Evaluation in synthetic data shows that correspondences recovered by fusion methods are more accurate than those based on registration to a population template.  ...  , to establish group-wise correspondences.  ... 
doi:10.1109/cvpr.2012.6247771 pmid:24457950 pmcid:PMC3896982 fatcat:2zrbiatfmjbrdprvnju6iuzcfu

Non-rigid image registration: theory and practice

W R Crum, T Hartkens, D L G Hill
2004 British Journal of Radiology  
In this paper we discuss the current state of the art of non-rigid registration to put on-going research in context and to highlight current and future clinical applications that might benefit from this  ...  Image registration is an important enabling technology in medical image analysis.  ...  Images comprising Figures 2-6 were provided by members of the Computational Imaging Science Group at Guy's Hospital: K Leung, funded by EPSRC and  ... 
doi:10.1259/bjr/25329214 pmid:15677356 fatcat:fgcrow4uzjf27arer4yb2ifyve

System for Integrated Neuroimaging Analysis and Processing of Structure

Bennett A. Landman, John A. Bogovic, Aaron Carass, Min Chen, Snehashis Roy, Navid Shiee, Zhen Yang, Bhaskar Kishore, Dzung Pham, Pierre-Louis Bazin, Susan M. Resnick, Jerry L. Prince
2012 Neuroinformatics  
Recent developments with MRI analysis of structural connectivity, anatomical brain segmentation, cortical surface parcellation, and functional imaging have yielded fantastic advances in our ability to  ...  This effort combines and extends state-of-the-art techniques to simultaneously consider and analyze structural and diffusion information alongside quantitative and functional imaging data.  ...  Acknowledgments The authors are appreciative of the careful feedback from the anonymous reviewers and editor (Dr. David Kennedy).  ... 
doi:10.1007/s12021-012-9159-9 pmid:22932976 pmcid:PMC3511612 fatcat:krgqmregs5hqnm3isklageiqi4

Multi-contrast anatomical subcortical structures parcellation

Pierre-Louis Bazin, Anneke Alkemade, Martijn J Mulder, Amanda G Henry, Birte U Forstmann
2020 eLife  
It has been carefully validated against expert human raters and previous methods, and can easily be extended to other subcortical structures and applied to any quantitative MRI dataset.  ...  In sum, we hope this novel parcellation algorithm will facilitate functional and structural neuroimaging research into small subcortical nuclei and help to chart terra incognita.  ...  We also thank Steven Miletić and Dagmar Timmann for stimulating discussions around this topic, and all undergraduate students who contributed to the manual delineations.  ... 
doi:10.7554/elife.59430 pmid:33325368 pmcid:PMC7771958 fatcat:bblosvpn35bcpjdydulognwheu

Evaluation of group-specific, whole-brain atlas generation using Volume-based Template Estimation (VTE): Application to normal and Alzheimer's populations

Yajing Zhang, Jiangyang Zhang, Johnny Hsu, Kenichi Oishi, Andreia V. Faria, Marilyn Albert, Michael I. Miller, Susumu Mori
2014 NeuroImage  
MRI-based human brain atlases, which serve as a common coordinate system for image analysis, play an increasingly important role in our understanding of brain anatomy, image registration, and segmentation  ...  It has been tested for segmented brain structures, such as the hippocampus, but its validity on whole-brain MR images has not been examined.  ...  Institute of Biomedical Imaging and Bioengineering.  ... 
doi:10.1016/j.neuroimage.2013.09.011 pmid:24051356 pmcid:PMC3860098 fatcat:utxce5q4rbdbrfgj7isylg7cgy
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