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Image Registration Driven by Combined Probabilistic and Geometric Descriptors [chapter]

Linh Ha, Marcel Prastawa, Guido Gerig, John H. Gilmore, Cláudio T. Silva, Sarang Joshi
2010 Lecture Notes in Computer Science  
Deformable image registration in the presence of considerable contrast differences and large-scale size and shape changes represents a significant challenge for image registration.  ...  We show preliminary results on the registrations of neonatal brain MRIs to two-year old infant MRIs using class posteriors and surface boundaries of structures undergoing major changes.  ...  Conclusions We have proposed a registration framework that makes use of the probabilistic and geometric structures of anatomies embedded in the images.  ... 
doi:10.1007/978-3-642-15745-5_74 fatcat:gycnqzijsbf2rp66erm5k6xx44

Efficient Morphometric Techniques in Alzheimer's Disease Detection: Survey and Tools

Vinutha N., P. Deepa Shenoy, P. Deepa Shenoy, K.R. Venugopal
2016 Neuroscience International  
The different types of segmentation techniques such as Tissue Segmentation, Atlas based Segmentation, Hippocampus Segmentation and other segmentation techniques have been discussed.  ...  The registered images are then subjected to the process of segmentation in order to segment relevant tissues or desired region of interest that are significant in AD detection.  ...  Author's Contributions All authors were involved in the manuscript preparation. Ethics This article is original and contains unpublished material.  ... 
doi:10.3844/amjnsp.2016.19.44 fatcat:3zeb2s5pjzfv7mptqi7cy2a3au

Automated Brain Structure Segmentation Based on Atlas Registration and Appearance Models

Fedde van der Lijn, Marleen de Bruijne, Stefan Klein, Tom den Heijer, Yoo Y. Hoogendam, Aad van der Lugt, Monique M. B. Breteler, Wiro J. Niessen
2012 IEEE Transactions on Medical Imaging  
The spatial model is implemented by registering multiple atlas images to the target image and creating a spatial probability map.  ...  The method is tested in cross-validation experiments on two datasets acquired with different magnetic resonance sequences, in which the hippocampus and cerebellum were segmented by an expert.  ...  In conclusion, we have presented a brain structure segmentation method based on atlas registration and multi-feature classification.  ... 
doi:10.1109/tmi.2011.2168420 pmid:21937346 fatcat:3wbcuchrq5flrbo7br4fqnldpq

Enhancing atlas based segmentation with multiclass linear classifiers

Michaël Sdika
2015 Medical Physics (Lancaster)  
Purpose To present a method to enrich atlases for atlas based segmentation. Such enriched atlases can then be used as a single atlas or within a multi-atlas framework. b.  ...  We also propose to use these images of classifiers within a multi-atlas framework: results produced by a set of such local classifier atlases can be combined using a label fusion method. c.  ...  A Bayes classifier with Markov prior is used in [38] to segment a single structure using multi-scale Gaussian derivatives features.  ... 
doi:10.1118/1.4935946 pmid:26632071 fatcat:6b63iq4evzcqvcszwdhdvsl7gi

A fast stochastic framework for automatic MR brain images segmentation

Marwa Ismail, Ahmed Soliman, Mohammed Ghazal, Andrew E. Switala, Georgy Gimel'farb, Gregory N. Barnes, Ashraf Khalil, Ayman El-Baz, Dzung Pham
2017 PLoS ONE  
The proposed segmentation framework is based on a shape prior built using a subset of co-aligned training images that is adapted during the segmentation process based on first-and second-order visual appearance  ...  To accurately account for the large inhomogeneity in infant MRIs, a higher-order Markov-Gibbs Random Field (MGRF) spatial interaction model that integrates third-and fourth-order families with a traditional  ...  Acknowledgments This work has been supported by the University of Louisville 21st Century University Initiative on Big Data in Medicine.  ... 
doi:10.1371/journal.pone.0187391 pmid:29136034 pmcid:PMC5685492 fatcat:kvx3gpreirbyliuhi74nrcky5a

Learning Deformable Image Registration from Optimization: Perspective, Modules, Bilevel Training and Beyond [article]

Risheng Liu, Zi Li, Xin Fan, Chenying Zhao, Hao Huang, Zhongxuan Luo
2021 arXiv   pre-print
We conduct two groups of image registration experiments on 3D volume datasets including image-to-atlas registration on brain MRI data and image-to-image registration on liver CT data.  ...  and image segmentation.  ...  These self-similarity context-based descriptors may transform images into representations independent of the underlying image acquisition and have been frequently used in multi-modal registration.  ... 
arXiv:2004.14557v3 fatcat:22p4ui6zjjh5fkxtpzolln2eqy

Atlas Guided Identification of Brain Structures by Combining 3D Segmentation and SVM Classification [chapter]

Ayelet Akselrod-Ballin, Meirav Galun, Moshe John Gomori, Ronen Basri, Achi Brandt
2006 Lecture Notes in Computer Science  
These features include in particular the prior probability knowledge of anatomic structures due to the use of an MRI probabilistic atlas.  ...  This study presents a novel automatic approach for the identification of anatomical brain structures in magnetic resonance images (MRI).  ...  We incorporate prior knowledge of anatomic structures using an MRI brain atlas.  ... 
doi:10.1007/11866763_26 fatcat:pxkcej3oabh3dd6m5eshvsu57m

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  
We also summarize publically available infant-dedicated resources, including MRI datasets, computational tools, grand challenges, and brain atlases.  ...  In this review paper, we provide a comprehensive review of the state-of-the-art computational methods for infant brain MRI processing and analysis, which have advanced our understanding of early postnatal  ...  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

The Brain/MINDS 3D digital marmoset brain atlas [article]

Alexander Woodward, Tsutomu Hashikawa, Masahide Maeda, Takaaki Kaneko, Keigo Hikishima, Atsushi Iriki, Hideyuki Okano, Yoko Yamaguchi
2017 bioRxiv   pre-print
To the best of our knowledge this is the first comprehensive digital 3D brain atlas of the common marmoset having nor- malized multi-modal data, cortical and sub-cortical segmentation, and in a common  ...  Nissl histology images were processed to remove illumination and shape artifacts and then normalized to the MRI data. Brain region segmentation is provided for both hemispheres.  ...  T.H. and A.I created the Nissl stained images and drew the original brain region boundaries in the TIF files. K.H. created the MRI T 2 data. Competing Financial Interests  ... 
doi:10.1101/228676 fatcat:thcwtyu6njfrbay7jzvn2dq2oa

The Brain/MINDS 3D digital marmoset brain atlas

Alexander Woodward, Tsutomu Hashikawa, Masahide Maeda, Takaaki Kaneko, Keigo Hikishima, Atsushi Iriki, Hideyuki Okano, Yoko Yamaguchi
2018 Scientific Data  
To the best of our knowledge this is the first comprehensive digital 3D brain atlas of the common marmoset having normalized multi-modal data, cortical and sub-cortical segmentation, and in a common file  ...  Nissl histology images were processed to remove illumination and shape artifacts and then normalized to the MRI data. Brain region segmentation is provided for both hemispheres.  ...  We thank Noritaka Ichinohe at RIKEN BSI for his advice on landmarks and on marmoset brain anatomy. We thank Reiko Nakatomi at RIKEN BSI for helping create the Nissl stained images.  ... 
doi:10.1038/sdata.2018.9 pmid:29437168 pmcid:PMC5810420 fatcat:ktaam3rnxnh77bvuoli73dgkom

A Three-dimensional MRI Atlas of the Mouse Brain with Estimates of the Average and Variability

N. Kovačević, J.T. Henderson, E. Chan, N. Lifshitz, J. Bishop, A.C. Evans, R.M. Henkelman, X.J. Chen
2004 Cerebral Cortex  
A three-dimensional annotation of the average image was performed and used to estimate the mean and standard deviation of volumes in a variety of structures across the individual brains; these volumes  ...  Magnetic resonance imaging (MRI) is ideally suited to probe fine structures in mice.  ...  For nonlinear registrations we used the multi-resolution, multi-scale ANIMAL methodology developed at the Montreal Neurological Institute (MNI) (Collins and Evans, 1997) .  ... 
doi:10.1093/cercor/bhh165 pmid:15342433 fatcat:o4n6qvjl2rcglbenkfbm46o5fu

A review on brain structures segmentation in magnetic resonance imaging

Sandra González-Villà, Arnau Oliver, Sergi Valverde, Liping Wang, Reyer Zwiggelaar, Xavier Lladó
2016 Artificial Intelligence in Medicine  
Future trends should combine multi-atlas with learning-based or deformable approaches Abstract Background and objectives: Automatic brain structures segmentation in magnetic resonance images has been widely  ...  We present a review of automatic brain structures segmentation methods. We provide a classification according to the strategy used to segment the structures.  ...  This work has been partially supported by "La Fundació la Marató de TV3", by Retos de Investigación TIN2014-55710-R, and by MPC UdG 2016/022 grant."  ... 
doi:10.1016/j.artmed.2016.09.001 pmid:27926381 fatcat:morzi7uy6zch7p73l7t7mrq2ti

A review on automatic fetal and neonatal brain MRI segmentation

Antonios Makropoulos, Serena J. Counsell, Daniel Rueckert
2018 NeuroImage  
In recent years, a variety of segmentation methods have been proposed for automatic delineation of the fetal and neonatal brain MRI.  ...  Brain atlases are commonly utilised as training data in the segmentation process.  ...  With advances in Magnetic Resonance Imaging (MRI), detailed images of the fetal and neonatal brain can be visualized non-invasively at a millimeter scale.  ... 
doi:10.1016/j.neuroimage.2017.06.074 pmid:28666878 fatcat:7fbaimevcfc67eqpdi2zx7l5ey

Multi-scale radiomic analysis of sub-cortical regions in MRI related to autism, gender and age

Ahmad Chaddad, Christian Desrosiers, Matthew Toews
2017 Scientific Reports  
We propose using multi-scale image textures to investigate links between neuroanatomical regions and clinical variables in MRI.  ...  Such features have been successfully applied in a variety of image analysis contexts, including segmentation and computer-aided diagnosis [16] [17] [18] [19] [20] [21] [22] .  ...  The funding agency has no role in the conceptualization of the study, data collection and analysis, or the decision to publish these results.  ... 
doi:10.1038/srep45639 pmid:28361913 pmcid:PMC5374503 fatcat:s37vg5clpzbxtndmbp7qm67lqa

Cortical Foldingprints for Infant Identification

Dingna Duan, Shunren Xia, Zhengwang Wu, Fan Wang, Li Wang, Weili Lin, John H Gilmore, Dinggang Shen, Gang Li
2019 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)  
To this end, we propose a novel discriminative descriptor of regional cortical folding based on multi-scale analysis of curvature maps via spherical wavelets, called FoldingPrint.  ...  Cortical folding of the adult brain is highly convoluted and encodes inter-subject variable characteristics. Recent studies suggest that it is useful for individual identification in adults.  ...  Acknowledgments This work was partially supported by NIH grants (MH100217, MH107815, MH108914, MH109773, MH110274, MH116225, MH117943, MH070890, MH064065, and HD053000).  ... 
doi:10.1109/isbi.2019.8759429 pmid:31938450 pmcid:PMC6959198 fatcat:3aa7hzy62bezrbdey3ocriclsa
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