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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  
Accurate automated brain structure segmentation methods facilitate the analysis of large-scale neuroimaging studies.  ...  The structure's appearance is modeled by a classifier based on Gaussian scale-space features.  ...  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

Multi-organ Abdominal CT Segmentation Using Hierarchically Weighted Subject-Specific Atlases [chapter]

Robin Wolz, Chengwen Chu, Kazunari Misawa, Kensaku Mori, Daniel Rueckert
2012 Lecture Notes in Computer Science  
The method is based on a hierarchical atlas registration and weighting scheme that generates target specific priors from an atlas database by combining aspects from multi-atlas registration and patch-based  ...  segmentation, two widely used methods in brain segmentation.  ...  Subject-specific, automated segmentation methods based on multi-atlas registration have been pioneered and are now widely used for brain segmentation of magnetic resonance (MR) imaging [6] , [7] .  ... 
doi:10.1007/978-3-642-33415-3_2 fatcat:rhlh3yrwanhcdafuuqgw4sbz4m

Front Matter: Volume 10133

Proceedings of SPIE, Martin A. Styner, Elsa D. Angelini
2017 Medical Imaging 2017: Image Processing  
Sulci segmentation using geometric active contours 0J Multi-modal and targeted imaging improves automated mid-brain segmentation 10133 0K An algorithm for automatic parameter adjustment for brain  ...  boundaries [10133-76] 10133 24 Automated segmentation of 3D anatomical structures on CT images by using a deep convolutional network based on end-to-end learning approach [10133-77] 10133 25 Microscopic  ...  SESSION 4 SEGMENTATION: BRAIN Session Chairs  ... 
doi:10.1117/12.2270368 dblp:conf/miip/X17 fatcat:resfpzholvbtbalfkbg3pj64gu

Vision 20/20: Perspectives on automated image segmentation for radiotherapy

Gregory Sharp, Karl D. Fritscher, Vladimir Pekar, Marta Peroni, Nadya Shusharina, Harini Veeraraghavan, Jinzhong Yang
2014 Medical Physics (Lancaster)  
Automated segmentation methods seek to reduce delineation workload and unify the organ boundary definition.  ...  In the nearest future, improvements in CT-based autosegmentation tools will be achieved through standardization of imaging and contouring protocols.  ...  Supplier Product name Method Included atlases Integrated with TPS Reference Accuray MultiPlan 5.0 Atlas-based model-based Brain, M pelvis Yes Reference 101 BrainLab iPlan Atlas-based Brain  ... 
doi:10.1118/1.4871620 pmid:24784366 pmcid:PMC4000389 fatcat:4chtxzqojfeyfan5fjloq6e7p4

Automated Segmentation of Mouse Brain Images Using Multi-Atlas Multi-ROI Deformation and Label Fusion

Jingxin Nie, Dinggang Shen
2012 Neuroinformatics  
We propose an automated multi-atlas and multi-ROI based segmentation method for both skullstripping of mouse brain and the ROI-labeling of mouse brain structures from the three dimensional (3D) magnetic  ...  Then, a multi-atlas and multi-ROI based deformable segmentation method is adopted to refine the ROI labeling result by deforming each ROI surface via boundary recognizers (i.e., SVM classifiers) trained  ...  Acknowledgments This work was supported in part by NIH grants EB006733, EB008374, EB009634, AG041721, and CA140413, by National Science Foundation of China under grant No. 61075010, and also by The National  ... 
doi:10.1007/s12021-012-9163-0 pmid:23055043 pmcid:PMC3538942 fatcat:llo6muovm5ay7fobxxsurvnjly

Eyeing the Human Brain's Segmentation Methods

Lilian Chirukawala et al., Lilian Chirukawala et al.,
2019 International Journal of Electrical and Electronics Engineering Research  
Among other uses, it helps us perform the following tasks in images: to measure and visualize the anatomical structures of the brain; to highlight brain structural changes; and to delineate regions with  ...  To date, a considerable body of research has burgeoned, which focuses on improving segmentation accuracy and reducing complexity.  ...  Multi-Atlas Registration Based Method Generally segmentation methods rely on intensity information and higher order structural information of objects.  ... 
doi:10.24247/ijeeerjun20195 fatcat:5cacelevgvci3n5wyiq6lr2jay

Atlas-Based Segmentation of the Brain for 3-Dimensional Treatment Planning in Children with Infratentorial Ependymoma [chapter]

Pierre-François D'Haese, Valerie Duay, Thomas E. Merchant, Benoit Macq, Benoit M. Dawant
2003 Lecture Notes in Computer Science  
The purpose of the study was to test the hypothesis that fully-automated atlas-based segmentation methods provide useful normal tissue dosimetry from which dose-volume modeling may be performed in a manner  ...  This paper presents a fully automated brain segmentation method that has been applied to a group of patients with infratentorial ependymoma.  ...  Pierre-François D'Haese is working towards a Ph.D. degree with awards from FRIA and FNRS (Belgian Science Foundation).  ... 
doi:10.1007/978-3-540-39903-2_77 fatcat:5djtrpwn45bdzlrset6hvw7yg4

Front Matter: Volume 9784

2016 Medical Imaging 2016: Image Processing  
shape analysis for cerebellar ataxia classification and cerebellar atrophy pattern visualization [9784-24] 9784 0Q Multi-object model-based multi-atlas segmentation for rodent brains using dense discrete  ...  correspondences [9784-25] 9784 0R Fast correspondences for statistical shape models of brain structures [9784-26] 9784 0S Robust group-wise rigid registration of point sets using t-mixture model [9784  ...  [9784-88] 9784 2I Active appearance model and deep learning for more accurate prostate segmentation on MRI [9784-89] 9784 2J Automated segmentation of MS lesions in FLAIR, DIR and T2-w MR images  ... 
doi:10.1117/12.2240619 fatcat:kot6cogf4rf6dcjhkzdrr5gahi

Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy

Anjum A. Sharief, Alexandra Badea, Anders M. Dale, G. Allan Johnson
2008 NeuroImage  
The mouse brain was segmented into 33 structures, including the hippocampus, amygdala, hypothalamus, thalamus, as well as fiber tracts and ventricles.  ...  We describe here a Markov Random Fields based segmentation of the actively-stained mouse brain, as a prerequisite for morphological phenotyping.  ...  Laurence Hedlund for numerous discussions and suggestions.  ... 
doi:10.1016/j.neuroimage.2007.08.028 pmid:17933556 pmcid:PMC2139901 fatcat:u3l273f7sze2zctjeqwjiuwktq

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  ...  This paper introduces a new framework for the segmentation of different brain structures (white matter, gray matter, and cerebrospinal fluid) from 3D MR brain images at different life stages.  ...  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

Automatic Labeling of Anatomical Structures in MR FastView Images Using a Statistical Atlas [chapter]

Matthias Fenchel, Stefan Thesen, Andreas Schilling
2008 Lecture Notes in Computer Science  
In our implementation, the statistical models of deformation and appearance are both implemented on the GPU (graphics processing unit), which permits computing the atlas based labeling using GPU hardware  ...  The statistical atlas consists of a statistical model of deformation and a statistical model of grey value appearance.  ...  Cootes introduced active shape models and active appearance models and published their application to atlas based matching in [8] .  ... 
doi:10.1007/978-3-540-85988-8_69 fatcat:zbrw3yfav5flbjukn6wf2ojqgu

Quantitative comparison of AIR, SPM, and the fully deformable model for atlas-based segmentation of functional and structural MR images

Minjie Wu, Owen Carmichael, Pilar Lopez-Garcia, Cameron S. Carter, Howard J. Aizenstein
2006 Human Brain Mapping  
structural segmentation and a more reliable functional signal colocalization than does AIR or SPM.  ...  Typical packages used for coregistration in functional image analyses include automated image registration (AIR) and statistical parametric mapping (SPM).  ...  .), and the NIMH. We thank the IMAGe (Imaging Methods and Analysis in Geriatrics) group and the Clinical Cognitive Neuroscience Laboratory at the University of Pittsburgh for their assistance.  ... 
doi:10.1002/hbm.20216 pmid:16463385 pmcid:PMC2886594 fatcat:exexak3lcrffxf6duchjxzlus4

A review of atlas-based segmentation for magnetic resonance brain images

Mariano Cabezas, Arnau Oliver, Xavier Lladó, Jordi Freixenet, Meritxell Bach Cuadra
2011 Computer Methods and Programs in Biomedicine  
In this paper we present a review of the automated approaches for atlas-based segmentation of magnetic resonance brain images.  ...  In recent years, researchers have investigated registration algorithms to match atlases to query subjects and also strategies for atlas construction.  ...  This study is also supported by the Center for Biomedical Imaging (CIBM) of the Geneva and Lausanne Universities and the EPFL, as well as the Leenaards and Louis Jeantet foundations.  ... 
doi:10.1016/j.cmpb.2011.07.015 pmid:21871688 fatcat:b4k343jqvbccjj2ps5lpqb2raq

An End-To-End Pipeline for Fully Automatic Morphological Quantification of Mouse Brain Structures From MRI Imagery

Shahinur Alam, Tae-Yeon Eom, Jeffrey Steinberg, David Ackerman, J. Eric Schmitt, Walter J. Akers, Stanislav S. Zakharenko, Khaled Khairy, Khaled Khairy
2022 Frontiers in Bioinformatics  
Segmentation of mouse brain magnetic resonance images (MRI) based on anatomical and/or functional features is an important step towards morphogenetic brain structure characterization of murine models in  ...  from T2w MRI images using an improved deep learning-based skull-stripping and data augmentation strategy, which enables segmentation of large brain regions by atlas or template registration, and 2) address  ...  T-YE and JS: conceptualization, data collection, data curation and neurobiological expert validation. WA and SZ: conceptualization, administration, supervision and editing.  ... 
doi:10.3389/fbinf.2022.865443 doaj:aac3d470352c401981a4b0f9a087742b fatcat:5tgq6ah77jdtheav5vxon2rsgm

Automatic brain tumor segmentation by subject specific modification of atlas priors1

Marcel Prastawa, Elizabeth Bullitt, Nathan Moon, Koen Van Leemput, Guido Gerig
2003 Academic Radiology  
The segmentation is guided by a spatial probabilistic atlas that contains expert prior knowledge about brain structures.  ...  This atlas is modified with the subject-specific brain tumor prior that is computed based on contrast enhancement. Results. Five cases with different types of tumors are selected for evaluation.  ...  Leuven for providing the MIRIT image registration software.  ... 
doi:10.1016/s1076-6332(03)00506-3 pmid:14697002 pmcid:PMC2430604 fatcat:tayzonl4pff4znrpmg6wzkriza
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