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Automatic segmentation of the hippocampus and the amygdala driven by hybrid constraints: Method and validation

M. Chupin, A. Hammers, R.S.N. Liu, O. Colliot, J. Burdett, E. Bardinet, J.S. Duncan, L. Garnero, L. Lemieux
2009 NeuroImage  
The segmentation from MRI of macroscopically ill-defined and highly variable structures, such as the hippocampus (Hc) and the amygdala (Am), requires the use of specific constraints.  ...  Here, we describe and evaluate a fast fully automatic hybrid segmentation that uses knowledge derived from probabilistic atlases and anatomical landmarks, adapted from a semi-automatic method.  ...  segmentation of the hippocampus and the amygdala.  ... 
doi:10.1016/j.neuroimage.2009.02.013 pmid:19236922 pmcid:PMC2677639 fatcat:xiae64dwgfeqpdwhkur5ispnx4

Hippocampus Segmentation Using A Local Prior Model On Its Boundary

Dimitrios Zarpalas, Anastasios Zafeiropoulos, Petros Daras, Nicos Maglaveras
2011 Zenodo  
Hippocampus segmentation is a very challenging task, due to the multivariate surrounding region and the missing boundary with the neighboring amygdala, whose intensities are identical.  ...  The proposed method, mimics the human segmentation way and thus shows enhancements in the segmentation accuracy.  ...  the manual segmentations of hippocampus and amygdala.  ... 
doi:10.5281/zenodo.1330622 fatcat:uzyghvpijnallogboeltwrcgqq

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  
Here, we present a review of the state-of-the-art of automatic methods available in the literature ranging from structure specific segmentation methods to whole brain parcellation approaches.  ...  , deformable, region-based and hybrid methods.  ...  González-Villà holds a UdG-BRGR2015 grant from the University of Girona.  ... 
doi:10.1016/j.artmed.2016.09.001 pmid:27926381 fatcat:morzi7uy6zch7p73l7t7mrq2ti

Fully automatic hippocampus segmentation and classification in Alzheimer's disease and mild cognitive impairment applied on data from ADNI

Marie Chupin, Emilie Gérardin, Rémi Cuingnet, Claire Boutet, Louis Lemieux, Stéphane Lehéricy, Habib Benali, Line Garnero, Olivier Colliot
2009 Hippocampus  
We proposed a fully automatic method using probabilistic and anatomical priors for hippocampus segmentation.  ...  Hippocampal magnetic resonance imaging volumetry is a potential biomarker for AD but is hindered by the limitations of manual segmentation.  ...  The grantee organization is the Northern California Institute for Research and Education, and the study is coordinated by the Alzheimer's Disease Cooperative Study at the University of California, San  ... 
doi:10.1002/hipo.20626 pmid:19437497 pmcid:PMC2837195 fatcat:2am6d4zacbgwrpnmgi4h5g72fe


2017 International Journal of Recent Trends in Engineering and Research  
We are presenting some survey and review of the current technologies and approaches of semi-automated and automated methods for the segmentation of medical images.  ...  The segmentation of the hippocampus in Magnetic Resonance Imaging (MRI) has been an important procedure to diagnose and monitor several clinical situations.  ...  The level set method is boundary driven and region driven model free segmentation. E. Atlas-based segmentation Atlas-based segmentation is a widely used technique for supervised methods.  ... 
doi:10.23883/ijrter.2017.3408.j1y8t fatcat:idtyppq4yjdcljlhlhf3qwrcee

Multi-domain potential biomarkers for post-traumatic stress disorder (PTSD) severity in recent trauma survivors

Ziv Ben-Zion, Yoav Zeevi, Nimrod Jackob Keynan, Roee Admon, Tal Kozlovski, Haggai Sharon, Pinchas Halpern, Israel Liberzon, Arieh Y. Shalev, Yoav Benjamini, Talma Hendler
2020 Translational Psychiatry  
Cross-validation established the results' robustness and consistency within this sample.  ...  The neural and cognitive potential biomarkers revealed by the 3C analytics offer objective classifiers of post-traumatic morbidity shortly following trauma.  ...  (co-Investigators, subcontractors), and had undergone critical review by the NIMH Adult Psychopathology and Disorders of Aging study section.  ... 
doi:10.1038/s41398-020-00898-z pmid:32594097 fatcat:f4axtnbsrfhipcxl6u3ojp3arq

Multi-Template Mesiotemporal Lobe Segmentation: Effects of Surface and Volume Feature Modeling

Hosung Kim, Benoit Caldairou, Andrea Bernasconi, Neda Bernasconi
2018 Frontiers in Neuroinformatics  
Numerous neurological disorders are associated with atrophy of mesiotemporal lobe structures, including the hippocampus (HP), amygdala (AM), and entorhinal cortex (EC).  ...  To further improve the method, we introduced two new modules: (1) a non-linear registration that is driven by volume-based intensities and features sampled on deformable template surfaces; (2) a shape  ...  HK was funded by the Baxter Foundation Fellowship Awards and the National Institutes of Health.  ... 
doi:10.3389/fninf.2018.00039 pmid:30050423 pmcid:PMC6052096 fatcat:yz3eleqagjgq7grvbvfxi42kcy


Bruce Fischl
2012 NeuroImage  
FreeSurfer is a suite of tools for the analysis of neuroimaging data that provides an array of algorithms to quantify the functional, connectional and structural properties of the human brain.  ...  It has evolved from a package primarily aimed at generating surface representations of the cerebral cortex into one that automatically creates models of most macroscopically visible structures in the human  ...  Disorders and Stroke (R01 NS052585-01, 1R21NS072652-01, 1R01NS070963), and was made possible by the resources provided by Shared Instrumentation Grants 1S10RR023401, 1S10RR019307, and 1S10RR023043.  ... 
doi:10.1016/j.neuroimage.2012.01.021 pmid:22248573 pmcid:PMC3685476 fatcat:nkxyxri74vgvzlnorxduawgsca

Evidence for Model-based Computations in the Human Amygdala during Pavlovian Conditioning

Charlotte Prévost, Daniel McNamee, Ryan K. Jessup, Peter Bossaerts, John P. O'Doherty, Olaf Sporns
2013 PLoS Computational Biology  
After fitting a model-based algorithm and a variety of model-free algorithms to the fMRI data, we found evidence for the superiority of a model-based algorithm in accounting for activity in the amygdala  ...  These findings support an important role for model-based algorithms in describing the processes underpinning Pavlovian conditioning, as well as providing evidence of a role for the human amygdala in model-based  ...  Author Contributions Conceived and designed the experiments: CP JPOD. Performed the experiments: CP. Analyzed the data: CP DM RKJ PB. Contributed reagents/materials/analysis tools: PB.  ... 
doi:10.1371/journal.pcbi.1002918 pmid:23436990 pmcid:PMC3578744 fatcat:hems43yvyfbytgk4xv5s5h4fzi

Appearance-Based Segmentation of Medial Temporal Lobe Structures

S Duchesne
2002 NeuroImage  
Experimental results demonstrated the robustness and flexibility of the new method.  ...  The proposed method was tested on a data set of 80 normal subjects and compared against manual segmentation as well as automated segmentation results from ANIMAL, a nonlinear registration and segmentation  ...  ACKNOWLEDGMENTS This study was supported by Fonds pour les Chercheurs et l'Aide à la Recherche (Government of Québec) and ICBM.  ... 
doi:10.1016/s1053-8119(02)91188-2 pmid:12377131 fatcat:rtnnqgpqmbbthip6dbezxkilwe

Appearance-Based Segmentation of Medial Temporal Lobe Structures

S. Duchesne, J.C. Pruessner, D.L. Collins
2002 NeuroImage  
Experimental results demonstrated the robustness and flexibility of the new method.  ...  The proposed method was tested on a data set of 80 normal subjects and compared against manual segmentation as well as automated segmentation results from ANIMAL, a nonlinear registration and segmentation  ...  ACKNOWLEDGMENTS This study was supported by Fonds pour les Chercheurs et l'Aide à la Recherche (Government of Québec) and ICBM.  ... 
doi:10.1006/nimg.2002.1188 pmid:12377131 fatcat:kyw23xbndfhzdphvfm76tqqggm

Combined Volumetric and Surface Registration

G. Postelnicu, L. Zollei, B. Fischl
2009 IEEE Transactions on Medical Imaging  
In this paper, we propose a novel method for the registration of volumetric images of the brain that optimizes the alignment of both cortical and subcortical structures.  ...  In order to achieve this, relevant geometrical information is extracted from a surface-based morph and diffused into the volume using the Navier operator of elasticity, resulting in a volumetric warp that  ...  ACKNOWLEDGMENT The authors would like to thank Prof. R. Buckner for the 40 volume data set [48] .  ... 
doi:10.1109/tmi.2008.2004426 pmid:19273000 pmcid:PMC2761957 fatcat:zrfvjvbhdvhildnapa5y2zmifm

Elastic model-based segmentation of 3-D neuroradiological data sets

A. Kelemen, G. Szekely, G. Gerig
1999 IEEE Transactions on Medical Imaging  
The results have been validated by comparison of automatic segmentation with the results obtained by interactive expert segmentation.  ...  The technique has been applied to automatically segment left and right hippocampus, thalamus, putamen, and globus pallidus from volumetric magnetic resonance scans taken from schizophrenia studies.  ...  ACKNOWLEDGMENT The authors thank R. Kikinis and M. Shenton, Brigham and Women's Hospital, Harvard Medical School, Boston, for kindly provided the original MR and segmented data sets.  ... 
doi:10.1109/42.811260 pmid:10628943 fatcat:mgd7iiboszd6phmf3itul7jskm

Deformable Templates Guided Discriminative Models for Robust 3D Brain MRI Segmentation

Cheng-Yi Liu, Juan Eugenio Iglesias, Zhuowen Tu
2013 Neuroinformatics  
Automatically segmenting anatomical structures from 3D brain MRI images is an important task in neuroimaging.  ...  The proposed algorithm achieves both robustness and efficiency, and can be used to segment brain MRI images with large anatomical variations.  ...  Data collection and sharing for this project was also funded by the ADNI (National Institutes of Health grant U01 AG024904).  ... 
doi:10.1007/s12021-013-9190-5 pmid:23836390 pmcid:PMC5966025 fatcat:yvb3w7afybfavbbvu52axx6a5q

Spatial Frequency Tuning during the Conscious and Non-Conscious Perception of Emotional Facial Expressions – An Intracranial ERP Study

Verena Willenbockel, Franco Lepore, Dang Khoa Nguyen, Alain Bouthillier, Frédéric Gosselin
2012 Frontiers in Psychology  
We examined which SFs in disgusted and fearful faces modulate activation in the insula and amygdala over time and as a function of awareness, using a combination of intracranial event-related potentials  ...  The data were analyzed by performing multiple linear regressions on the SF filters from each trial and the transformed ERP amplitudes across time.  ...  et al., 2009 ; see also Pourtois et al., 2005) are probably not driven by the amygdala or insula.  ... 
doi:10.3389/fpsyg.2012.00237 pmid:23055988 pmcid:PMC3458489 fatcat:6moxejojuve7tawegtsiciezde
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