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Use of Simulated Atrophy for Performance Analysis of Brain Atrophy Estimation Approaches [chapter]

Swati Sharma, Vincent Noblet, François Rousseau, Fabrice Heitz, Lucien Rumbach, Jean-Paul Armspach
2009 Lecture Notes in Computer Science  
In this paper, we study the performance of popular brain atrophy estimation algorithms using a simulated gold standard.  ...  Firstly, we propose an approach for the construction of a gold standard.  ...  A quantitative analysis of the ability of the proposed algorithm for simulating the desired atrophy has also been performed (see Table 1 ).  ... 
doi:10.1007/978-3-642-04271-3_69 fatcat:cst6gqe46rc3vpge5hmpkfwmme

Evaluation of brain atrophy estimation algorithms using simulated ground-truth data

S. Sharma, V. Noblet, F. Rousseau, F. Heitz, L. Rumbach, J.-P. Armspach
2010 Medical Image Analysis  
A number of analysis tools have been developed for the estimation of brain atrophy using MRI.  ...  In order to create gold standards, we first propose an approach for the realistic simulation of brain tissue loss that relies on the estimation of a topology preserving B-spline based deformation fields  ...  We are thankful to Alsace Region and ARSEP for supporting this study. We also thank Dr. Evan Fletcher (University of California, Davis) for his support on the BSI-UCD software.  ... 
doi:10.1016/ pmid:20219411 fatcat:txytawsghjetrl6fojzfatz66u

Voxel-Based Morphometry Using the RAVENS Maps: Methods and Validation Using Simulated Longitudinal Atrophy

Christos Davatzikos, Ahmet Genc, Dongrong Xu, Susan M. Resnick
2001 NeuroImage  
A new method for elastic, volume-preserving spatial normalization, which allows for accurate quantification of very localized atrophy, is used.  ...  This paper presents an extension and validation of a previously published methodology, referred to as RAVENS, for characterizing regional atrophy in the brain.  ...  Our initial studies of the accuracy of the RAVENS approach for analysis of localized brain atrophy yielded encouraging results.  ... 
doi:10.1006/nimg.2001.0937 pmid:11707092 fatcat:jzjvqbvxarcoffnunu7gkem43a

Regional expression of genes mediating trans-synaptic alpha-synuclein transfer predicts regional atrophy in Parkinson disease

Benjamin Freeze, Diana Acosta, Sneha Pandya, Yize Zhao, Ashish Raj
2018 NeuroImage: Clinical  
Regional brain atrophy and genetic expression was co-registered to a common 86 region brain atlas and robust multivariable regression analysis was performed to identify genetic predictors of regional brain  ...  We identify three genes with expression patterns that are highly significant predictors of regional brain atrophy.  ...  Fox Foundation for Parkinson's Research funding partners Abbvie, Avid Radiopharmaceuticals, Biogen Idec, BioLegend, Bristol-Myers Squibb, Eli Lilly and Company, F.  ... 
doi:10.1016/j.nicl.2018.01.009 pmid:29868450 pmcid:PMC5984599 fatcat:uc7ss4ojgrevhhtyxs7mrni2ru

The Impact of Lesion In-Painting and Registration Methods on Voxel-Based Morphometry in Detecting Regional Cerebral Gray Matter Atrophy in Multiple Sclerosis

A. Ceccarelli, J.S. Jackson, S. Tauhid, A. Arora, J. Gorky, E. Dell'Oglio, A. Bakshi, T. Chitnis, S.J. Khoury, H.L. Weiner, C.R.G. Guttmann, R. Bakshi (+1 others)
2012 American Journal of Neuroradiology  
Our aim was to compare the performance of VBM-DARTEL versus VBM-USM and the effect of LI in the regional analysis of GM atrophy in MS.  ...  VBM analysis was performed in SPM8 by using DARTEL and USM with and without LI, allowing the comparison of 4 VBM methods (DARTEL ϩ LI, DARTEL Ϫ LI, USM ϩ LI, and USM Ϫ LI).  ...  Acknowledgments We thank Dr Christos Davatzikos and the biomedical image analysis center at the University of Pennsylvania for providing the atrophy simulation software package.  ... 
doi:10.3174/ajnr.a3083 pmid:22460341 pmcid:PMC3425668 fatcat:7bluima2wjajhngycg5da2j46y

Distinguishing Healthy Ageing from Dementia: a Biomechanical Simulation of Brain Atrophy using Deep Networks [article]

Mariana Da Silva, Carole H. Sudre, Kara Garcia, Cher Bass, M. Jorge Cardoso, Emma C. Robinson
2021 arXiv   pre-print
Biomechanical modeling of tissue deformation can be used to simulate different scenarios of longitudinal brain evolution.  ...  In this work,we present a deep learning framework for hyper-elastic strain modelling of brain atrophy, during healthy ageing and in Alzheimer's Disease.  ...  Acknowledgements The data used in this work was funded by the Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904) and DOD ADNI (Department of Defense award  ... 
arXiv:2108.08214v1 fatcat:ub56htvwd5cndoarpowmssgjlq

Agreement of MSmetrix with established methods for measuring cross-sectional and longitudinal brain atrophy

Martijn D. Steenwijk, Houshang Amiri, Menno M. Schoonheim, Alexandra de Sitter, Frederik Barkhof, Petra J.W. Pouwels, Hugo Vrenken
2017 NeuroImage: Clinical  
Here we perform a validation of MSmetrix against established methods in simulated and in vivo MRI data.  ...  For this comparison we investigated 20 simulated brain images, as well as in vivo data from 100 MS patients and 20 matched healthy controls.  ...  Although FreeSurfer is specifically optimized for cortical thickness measurements, the pipeline has also been used for quantification of whole-brain atrophy.  ... 
doi:10.1016/j.nicl.2017.06.034 pmid:28794970 pmcid:PMC5540882 fatcat:lsgvfselnjdg7dilkzc23yoibu

Simulating Longitudinal Brain MRIs with Known Volume Changes and Realistic Variations in Image Intensity

Bishesh Khanal, Nicholas Ayache, Xavier Pennec
2017 Frontiers in Neuroscience  
In this work, we propose a novel way of reproducing realistic intensity variation in longitudinal brain MRIs, which is inspired by an approach used for the generation of synthetic cardiac sequence images  ...  The simulator is based on a previously proposed biophysical model of brain deformation due to atrophy in AD.  ...  Since the proposed approach to simulate images may need deformations estimated from image registration, the use of these simulated images for the evaluation of some registration algorithms can bring an  ... 
doi:10.3389/fnins.2017.00132 pmid:28381986 pmcid:PMC5360759 fatcat:kyowvuw6u5cgxoraqyvgqn7qom

Simulating Patient Specific Multiple Time-Point MRIs from a Biophysical Model of Brain Deformation in Alzheimer's Disease [chapter]

Bishesh Khanal, Marco Lorenzi, Nicholas Ayache, Xavier Pennec
2016 Computational Biomechanics for Medicine  
We use a biophysical model of brain deformation due to atrophy that can generate biologically plausible deformation for any given desired volume changes at the voxel level of the brain MRI.  ...  These atrophy maps are prescribed to the baseline images to simulate the middle time-point images by using the biophysical model of brain deformation.  ...  A detailed analysis must be done to find out the regions that are the most reliable ones in estimating volume changes for both the real and simulated images.  ... 
doi:10.1007/978-3-319-28329-6_15 fatcat:t6n7bkij6zbipdysfb7s7xcwdm

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

Evaluation of Multiple Voxel-Based Morphometry Approaches and Applications in the Analysis of White Matter Changes in Temporal Lobe Epilepsy [chapter]

Wenjing Li, Huiguang He, Jingjing Lu, Bin Lv, Meng Li, Zhengyu Jin
2013 Lecture Notes in Computer Science  
Our study demonstrated that DARTEL was the most robust and reliable approach for VBM analysis.  ...  The results from simulation show that VBM-DARTEL performs the best among these VBM approaches.  ...  Materials and Methods Simulation of Atrophy Images with simulated atrophy can act as the gold standard for evaluating the relative merits of various VBM approaches.  ... 
doi:10.1007/978-3-642-40843-4_29 fatcat:p6nxw7amqnb55fnvxlba2hw5um

Phenomenological Model of Diffuse Global and Regional Atrophy Using Finite-Element Methods

O. Camara, M. Schweiger, R.I. Scahill, W.R. Crum, B.I. Sneller, J.A. Schnabel, G.R. Ridgway, D.M. Cash, D.L.G. Hill, N.C. Fox
2006 IEEE Transactions on Medical Imaging  
The main goal of this work is the generation of ground-truth data for the validation of atrophy measurement techniques, commonly used in the study of neurodegenerative diseases such as dementia.  ...  The method produces cohorts of brain images with known change that is physically and clinically plausible, providing data for objective evaluation of atrophy measurement techniques.  ...  Frost for his statistical advice, and Dr. J. Kennedy and Dr. J. Rohrer for their contribution to the atrophy rating study.  ... 
doi:10.1109/tmi.2006.880588 pmid:17117771 fatcat:sxie63u57zfp5edyxurlrow4ce

Simulation of Acquisition Artefacts in MR Scans: Effects on Automatic Measures of Brain Atrophy [chapter]

Oscar Camara-Rey, Beatrix I. Sneller, Gerard R. Ridgway, Ellen Garde, Nick C. Fox, Derek L. G. Hill
2006 Lecture Notes in Computer Science  
Automatic algorithms in conjunction with longitudinal MR brain images can be used to measure cerebral atrophy, which is particularly pronounced in several types of dementia.  ...  The original images were 7 MR scans of healthy elderly controls, each of which had two levels of simulated atrophy.  ...  In this work, we only make use of the atrophy simulation's ground truth values for the whole brain volume change since SIENA only gives an estimation of the global atrophy rate.  ... 
doi:10.1007/11866565_34 fatcat:ntorlccuovaxpl3pxdalqh7jze

A biophysical model of brain deformation to simulate and analyze longitudinal MRIs of patients with Alzheimer's disease

Bishesh Khanal, Marco Lorenzi, Nicholas Ayache, Xavier Pennec
2016 NeuroImage  
We use this model to simulate longitudinal MRIs by prescribing complex patterns of atrophy.  ...  We also present a pipeline that allows evaluating atrophy estimation algorithms by simulating longitudinal MRIs from large number of real subject MRIs with complex subjectspecific atrophy patterns.  ...  We would like to thank neurologist David Bensamoun of the Nice Resource & Research Memory Centre (Nice, France) for providing qualitative assessment of our simulations of atrophy progression in the brain  ... 
doi:10.1016/j.neuroimage.2016.03.061 pmid:27039699 fatcat:q4g6hsbu35dttpyt6iv6yelhuu

Multi-channel registration of fractional anisotropy and T1-weighted images in the presence of atrophy: application to multiple sclerosis

Eloy Roura
2015 Functional Neurology  
In this work, we test the performance of an MC registration approach applied to T1w and FA data using simulated brain atrophy images.  ...  can be used for brain segmentation while DTI can provide microstructural tissue information.  ...  The International Federation of MS (Du Pré Grant 2012) granted E. Roura for a research stay in IoN/UCL.  ... 
doi:10.11138/fneur/2015.30.4.245 fatcat:rtsyylwckbhznmn623xmez3tay
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