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Refereed journal publications
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Refereed journal publications
S. Lee, N. Charon, B. Charlier, K. Popuri, E. Lebed, M. V. Sarunic, A. Trouvé, and M. F. Beg. Atlas-based shape analysis and classification of retinal optical coherence tomography images using the functional shape (fshape) framework. Medical Image Analysis, August 2016, doi.org/10.1016/j.media.2016.08.012 http://www.sciencedirect.com/science/article/pii/S1361841516301608
P. Prentašić, M. Heisler, Z. Mammo, S. Lee, A. Merkur, E. Navajas,
M. F. Beg, M. V. Šarunic, and S. Lončarić. Segmentation of the foveal
microvasculature using deep learning networks. J Biomed Optics,
21(7):075008, 2016.
Z. Mammo, M. Heisler, C. Balaratnasingam, S. Lee, D. Y. Yu, P. Mackenzie, S. Schendel, A. Merkur, A. Kirker, D. Albiani, E. Navajas, M. F. Beg, W. Morgan, and M. V. Sarunic. Quantitative optical coherence tomography angiography of radial peripapillary capillaries in glaucoma, glaucoma suspect and normal eyes. Am J Ophthalmol, 170:41-49, 2016. https://www.ncbi.nlm.nih.gov/pubmed/27470061
Amanmeet Garg, Silke Cresswell, Karteek Popuri, Martin McKeown, Mirza Faisal Beg, Morphological Alterations in Caudate, Putamen, Pallidum and Thalamus in Parkinson’s disease, Frontiers in Neurology, volume 9, pages 101.1 – 101.14., 2015, http://journal.frontiersin.org/article/10.3389/fnins.2015.00101
Eric Lin, Calvin Craig, Marcel Lamothe,
Marinko Sarunic, Mirza Faisal Beg, Glen Tibbits, Construction and use of a
zebrafish heart voltage and calcium optical mapping system, with integrated
electrocardiogram and programmable electrical stimulation, American Journal
of Physiology, May 1;308(9):R755-68. doi: 10.1152/ajpregu.00001.2015
Adam Christensen, Kathryn Alpert, Emily Rogalski, Derin Cobia, Julia Rao, Mirza Faisal Beg, Sandra Weintraub, M.-Marsel Mesulam, and Lei Wang. "Hippocampal subfield surface deformity in nonsemantic primary progressive aphasia" Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring, In press, October 17, 2014 https://www.ncbi.nlm.nih.gov/pubmed/25893207
Michelle Cua, Eric Lin, Ling Lee, Xiaoye Sheng, Kevin
Wong, Glen Tibbits, Mirza Faisal Beg, Marinko Sarunic, "Morphological
Phenotyping of Mouse Hearts using Optical Coherence Tomography" , Accepted
for publication in the Journal of Biomedical Optics, September 26, 2014
Amanmeet Garg, Darren Wong, Karteek Popuri, Kenneth
J. Poskitt, Kevin Fitzpatrick, Bruce Bjornson, Ruth E. Grunau, Mirza Faisal
Beg
Sieun Lee, Sherry Xan, Mirza Faisal Beg, Marinko Sarunic, Paul Mackenzie, “Optic Nerve Head and Peripapillary Morphometrics in Myopic Glaucoma”, Invest. Ophthalmol. Vis. Sci., 55(7):4378-93, 2014
Jing Ming,Michael Harms,Matthew Colvin,Mirza Faisal Beg,John Morris,John
Csernansky,Lei Wang
Bruce Bjornson, Kenneth
Poskitt, Kevin Fitzpatrick, Anne R. Synnes, Steven P. Miller, Ruth E.
Grunau, Neonatal
Pain-Related Stress Predicts Cortical Thickness at Age 7 Years in Children
Born Very Preterm, Plos One, 8(10):e76702, 2013
Evgeniy Lebed, Sieun Lee, Marinko Sarunic, Mirza Faisal Beg, "Rapid Radial Optical Coherence Tomography Image Acquisition", Journal of Biomedical Optics, 0001;18(3):036004-036004, 2013
Evgeniy Lebed, Claudia Jacova, Lei Wang, Mirza Faisal Beg, “Novel surface-smoothing based local gyrification index and its use in localizing changes in cortical folding in Alzheimer’s Disease”, IEEE Transactions in Medical Imaging, vol.32, no.4, pp.660,669, 2013
Ali Khan, Lei Wang and Mirza Faisal Beg,
Multi-structure large deformation diffeomorphic brain registration,
IEEE Transactions in Biomedical
Engineering, vol.60, no.2, 544-553,
2013
Elvan Ceyhan, Mirza Faisal Beg, Can Ceritoglu, Lei Wang, John C. Morris, John G. Csernansky, Michael I. Miller, J. Tilak Ratnanather, Metric Distances between Hippocampal Shapes Indicate Different Rates of Change over Time in Nondemented and Demented Subjects, Journal of Current Alzheimer’s Research, 9(8):972-981, 2012
Wang L, Fagan AM, Shah AR, Beg MF, Csernansky JG, Morris JC, Holtzman DM, CSF Proteins Predict Longitudinal Hippocampal Degeneration in Early Stage Dementia of the Alzheimer Type, Alzheimer Disease & Associated Disorders, 26(4):314-21, 2012
Bo Wu, Evgeniy Lebed, Marinko Sarunic, Mirza Faisal Beg, “Quantitative evaluation of transform domains for compressive sampling-based recovery of sparsely sampled volumetric OCT images”, Accepted May 15, 2012, IEEE Transactions in Biomedical Engineering, 2012
Naznin Virji-Babul, Alexander Moiseev, Wenqi Sun, A. Fesharaki, Mirza Faisal Beg, Urs Ribary, Dynamics of oscillatory changes associated with the perception of human motion, Neuroreport, 23(13)L 793-798, 2012
Salimah Ismail, Wenqi Sun, Farouk S. Nathoo, Arif Babul, Alexader Moiseev, Mirza Faisal Beg, Naznin Virji-Babul A Skew-t Space-Varying Regression Model for the Spectral Analysis of Resting State Brain Activity, Journal of Statistical Methods in Medical Research, 2012
Mirza Faisal Beg, Pradeep Kumar, Sebastiano Barbieri, Lei Wang, Comparison of four shape features for detecting hippocampal shape changes in early Alzheimer’s, Stat Methods Med Res. 22(4):439-62, 2012
Yue Cui, Darren M Lipnicki, Mirza Faisal Beg, Jesse S Jin, Suhuai Luo, Wanlin Zhu, Nicole A Kochan, Simone Reppermund, Lin Zhuang, Pradeep R Ramana, Tao Liu, Julian N Trollor, Lei Wang, Henry Brodaty, Perminder S Sachdev, Automated detection of amnestic mild cognitive impairment in community-dwelling elderly adults: a combined spatial atrophy and white matter alteration approach, ISSN 1053-8119, 10.1016/j.neuroimage.2011.08.013
Heather L. More, Jingyun Chen, Eli Gibson, J. Maxwell Donelan, Mirza Faisal Beg, A semi-automated method for identifying and measuring myelinated nerve fibers in scanning electron microscope images, Journal of Neuroscience Methods, 201(1):149-58, 2011
Mei Young, Evgeniy Lebed, Yifan Jian, Paul J. Mackenzie, Mirza Faisal Beg, and Marinko V. Sarunic, Real-time high-speed volumetric imaging using compressive sampling optical coherence tomography Biomedical Optics Express, 2 (9), 2690-2697, 2011
Ali Khan, Nicolas Cherbuin, Kaarin Anstey, Perminder Sachdev, Mirza Faisal Beg, Optimal weights for local multi-atlas fusion using supervised learning and dynamic information (SuperDyn): validation on hippocampus segmentation, Neuroimage, 56(1), 126-139, 2011
Michael Valenzuela, David Bartes-Faz, Mirza Faisal Beg, Alex Fornito, Emilio Merlo-Pich, Ulrich Müller, Dost Öngür, Arthur Toga, Murat Yücel, Neuroimaging as Endpoints in Clinical Trials: Perspective from the first Provence Workshop, Journal of Molecular Psyciatry, 16(11):1064-6, 2011
Sieun Lee, Mei Young, Marinko Sarunic, Mirza Faisal Beg, "End-to-end pipeline for spectral domain optical coherence tomography and morphometric analysis of human optic nerve head". Accepted in the Special Issue "Advances in Clinical and Biomedical engineering", Journal of Medical and Biomedical Engineering, 2010
M. Sulman, JF Williams, Mirza Faisal Beg and Bob Russell, Volumetric Image Registration Methods based on Solving the Monge-Ampere Equation, Canadian Applied Mathematics Quarterly, Vol 17, Number 3, 2010
Elvan Ceyhan, Mirza Faisal Beg, Can Ceritoglu, Lei Wang, John C. Morris, John G. Csernansky, Michael I. Miller, J. Tilak Ratnanather, Quantization and Analysis of Hippocampal Morphometric Changes Due to Dementia of Alzheimer Type Using Metric Distances Based on Large Deformation Diffeomorphic Metric Mapping, Journal of Computerized Medical Imaging and Graphics, Jan 21, 2011
Paul R. Borghesania, Kurt E. Weaver, Elizabeth H. Aylward, Anne L. Richards, Tara M. Madhyastha, Ali R. Khan, Olivia Liang, Rachel L. Ellenbogen, Mirza Faisal Beg, K. Warner Schai and Sherry L. Willis, Midlife memory improvement predicts preservation of hippocampal volume in old age, Neurobiology of Aging”, November 2010
Marinko Sarunic, Azadeh Yazdanpanah, Eli Gibson, Jing Xu, Yujing Bai, Sieun Lee, Uri Saragovi, Mirza Faisal Beg, Longitudinal Study of Retinal Degeneration in Rats using Spectral Domain Optical Coherence Tomography, Opt. Express 18, 23435-23441 (2010)
Eli Gibson, Mei Young, Marinko Sarunic, Mirza Faisal Beg. Optic Nerve Head Registration via Hemispherical Surface and Volume Registration. IEEE Trans Biomed Eng. 57(10), 2592 – 2595, 2010
Evgeniy Lebed, Paul Mackenzie, Marinko Sarunic, Mirza.Faisal Beg, “Rapid Volumetric OCT Image Acquisition Using Compressive Sampling”, Optics Express, 18, 21003-21012 (2010)
Lei Wang, Ali Khan, John Csernansky, Bruce Fischl, Michael Miller, John Morris, Mirza Faisal Beg. Fully-Automated, Multi-Stage Hippocampus Mapping in Very Mild Alzheimer Disease. Hippocampus, Special Issue on Computational Anatomy and Physiology of the Hippocampus, Volume 19, Issue 6, pages 541–548, June 2009
Mirza Faisal Beg, Stephen Wong, Ali Khan, Teresa Cheung, Naznin Virji-Babul, Anthony Herdman. External Landmark and Head Shape based Functional Data Normalization” in the Journal of Computerized Medical Imaging and Graphics, Journal of Computerized Medical Imaging and Graphics, Volume 33, Issue 7, Pages 501–509, 2009.
Ali Khan, Lei Wang and Mirza Faisal Beg, FreeSurfer-Initiated Fully-Automated Sub-cortical Brain Segmentation in MRI Using Large Deformation Diffeomorphic Metric Mapping, NeuroImage (impact factor 5.559)
Pankaj Sadaphal, Josna Rao and Mirza Faisal Beg, Image Processing Techniques for Identifying Mycobacterium Tuberculosis in Ziehl-Neelsen Stains, International Journal of Tuberculosis and Lung Disease (impact factor 2.035)
Mirza Faisal Beg and Ali Khan. Symmetric Data Attachment Terms for Large Deformation Image Registration, IEEE Transactions on Medical Imaging 26(9), 1179-1189, 2007
Lei Wang, Mirza Faisal Beg, J.T. Ratnanather, Can Ceritoglu, Laurent Younes, J.C. Morris, J.G. Csernansky, M. I. Miller, Large Deformation Diffeomorphism and Momentum Based Hippocampal Shape Discrimination in Dementia of the Alzheimer Type, IEEE Transactions on Medical Imaging, 26(4), 462-470, 2007
Patrick Helm, Laurent Younes, Mirza Faisal Beg, Daniel Ennis, Christophe Leclercq, Owen Faris, Elliot McVeigh, David Kass, Michael I. Miller and Raimond Winslow, Evidence of Structural Remodeling in the Dyssynchronous Failing Heart, Circulation Research, volume 98, pages 125-132, 2006. (18 Citations as of 11/18/2007)
Patrick Helm, Mirza Faisal Beg, Michael I. Miller, and R. L. Winslow (2005). Measuring and Mapping Cardiac Fiber and Laminar Architecture Using Diffusion Tensor MR Imaging. Annals of the New York Academy of Sciences 2005 1047: 296-307 (17 Citations as of 11/18/2007)
Michael Miller, Mirza Faisal Beg, Can Ceritogulu, and Craig Stark, Increasing the power of functional maps of the Medial Temporal Lobe using Large Deformation Metric Mapping, Proceedings of the National Academy of Sciences (PNAS)USA, volume 102, pages 9685-9690, 2005. (8 Citations as of 11/18/2007)
Mirza Faisal Beg, Patrick Helm, Elliot McVeigh, Raimond Winslow and Michael Miller, Computational Cardiac Anatomy Using Magnetic Resonance Imaging, Magnetic Resonance in Medicine, volume 52, issue 5, pages 1167-1174, 2004. (8 Citations as of 11/18/2007)
Mirza Faisal Beg, Michael I. Miller, Laurent Younes, Alain Trouvé. “Computing Metrics via Geodesics on Flows of Diffeomorphisms.” International Journal of Computer Vision, volume 61, issue 2, pages 139-157, 2005. (47 citations as of 11/18/2007)
Zeynep Erim, Mirza Faisal Beg, David Burke and Carlo De Luca, Effects of Aging on motor unit firing behaviour, Journal of Neurophysiology, 82, 2081-2091, 1999. (63 citations as of 11/18/2007)
Refereed Conference Papers
Jingyun Chen, Martin McKeown, Mirza Faisal Beg, Momentum-based morphometric analysis with application to Parkinson's disease, "Visualization, Image-Guided Procedures, and Modeling", SPIE 2010 Florida, USA.
Ali Khan, Alain Trouve and Mirza Faisal Beg. Cross-sectional analysis of anatomical shape change over time via statistics on 4D within-subject flows, MICCAI 2010 Workshop on Spatio-Temporal Image Analysis for Longitudinal and Time-Series Image Data, September 2010.
Mei Young, Sieun Lee, Eli Gibson, Kevin Hsu, Mirza Faisal Beg, Paul J. Mackenzie, Marinko V. Sarunic, “Morphometric analysis of the optic nerve head with optical coherence tomography,” Coherence Domain Optical Methods and Optical Coherence Tomography in Biomedicine XII, Photonics West, J. A. Izatt; J. G. Fujimoto; V.V. Tuchin, Editors, Proc. SPIE, Vol. 7554, 75542L, (2010).
Jingyun Chen, Martin McKeown, and Mirza Faisal Beg, Variability of basal ganglia morphology after spatial normalization: Implications for group studies. 33rd Conference of the Canadian Medical and Biological Engineering Society. Vancouver Canada.
Jingyun Chen, Heather More, Max Donelan, and Mirza Faisal Beg, Automated methods for neuron segmentation and analysis of electron microscope images. 33rd Conference of the Canadian Medical and Biological Engineering Society. Vancouver Canada.
Sieun Lee, Mei Young, Paul Mackenzie, Mirza Faisal Beg, Marinko Sarunic, "Morphometry of the myopic optic never head using Fourier domain optical coherence tomography," Optical Coherence Tomography and Coherence Domain Optical Methods in Biomedicine XIV, Photonics West, J. G. Fujimoto; J. A. Izatt; V. V. Tuchin, Editors, Proc. SPIE, Vol. 7889, (Jan 2011).
Sieun Lee, Mei Young, Marinko V. Sarunic, Mirza Faisal Beg, "End-to-end pipeline for Fourier domain optical coherence tomography of human optic nerve head" presented at The 33rd Conference of the Canadian Medical and Biological Engineering Society (CMBEC33), Vancouver, BC. July 12, 2010.
Ali Khan and Mirza Faisal Beg. Multi-structure LDDMM Brain Registration and Population Average. Accepted in the IEEE-EMBC Conference 2009.
Eli Gibson, Ali Khan and Mirza Faisal Beg. A combined Surface and VOlumetric registration (SAVOR) framework to study cortical biomarkers and functional neuroimaging data. Volume 5761, Pages 713-720, Proceedings of the Medical Image Computing and Computer-Assisted Intervention – MICCAI 2009.
Ali Khan, Moo Chung and Mirza Faisal Beg, Robust atlas-based brain segmentation using multi-structure confidence-weighted registration Volume 5762, Pages 549-557, Proceedings of the Medical Image Computing and Computer-Assisted Intervention – MICCAI 2009.
Yonas Weldeselassie, Ghassan Hamarneh, Mirza Faisal Beg, and Stella Atkins. Novel Decomposition of Tensor Distance into Shape and Orientation Distances. In Medical Image Computing and Computer-Assisted Intervention Workshop on Diffusion Modelling and the Fibre Cup (MICCAI DMFB), 2009.
Jingyun Chen, Samantha J. Palmer, Ali R. Khan, Martin J. McKeown, Mirza Faisal Beg, Freesurfer-Initialized Large Deformation Diffeomorphic Metric Mapping with application to Parkinson's Disease, SPIE Symposium on Medical Imaging 2009.
Joaquin Andres Hoffer, Eli Gibson, Burkhard Mädler, Mirza Faisal Beg. Estimation of Nerve Dimensions from MRI of the Human Thigh. Int’l. Functional Electrical Stimulation Soc., 13th Ann. Conf., Freiburg, Germany, Pages 51-53, Sept. 2008.
Lei Wang, Ali Khan, John Csernansky, Bruce Fischl, Michael Miller, John Morris and Mirza Faisal Beg. Fully-automated multi-stage Hippocampus Mapping in very mild Alzheimer Disease. Proceedings of the Medical Image Computing and Computer Assisted Intervention 2008 workshop on Computational Anatomy and Physiology of the hippocampus, Pages 28-40, September 2008.
Ryan Dickie and Mirza Faisal Beg, Two Novel Methods of Computing the Cardiac Mid-Wall, International Symposium of Biomedical Imaging, May 2008
Ali Khan and Mirza Faisal Beg, Representation of Time-varying shapes in the Large Deformation Diffeomorphic Metric Mapping Framework, International Symposium of Biomedical Imaging, May 2008
Vinay Kotamraju and Mirza Faisal Beg, Automated Detection of Cardiac MR tags and calculation of cardiac strain using Large Deformation Metric Mapping. Proceedings of SPIE - Volume 6512, March 2007, Medical Imaging
Mirza Faisal Beg, Ryan Dickie and Laurent Younes. Consistent realignment of Diffusion Tensor Eigenvectors. Proceedings of SPIE - Volume 6512, March 2007, Medical Imaging
Elvan. Ceyhan, L. Fong, T. N. Tasky, Monica. Hurdal, Mirza Faisal Beg, Maryanne Martone, and John. Ratnanather, Type-Specific Analysis of Morphometry of Dendrite Spines of Mice, Proceedings of the 5th International Symposium on Image and Signal Processing and Analysis, 2007.
Elvan Ceyhan, R. Ç. Ölken, L. Fong, T. N. Tasky, Monica Hurdal, Mirza Faisal Beg, Maryanne E. Martone, John Ratnanather, Modeling metric distances of dendrite spines of mice based on morphometric measures in L. E. Akman, N. Baykal, T. Can, M. Iscan, U. E. Mumcuoglu (eds), Proceedings of the International Symposium on Health Informatics and Bioinformatics (HIBIT'07), 2007.
Mirza Faisal Beg and Ali Khan (Invited Paper). Computation of Average Atlas using LDDMM and Geodesic Shooting. IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Special Session on the use of shape in biomedical image formation, modeling, and analysis, April, 2006.
Ali Khan, Elizabeth Aylward, Patrick Barta, Michael Miller, Mirza Faisal Beg, Semi-automated Basal Ganglia Segmentation Using Large Deformation Diffeomorphic Metric Mapping, Medical Image Computing and Computer Assisted Intervention - Lecture Notes in Computer Science, Volume 3749, Sep 2005, Pages 238 - 245.
Gregory Golds and Mirza Faisal Beg, Computing the thickness of 3D ventricular wall from MRI images and morphological segmentation of the ventricles from binary anatomical cardiac images. Proceedings of the SPIE-Medical Imaging Conference, Volume 5747, April, 2005, pp 1925-1932.
Jorge Jovicich, Mirza Faisal Beg, Steve Pieper, Carey Priebe, Michael Miller, Randy Buckner, Bruce Rosen, Morphometry BIRN (2005) "Biomedical Informatics Research Network: Integrating Multi-Site Neuroimaging Data Acquisition, Data Sharing and Brain Morphometric Processing." Proceedings of the 18th IEEE International Symposium on Computer-Based Medical Systems, June 2005.
Gregory Golds and Mirza Faisal Beg, Computational Cardiac Anatomy: Computing the thickness of the heart wall using Laplace's equation. Canadian Medical and Biological Engineering Conference, Quebec City, November 2004.
Mirza Faisal Beg, Michael Miller, Alain Trouve, and Laurent Younes. The Euler-Lagrange equations for interpolating sequence of landmark datasets. Medical Image Computing and Computer-Assisted Intervention - MICCAI 2003, 6th International Conference, Montréal, Canada, November 15-18, 2003, Proceedings, Part II. Lecture Notes in Computer Science 2879 Springer 2003, pages 918-925.
Mirza Faisal Beg, Michael Miller, Alain Trouvé, Laurent Younes, July 2002. “Computational Anatomy: Computing Metrics on Anatomical Shapes,” Proceedings of the 2002 IEEE Symposium on Biomedical Imaging, Washington D.C.