Research  Home
Journal Papers
  1. G. Tran, Y. Shi, Fiber Orienation and Compartment Parameter Estimation from Multi-shell Diffusion Imaging, IEEE Trans. Medical Imaging, 2015. In press.
  2. X. Ge, Y. Shi, J. Li, Z. Zhang, X. Lin, J. Zhan, H. Ge, J. Xu, Q. Yu, Y. Leng, G. Teng, L. Feng, H. Meng, Y. Tang, F. Zang, A. W. Toga, S. Liu, Development of the human fetal hippocampal formation during early second trimester, NeuroImage, 2015. In press.
  3. Y. Shi, R. Lai, D. Wang, D. Pelletier, D. Mohr, N. Sicotte, A.W. Toga, Metric Optimization for Surface Analysis in the Laplace-Beltrami Embedding Space, IEEE Trans. Medical Imaging, 33(7), pp. 1447-1463, 2014. (Software Download: MOCA)
  4. Y. Jin, Y. Shi, L. Zhan, B. Gutman, G.I de Zubicaray, K. L. McMahon, M. J. Wright, A. W. Toga, P. M. Thompson, Automatic clustering of white matter fibers in brain diffusion MRI with an application to genetics, NeuroImage, 100(15), pp. 75-90, 2014.
  5. J. Li, Y. Shi, G. Tran, I. Dinov, D. J. Wang, and A. W. Toga, Fast Local Trust Region Techniques for Diffusion Tensor Registration using Exact Reorientation and Regularization, IEEE Trans. Medical Imaging, 33(5), pp.1005-22, 2014.
  6. JS Labus, ID Dinov, Z Jiang, C Ashe-McNalley, A Zamanyan, Y Shi, JY Hong, A Gupta, K Tillisch, B Ebrat, S Hobel, BA Gutman, S Joshi, PM Thompson, AW Toga, EA Mayer, Irritable bowel syndrome in female patients is associated with alterations in structural brain networks, PAIN, 155(1): pp. 137-149, 2014.
  7. JY Hong, JS Labus, Z Jiang, C Ashe-Mcnalley, ID Dinov, A Gupta, Y Shi, J Stains, N Heendeniya, SR Smith, K Tillisch, EA Mayer, Regional neuroplastic brain changes in patients with chronic inflammatory and non-inflammatory visceral pain, Plos One, 2014.
  8. Z Jiang, ID Dinov, J Labus, Y Shi, A Zamanyan, A Gupta, C Ashe-McNalley, JY Hong, K Tillisch, AW Toga, EA Mayer, Sex-related differences of cortical thickness in patients with chronic abdominal pain, PL0S One, 2013.
  9. J Zhan, ID Dinov, J Li, Z Zhang, S Hobel, Y Shi, X Lin, A Zamanyan, L Feng, G Teng, F Fang, Y Tang, F Zang, AW Toga, S Liu, Spatial–temporal atlas of human fetal brain development during the early second trimester, NeuroImage, 82,pp.115-126, 2013.
  10. Y. Shi, R. Lai, A. W. Toga, and the Alzheimer's Disease Neuroimaging Initiative, Cortical Surface Reconstruction via Unified Reeb Analysis of Geometric and Topological Outliers in Magnetic Resonance Images, IEEE Trans. Medical Imaging, 32(3), pp.511-530, 2013.
  11. S. M. Gold, M. F. O'Connor, R. Gill, K. C. Kern, Y. Shi, R. G. Henry, D. Pelletier, D. C. Mohr, N. L. Sicotte, Detection of altered hippocampal morphology in multiple sclerosis associated depression using automated surface mesh modeling. Human Brain Mapping, 2012.
  12. S. G. Costafreda , I. Dinov, Z. Tu, Y. Shi , C. Liu, I. Klowzewska, P. Mecocci, H. Soininen, M. Tsolaki, B. Vellas, L. Walhund, C. Spenger, A. W. Toga, S. Lovestone, A. Simmons, Automated hippocampal shape analysis predicts the onset of dementia in Mild Cognitive Impairment. NeuroImage, 56(1), pp:212-219, 2011.
  13. Y.Shi, R. Lai, J. Morra, I. Dinov, P. M. Thompson, A. W. Toga, Robust Surface Reconstruction via Laplace-Beltrami Eigen-Projection and Boundary Deformation, IEEE Trans. Medical Imaging, 29(12), pp. 2009-2022, 2010.
  14. V. Patel, Y. Shi, P. M. Thompson, A. W. Toga, Mesh-Based Spherical Deconvolution: A Flexible Approach to Reconstruction of Non-Negative Fiber Orientation Distributions, NeuroImage, 51(3), pp. 1071-1081, 2010 .
  15. X. Liu, Y. Shi, I. Dinov, W. Mio, A Computational Model of Multidimensional Shape, International Journal of Computer Vision, 89(1), pp. 69-83, 2010.
  16. N. Lepore, Y. Shi, F. Lepore, M. Fortin, P. Voss, Y. Chou, C. Lord, M. Lassonde, I. Dinov, A. W. Toga, P. M. Thompson, Patterns of Hippocampal Shape and Volume Differences in Blind Subjects, NeuroImage, 46(4), pp. 949-957, 2009 .
  17. Y. Shi , Z. Tu, A. L. Reiss, R. A. Dutton, A. D. Lee, A. Galaburda, I. Dinov, P. M. Thompson, A. W. Toga, Joint sulcal detection on cortical surfaces with graphical models and boosted priors, IEEE Trans. Medical Imaging, 28(3), pp.361-373, 2009 .
  18. Y. Shi, W. C. Karl, A real-time algorithm for the approximation of level-set-based curve evolution, IEEE Trans. Image Processing, 17(5), pp.645-656, 2008.
  19. Y. Shi, P. M. Thompson, I. Dinov, A. W. Toga, Hamilton-Jacobi Skeleton on Cortical Surfaces, IEEE Trans. Medical Imaging, 27(5), pp. 664-673, 2008 .
  20. Y. Shi, P. M. Thompson , G. I. de Zubicaray, S. Rose, Z. Tu, I. Dinov, A. W. Toga, Direct mapping of hippocampal surfaces with intrinsic shape context, NeuroImage, 37(3), pp. 792-807, 2007.
  21. Y. Shi, P. M. Thompson, I. Dinov, S. Osher, A. W. Toga, Direct cortical mapping via solving partial differential equations on implicit surfaces, Medical Image Analysis, 11(3), pp.207-223, 2007.

Peer-Reviewed Conference Papers

  1. D. Aydogan, Y. Shi, Track Filtering via Iterative Correction of TDI Topology, Proc. MICCAI, 2015.
  2. J. Li, Y. Shi, AW Toga, Controlling False Discovery Rate in Signal Space for Transformation-Invariant Thresholding of Statistical Maps , Proc. IPMI, 2015.
  3. Y. Shi, J. Li, AW Toga, Persistent Reeb Graph Matching for Fast Brain Search, Proc. MICCAI Workshop MLMI, 2014.
  4. J Li, Y. Shi, AW Toga,  Diffusion of fiber orientation distribution functions with a rotation-induced Riemannian Metric. Proc MICCAI, 2014
  5. Y. Shi, R. Lai, and  A.W. Toga,  Conformal Mapping via Metric Optimization with Application for Cortical Label Fusion. Proc. IPMI 2013: 244-255.
  6. G. Tran and Y. Shi, Adaptively Constrained Convex Optimization for Accurate Fiber Orientation Estimation with High Order Spherical Harmonics. Proc. MICCAI, 2013.
  7. J. Li, Y. Jin, Y. Shi, I. Dinov, D. J. Wang, A. W. Toga, and P. M. Thompson, Voxelwise Spectral Diffusional Connectivity and its Applications to Alzheimer's Disease and Intelligence Prediction, Proc. MICCAI, 2013.
  8. J. Li, Y. Shi, I. Dinov, and A. W. Toga, Locally weighted multi-atlas construction, Proc. MBIA, 2013.
  9. Y. Shi, R. Lai, A. W. Toga, Conformal Mapping via Metric Optimization with Application for Cortical Label Fusion, Proc. IPMI, 2013.
  10. Y. Shi, R. Lai, A. W. Toga, Unified Geometry and Topology Correction for Cortical Surface Reconstruction with Intrinsic Reeb Analysis, Proc. MICCAI, 2012.
  11. J. Li, Y. Shi, G. Tran, I. Dinov, D. J. Wang, A. W. Toga, Fast Diffusion Tensor Registration with Exact Reorientation and Regularization, Proc. MICCAI, 2012.
  12. R. Lai, Y. Shi, N. Sicotte, A.W. Toga, Automated Corpus Callosum Extraction via Laplace-Beltrami Nodal Parcellation and Intrinsic Geodesic Curvature Flows on Surfaces, Proc. ICCV, 2011.
  13. Y. Jin, Y. Shi, S. Joshi, N. Jahanshad, L. Zhan, G. de Zubicaray, K. McMahon, N. Martin, M. Wright, A. W. Toga, P. Thompson, Heritability of White Matter Fiber Tract Shapes: A HARDI Study of 198 Twins, Proc. MBIA, 2011.
  14. Y. Shi, R. Lai, R. Gill, D. Pelletier, D. Mohr, N. Sicotte, A. W. Toga, Conformal Metric Optimization on Surface (CMOS) for Deformation and Mapping in Laplace-Beltrami Embedding Space, Proc. MICCAI, 2011.
  15. Y. Shi, R. Lai, A. W. Toga, CoRPORATE: Cortical Reconstruction by Pruning Outliers with Reeb Analysis and Topology-preserving Evolution. Proc. IPMI, 2011.
  16. V. Patel, Y. Shi, P.M. Thompson, A. W. Toga. K-SVD for HARDI Denoising . Proc. ISBI, 2011.
  17. Y. Jin, Y. Shi, N. Jahanshad, I. Aganj, G. Sapiro, A.W. Toga, P.M. Thompson. 3D Elastic Registration Improves HARDI-Derived Fiber Alignment and Automated Tract Clustering . Proc . ISBI, 2011.
  18. Y. Shi, B. Sun, R.Lai, I.Dinov, A.W.Toga, Automated Sulci Identification via Intrinsic Modeling of Cortical Anatomy, MICCAI, 2010.
  19. R. Lai, Y. Shi, K. Scheibel, S. Fears, R. Woods, A. W. Toga, T.F.Chan, Metric-Induced Optimal Embedding for Intrinsic 3D Shape Analysis, CVPR, 2010.
  20. X. Liu, Y. Shi, Y. Wang, P. M. Thompson, W. Mio, A Riemannian model of regional degeneration of the hippocampus in Alzheimer's disease, ISBI, 2010.
  21. Y. Shi, I. Dinov, A. W. Toga, Cortical Shape Analysis in the Laplace-Beltrami Feature Space, MICCAI, 2009.
  22. Y. Shi, J. Morra, P. M. Thompson, A. W. Toga, Inverse-consistent surface mapping with Laplace-Beltrami eigen-features, IPMI, 2009. (Oral Presentation)
  23. R. Lai, Y. Shi , I. Dinov, T. F. Chan, A. W. Toga, LAPLACE-BELTRAMI nodal counts: a new signature for 3D shape analysis, ISBI, 2009.
  24. V. Patel, Y. Shi , P. M. Thompson, A. W. Toga, Mesh-based spherical deconvolution for physically valid fiber orientation reconstruction via diffusion-weighted MRI, ISBI, 2009.
  25. X. Liu, Y. Shi, J. Morra, X. Liu, P. M. Thompson, W. Mio, Mapping hippocampal atrophy with a multi-scale model of shape, ISBI , 2009.
  26. Y. Shi, R. Lai, S. Krishna, N. Sicotte, I. Dinov, A. W. Toga, Anisotropic Laplace-Beltrami Eigenmaps: Bridging Reeb Graphs and Skeletons, MMBIA, 2008. (Best Paper Award!)
  27. Y. Shi , R. Lai, K. Kern, N. Sicotte, I. Dinov, A. W. Toga, Harmonic Surface Mapping With Laplace-Beltrami Eigenmaps, MICCAI , 2008.
  28. X. Liu, W. Mio, Y. Shi , I. Dinov, Xiuwen Liu, N. Lepore, F. Lepore, M. Fortin, P. Voss, M. Lassonde, P. Thompson, Models of Normal Variation and Local Contrasts in Hippocampal Anatomy, MICCAI, 2008.
  29. Y. Shi , Z. Tu, A. L. Reiss, R. A. Dutton, A. D. Lee, A. Galaburda, I. Dinov, P. M. Thompson, A. W. Toga, Joint sulci detection using graphical models and boosted priors, Proc. IPMI, pp. 98-109, 2007. (Oral Presentation)
  30. Y. Shi , A. L. Reiss, A. D. Lee, R. A. Dutton, U. Bellugi, A.  Galaburda, J. Korenberg, D. Mills, I. Dinov, P. M. Thompson, A. W. Toga, Hamilton-Jacobi skeletons on cortical surfaces with applications in characterizing the gyrification pattern in Williams syndrome, Proc. ISBI, pp. 660 - 663, 2007.
  31. H. Shen, Y. Shi , Z. Peng, Applying prior knowledge in the segmentation of 3D complex anatomic structures, Proc. International Workshop on Computer Vision for Biomedical Image Applications ( CVBIA ), pp. 189-199, 2006.
  32. Y. Shi, W. C. Karl, Real-time tracking using level sets, Proc. CVPR, vol.2, pp.34-41, 2005.
  33. Y. Shi, W. C. Karl, A fast level set method without solving PDEs, Proc. ICASSP, vol.2, pp. 97-100,2005.
  34. Y. Shi, W. C. Karl, Shape reconstruction from unorganized points with a data-driven level set method, Proc. ICASSP, vol.3, pp. 17-21, 2004.
  35. S. Venkatesh, Y. Shi, W. C. Karl, Performance guarantees in sensor networks, Proc. ICASSP, vol.2, pp. 269-272, 2004.
  36. Y. Shi, W. C. Karl, Level set methods for dynamic tomography, (invited paper) Proc. ISBI, vol.1, pp. 620 - 623, 2004.
  37. Y. Shi, W. C. Karl, Differentiable minimin shape distance for incorporating topological priors in biomedical
    imaging, Proc. ISBI, vol.2, pp. 1247 - 1250, 2004.
  38. Y. Shi, J. Konrad, W. C. Karl, Multiple motion and occlusion segmentation with a multiphase level set method, Proc. VCIP, pp. 189-197, 2004.
  39. Y. Shi, W. C. Karl, D. A. Castanon, Dynamic tomography using curve evolution with spatial-temporal regularization, Proc. ICIP, vol.2, pp. 22-25 2002.

ABSTRACTS

  1. N. L. Sicotte, K. C. Kern, Y. Shi , A. Arshanapalli, M. Montag, B. S. Giesser, A. W. Toga, S. Y. Bookheimer, Structural and functional hippocampal changes in multiple sclerosis, 60th Annual Meeting of American Academy of Neurology ( AAN ), Chicago, IL, April 12-19, 2008.
  2. N. Lepore, Y. Shi , F. Lepore, P. Voss, M. Fortin, M. Lassonde, I. Dinov, A. W. Toga, P. M. Thompson , Hippocampal shape differences detected in blind versus sighted subjects, 13th Annual Meeting of the Organization for Human Brain Mapping ( OHBM ), Chicago, IL, June 10-14, 2007.