Publications/Brain Mapping

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Publications - Brain Mapping

Biological Brain Image Processing Image-Guided OCT
Motion Estimation Mapping and Analysis Interventions


FAIR ACADEMIC USE STATEMENT
Publications below are for individual use under the auspices and protection of FAIR ACADEMIC USE.
Please cite appropriately in references, and contact the publisher for subscription / purchase of original work.

2014

  • N.Shiee, P.-L. Bazin, J.L. Cuzzocreo, C. Ye, B. Kishore, A. Carass, P.A. Calabresi, D.S. Reich, J.L. Prince, and D.L. Pham, "Robust Reconstruction of the Human Brain Cortex in the Presence of the WM Lesions: Method and Validation", Human Brain Mapping, In Press, 2014. (doi)
  • A. Jog, A. Carass, D.L. Pham, and J.L. Prince, "Random Forest FLAIR reconstruction from T1, T2, and PD-weighted MRI", 11th IEEE International Symposium on Biomedical Imaging (ISBI 2014), Beijing, China, April 28 - May 2, 2014.
  • S. Roy, Q. He, A. Jog, A. Carass, J.L. Prince, and D.L. Pham, "Example based lesion segmentation", Proceedings of SPIE Medical Imaging (SPIE-MI 2014), San Diego, CA, February 15-20, 2014. (doi)
  • S. Roy, A. Carass, A. Jog, J.L. Prince, and J. Lee,, "MR to CT registration of brains using image synthesis", Proceedings of SPIE Medical Imaging (SPIE-MI 2014), San Diego, CA, February 15-20, 2014. (doi)
  • M.E. Ranta, M. Chen, D. Crocetti, J.L. Prince, K. Subramaniam, B. Fischl, W.E. Kaufmann, and S.H. Mostofsky, "Automated MRI parcellation of the frontal lobe", Human Brain Mapping, In Press, 2014. (doi)


2013

  • S. Roy, A. Carass, and J.L. Prince, "Magnetic Resonance Image Example Based Contrast Synthesis", IEEE Trans. on Medical Imaging, 32(12):2348-2363, 2013. (doi)
  • M. Chen, A. Carass, J. Oh, G. Nair, D.L. Pham, D.S. Reich, and J.L. Prince, "Automatic Magnetic Resonance Spinal Cord Segmentation with Topology Constraints for Variable Fields of View", NeuroImage, 83:1051-1062, 2013. (doi)
  • A. Jog, S. Roy, J.L. Prince, and A. Carass, "MR Brain Segmentation using Decision Trees", MICCAI Grand Challenge on MR Brain Image Segmentation (MRBrainS13), Nagoya, Japan, September 26, 2013..
  • S. Roy, A. Jog, A. Carass, and J.L. Prince, "Atlas Based Intensity Transformation of Brain MR Images", MICCAI Third International Workshop on Multimodal Brain Image Analysis (MBIA 2013). (doi)
  • Z. Yang, J.A. Bogovic, C. Ye, A. Carass, S.H. Ying, and J.L. Prince, "Automated Cerebellar Lobule Segmentation using Graph Cuts", MICCAI Challenge Workshop on Segmentation: Algorithms, Theory and Applications (SATA 2013), Nagoya, Japan, September 26, 2013.
  • A.K. Knutsen, E. Magrath, J. McEntee, J.L. Prince, P. Bayly, J. Butman, and D.L. Pham, "Improved measurement of Brain Deformation during a Mild Acceleration using Tagged MRI", Journal of Neurotrauma, 30(15):A114-A115, August 2013.
  • J.A. Bogovic, P.L. Bazin, S.H. Ying, and J.L. Prince, "Automated Segmentation of the Cerebellar Lobules using Boundary Specific Classification and Evolution", 23rd Conference on Information Processing in Medical Imaging (IPMI 2013), Asilomar California, USA, June 29 - July 3, 2013. (doi)
  • J. Stough, C. Ye, S.H. Ying, and J.L. Prince, "Thalamic Parcellation from Multi-Modal Data using Random Forest Learning", Tenth IEEE International Symposium on Biomedical Imaging (ISBI 2013), San Francisco, CA, April 7 - 11, 2013.
  • C. Ye, J.A. Bogovic, S.H. Ying, and J.L. Prince, "Segmentation of the Complete Superior Cerebellar Peduncles using a Multi-object Geometric Deformable Model", Tenth IEEE International Symposium on Biomedical Imaging (ISBI 2013), San Francisco, CA, April 7 - 11, 2013.
  • S. Roy, A. Carass, and J.L. Prince, "Patch Based Intensity Normalization of Brain MR Images", Tenth IEEE International Symposium on Biomedical Imaging (ISBI 2013), San Francisco, CA, April 7 - 11, 2013.
  • S. Roy, A. Carass, N. Shiee, D.L. Pham, P.A. Calabresi, D.S. Reich, and J.L. Prince, "Longitudinal Intensity Normalization in the presence of Multiple Sclerosis Lesions", Tenth IEEE International Symposium on Biomedical Imaging (ISBI 2013), San Francisco, CA, April 7 - 11, 2013.
  • A. Jog, S. Roy, A. Carass, and J.L. Prince, "Magnetic Resonance Image Synthesis through Patch Regression", Tenth IEEE International Symposium on Biomedical Imaging (ISBI 2013), San Francisco, CA, April 7 - 11, 2013.
  • Z. Yang, A. Carass, and J.L. Prince, "Covariance shrinking in active shape models with application to gyral labeling of the cerebral cortex", Tenth IEEE International Symposium on Biomedical Imaging (ISBI 2013), San Francisco, CA, April 7 - 11, 2013.
  • M. Bilgel, S. Roy, A. Carass, P.A. Nyquist, and J.L. Prince, "Automated Anatomical Labeling of the Cerebral Arteries using Belief Propagation", Proceedings of SPIE Medical Imaging (SPIE-MI 2013), Orlando, FL, February 9-14, 2013. (doi)
  • M. Chen, A. Carass, D.S. Reich, P.A. Calabresi, D.L. Pham, and J.L. Prince, "Voxel-Wise Displacement as Independent Features in Classification of Multiple Sclerosis", Proceedings of SPIE Medical Imaging (SPIE-MI 2013), Orlando, FL, February 9-14, 2013. (doi)
  • A. Jog, S. Roy, A. Carass, and J.L. Prince, "Pulse Sequence based Multi-acquisition MR Intensity Normalization", Proceedings of SPIE Medical Imaging (SPIE-MI 2013), Orlando, FL, February 9-14, 2013. (doi)
  • S. Roy, A. Carass, and J.L. Prince, "Longitudinal Intensity Normalization of Magnetic Resonance Images using Patches", Proceedings of SPIE Medical Imaging (SPIE-MI 2013), Orlando, FL, February 9-14, 2013. (doi)
  • C. Ye, J.A. Bogovic, S.H. Ying, and Jerry L. Prince, "Parcellation of the thalamus using diffusion tensor images and a multi-object geometric deformable model", Proceedings of SPIE Medical Imaging (SPIE-MI 2013), Orlando, FL, February 9-14, 2013. (doi)
  • J.A. Bogovic, B. Jedynak, R. Rigg, A. Du, B.A. Landman, J.L. Prince, and S.H. Ying, "Approaching expert results using a hierarchical cerebellum parcellation protocol for multiple inexpert human raters", NeuroImage, 64(1):616-629, 2013. (doi) (PubMed)


2012

  • B.A. Landman, J.A. Bogovic, A. Carass, M. Chen, S. Roy, N. Shiee, Z. Yang, B. Kishore, D. Pham, P.-L. Bazin, S.M. Resnick, and J.L. Prince, "System for Integrated Neuroimaging Analysis and Processing of Structure", Neuroinformatics, 11(1):91-103, 2012. (doi) (PubMed)
  • P.G. Unschuld, R.A.E. Edden, A. Carass, X. Liu, M. Shanahan, X. Wang, K. Oishi, J. Brandt, S.S. Bassett, G.W. Redgrave, R.L. Margolis, P.C.M. van Zijl, P.B. Barker, and C.A. Ross, "Brain metabolite alterations and cognitive dysfunction in early Huntington's disease", Movement Disorders, 27(7):895-902, June 2012. (doi) (PubMed)
  • S. Roy, A. Carass, P.-L. Bazin, S.M. Resnick, and J.L. Prince, "Consistent Segmentation using a Rician Classifier", Medical Image Analysis, 16(2):524-535, 2012. (doi) (PubMed)
  • Z. Yang, A. Carass, and J.L. Prince, "Automatic Sulcal Curve Extraction with MRF Based Shape Prior", Ninth IEEE International Symposium on Biomedical Imaging (ISBI 2012), Barcelona, Spain, May 2 - 5, 2012. (doi)
  • C. Ye, J.A. Bogovic, P-L Bazin, J.L. Prince, and S.H. Ying, "Fully Automatic Segmentation of the dentate nucleus using diffusion weighted images", Ninth IEEE International Symposium on Biomedical Imaging (ISBI 2012), Barcelona, Spain, May 2 - 5, 2012. (doi)
  • B.A. Landman, J.A. Bogovic, H. Wan, F. El Zahraa El-Shahaby, P.-L. Bazin, and J.L. Prince, "Resolution of crossing fibers with constrained compressed sensing using diffusion tensor MRI", NeuroImage, 59(3):2175–2186, 2012. (doi)
  • Z. Yang, A. Carass, C. Chen, and J.L. Prince, "Simultaneous Cortical Surface Labeling and Sulcal Curve Extraction", Proceedings of SPIE Medical Imaging (SPIE-MI 2012), San Diego, CA, February 4-9, 2012. (doi)
  • X. Liu, A. Carass, P.-L. Bazin, and J.L. Prince, "Topology Preserving Brain Tissue Segmentation Using Graph Cuts", IEEE Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA 2012), Breckenridge, CO, January 9, 2012. (doi)


2011

  • B.C. Jung, S.I. Choi, A.X. Du, J.L. Cuzzocreo, H.S. Ying, B.A. Landman, S.L. Perlman, R.W. Baloh, D.S. Zee and A.W. Toga, J.L. Prince, and S.H. Ying, "MRI Shows a Region-Specific Pattern of Atrophy in Spinocerebellar Ataxia Type 2", The Cerebellum, 1-8, 2011. (doi) (PubMed)
  • P.-L. Bazin, C. Ye, J.A. Bogovic, N. Shiee, D.S. Reich, J.L. Prince, and D.L. Pham, "Direct segmentation of the major white matter tracts in diffusion tensor images", NeuroImage, 58(2):458-468, September 2011. (doi) (PubMed)
  • A. Carass, J. Cuzzocreo, M.B. Wheeler, P.-L. Bazin, S.M. Resnick, and J.L. Prince, "Simple paradigm for extra-cerebral tissue removal: Algorithm and analysis", NeuroImage, 56(4):1982-1992, June 2011. (doi) (PubMed) (PMCID 3105165)
  • N. Shiee, P.-L. Bazin, J.L. Cuzzocreo, A. Blitz, and D.L. Pham, "Segmentation of brain images using adaptive atlases with application to ventriculomegaly", 22nd Conference on Information Processing in Medical Imaging (IPMI 2011), Monastery Irsee, Germany, July 3-8, 2011. (doi) (PubMed) (PMCID 3478153)
  • S. Roy, A. Carass, and J.L. Prince, "A Compressed Sensing Approach For MR Tissue Contrast Synthesis", 22nd Conference on Information Processing in Medical Imaging (IPMI 2011), Monastery Irsee, Germany, July 3-8, 2011. (doi) (PubMed) (PMCID 3398746)
  • H. Huang, J.L. Prince, V. Mishra, A. Carass, B. Landman, D.C. Park, C. Tamminga, R. King, M.I. Miller, P.C.M. van Zijl, and S. Mori, "A framework on surface-based connectivity quantification for the human brain", Journal of Neuroscience Methods, 197(2):324-332, April 2011. (doi) (PubMed) (PMCID 3081907)
  • A. Carass, M. Chen, J. Cuzzocreo, S.M. Resnick and J.L. Prince, "Skull Stripping Influence on Cortical Surface Reconstruction : A Landmark Validation", 17th Annual Meeting of the Organization for Human Brain Mapping (HBM 2011), Quebec, Canada, June 26-30, 2011.
  • N. Shiee, P.-L. Bazin, P.A. Calabresi, D.S. Reich, D.L. Pham, "Fiber tractography and tract segmentation in multiple sclerosis lesions", Eighth IEEE International Symposium on Biomedical Imaging (ISBI 2011), Chicago, IL, March 30 - April 2, 2011. (doi)
  • M. Chen, A. Carass, J. Cuzzocreo, P.-L. Bazin, D. Reich, and J.L. Prince, "Topology Preserving Automatic Segmentation of the Spinal Cord in Magnetic Resonance Images", Eighth IEEE International Symposium on Biomedical Imaging (ISBI 2011), Chicago, IL, March 30 - April 2, 2011. (doi)
  • S. Roy, A. Carass, and J.L. Prince, "Compressed Sensing Based Intensity Non-Uniformity Correction", Eighth IEEE International Symposium on Biomedical Imaging (ISBI 2011), Chicago, IL, March 30 - April 2, 2011. (doi)
  • M. Chen, A. Carass, P.-L. Bazin, J.A. Bogovic, and J.L. Prince, "Distance Transforms in Multi Channel MR Image Registration", Proceedings of SPIE Medical Imaging (SPIE-MI 2011), Orlando, FL, February 12-17, 2011. (doi)
  • S. Roy, A. Carass, P.-L. Bazin, and J.L. Prince, "Intensity Inhomogeneity Correction of Magnetic Resonance Images using Patches", Proceedings of SPIE Medical Imaging (SPIE-MI 2011), Orlando, FL, February 12-17, 2011. (doi)
  • F.E.A. ElShahaby, B.A. Landman, and J.L. Prince, "Effect of Regularization Parameter and Scan Time on Crossing Fibers with Constrained Compressed Sensing", Proceedings of SPIE Medical Imaging (SPIE-MI 2011), Orlando, FL, February 12-17, 2011. (doi) (PubMed) (PMCID 3087384)
  • B.A. Landman, A.J. Huang, A. Gifford, D.S. Vikram, I.A.L. Lim, J.A.D. Farrell, J.A. Bogovic, J. Hua, M. Chen, S. Jarso, S.A. Smith, S. Joel, S. Mori, J.J. Pekar, P.B. Barker, J.L. Prince, and P.C.M. van Zijl, "Multi-parametric neuroimaging reproducibility: A 3-T resource study", NeuroImage, 54(4):2854–2866, 2011. (doi) (PubMed) (PMCID 3020263)


2010

  • A.X. Du, J.L. Cuzzocreo, B.A. Landman, D.S. Zee, J.L. Prince, and S.H. Ying, "Diffusion tensor imaging reveals disease-specific deep cerebellar nuclear changes in cerebellar degeneration", Journal of Neurology, 257(8):1406-1408, August 2010. (doi) (PubMed) (PMCID 2963035)
  • B.A. Landman, K. Covington, E.S. McCreedy, M. Chen, A. Carass, N. Aucoin, J.L. Prince, and D.L.Pham, "JIST: An Open-Source, Java-Based Integrative Framework for Biomedical Image Analysis", NCI's NCRI, Washington D.C., June 21-22, 2010.
  • M. Thambisetty, J. Wan, A. Carass, Y. An, J.L. Prince and S.M. Resnick, "Longitudinal changes in cortical thickness associated with normal aging", NeuroImage, 52(4):1215-1223, October 2010. (doi) (PubMed) (PMCID 2910226)
  • K. Covington, E. McCreedy, M. Chen, A. Carass, N. Aucoin, and B.A. Landman, "Interfaces and Integration of Medical Image Analysis Frameworks: Challenges and Opportunities", Annual ORNL Biomedical Science and Engineering Conference (BSEC 2010), Oak Ridge, Tennessee, May 25-26, 2010. (doi) (PubMed) (PMCID 2998761)
  • N.Shiee, P.-L. Bazin, J. Bogovic, M. Chen, P.A. Calabresi, D.S. Reich, J.L. Prince, and D.L. Pham, "Cortical thinning in Multiple Sclerosis", 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.
  • N.Shiee, P.-L. Bazin, P.A. Calabresi, D.L. Pham, and D.S. Reich, "Brain sub-structure atrophy in Multiple Sclerosis measured by automated tissue-lesion segmentation", 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.
  • J.A. Bogovic, J.A. Barger, M. Thomson, X. Fan, J.L. Prince, and S.H. Ying, "Shape Variation of the Thalamic Nuclei Estimated from a Manual Parcellation", 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.
  • M. Chen, A. Carass, M.B. Wheeler, X. Liu, and J.L. Prince, "Multi-Channel Enhancement of the Adaptive Bases Algorithm", 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.
  • M. Chen, A. Carass, M.B. Wheeler, X. Liu, and J.L. Prince, "Implementation of the Adaptive Bases Algorithm in the Java Image Science Toolkit", 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.
  • C. Zhao, A. Carass, M. Chen, J. Bogovic, D. Chen, and J.L. Prince, "A Protocol for Manual Correction of Gyral Based Cortical Labels", 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.
  • C. Zhao, D. Chen, A. Carass, M. Chen, J. Bogovic, and J.L. Prince, "A Java Application for Manually Editing Cortical Labels", 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.
  • J. Vogelstein, J. Bogovic, A. Carass, W. Gray, J.L. Prince, B. Landman, D. Pham, L. Ferrucci, S. Resnick, C. Priebe, and R.J. Vogelstein, "Graph-Theoretical Methods for Statistical Inference on MR Connectome Data", 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.
  • J.A. Bogovic, M. Chen, A. Carass, P.-L. Bazin, D.L. Pham, S. Resnick, J.L. Prince, and B.A. Landman, "Multi-Modal Structural Networks: Mapping of Connectivity through Diffusion, Functional, and Structural Assessment of Intervening Pathways", 18th Annual meeting of the International Society for Magnetic Resonance in Medicine (ISMRM 2010), Stockholm, Sweden, May 1-7, 2010.
  • S. Roy, A. Carass, N. Shiee, D.L. Pham, S. Resnick, and J.L. Prince, "Longitudinal Changes of White Matter Lesions", 18th Annual meeting of the International Society for Magnetic Resonance in Medicine (ISMRM 2010), Stockholm, Sweden, May 1-7, 2010.
  • S. Roy, A. Carass, N. Shiee, D.L. Pham, and J.L. Prince, "MR Contrast Synthesis for Lesion Segmentation", Seventh IEEE International Symposium on Biomedical Imaging (ISBI 2010), Rotterdam, The Netherlands, April 14 - 17, 2010. (doi) (PubMed) (PMCID 2995277)
  • A. Ozturk, S.A. Smith, E.M. Gordon-Lipkin, D.M. Harrison, N. Shiee, D.L. Pham, B.S. Caffo, P.A. Calabresi, and D.S. Reich, "MRI of the Corpus Callosum in Multiple Sclerosis: Association with disability", Multiple Sclerosis, 16(2):166-77, 2010. (doi) (PubMed) (PMCID 2820126)
  • J.N. Ratchford, S. Farrell, N. Shiee, C. Warner, S.B. Syc, S. Newsome, D. Harrison, E.M. Frohman, L.J. Balcer, D. Pham, D.S. Reich, and P.A. Calabresi, "Retinal nerve fiber layer thickness correlates with gray and white matter volume in MS", Annual Meeting of the American Academy of Neurology (AAN 2010), Toronto, Canada, April 10-17, 2010.
  • B.C. Lucas, J.A. Bogovic, A. Carass, P.-L. Bazin, J.L. Prince, D.L. Pham, and B.A. Landman, "The Java Image Science Toolkit (JIST) for Rapid Prototyping and Publishing of Neuroimaging Software", Neuroinformatics, 8:5-17, March 2010. (doi) (PubMed) (PMCID 2860951)
  • J.A. Bogovic, B.A. Landman, P.-L. Bazin, and J.L. Prince, "Statistical Recombination of Rater Labels on Surfaces", Proceedings of SPIE Medical Imaging (SPIE-MI 2010), San Diego, CA, February 16-21, 2010. (doi) (PubMed) (PMCID 2997739)
  • S. Roy, A. Carass, and J.L. Prince, "Synthesizing MR contrast and resolution through a patch matching technique", Proceedings of SPIE Medical Imaging (SPIE-MI 2010), San Diego, CA, February 16-21, 2010. (doi) (PubMed) (PMCID 2860803)
  • X. Fan, J.A. Bogovic, P.-L. Bazin, and J.L. Prince, "A novel contrast for DTI visualization for thalamus delineation", Proceedings of SPIE Medical Imaging (SPIE-MI 2010), San Diego, CA, February 16-21, 2010. (doi)
  • B.A. Landmann, H. Wan, J.A. Bogovic, P.-L. Bazin, and J.L. Prince, "Resolution of crossing fibers with constrained compressed sensing using traditional diffusion tensor MRI", Proceedings of SPIE Medical Imaging (SPIE-MI 2010), San Diego, CA, February 16-21, 2010. (doi) (PubMed) (PMCID 2854412)
  • N. Shiee, P.-L. Bazin, A. Ozturk, D.S. Reich, P.A. Calabresi, and D.L. Pham, "A Topology-Preserving Approach to the Segmentation of Brain Images with Multiple Sclerosis Lesions", NeuroImage, 49(2):1524-1535, January 2010. (doi) (PubMed) (PMCID 2806481)


Publications/Brain Mapping/2000s


Publications/Brain Mapping/1990s

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