Publications

Assistant Professor  •  Computer Scientist  •  Imaging Expert  •   •  Home  •  Classes  •  CRCV  •  Research Blog  •  Publications  • 

Publications are grouped into Books, Journal Articles, Conference Papers, Meeting Abstracts and Technical Reports.

Download my ALL papers and/or bibliography at GOOGLE SCHOLAR

* indicates students under my direct supervision (including postdocs, postbacs, PhD students, and summer interns), and I am the corresponding author.


Journal Articles

  1. Quantitative Image Quality Comparison of Reduced and Standard Dose Dual Energy Multiphase Chest, Abdomen, and Pelvis CT.
    M.Buty, Z.Xu, A.Wu, M. Gao, C. Nelson, G.Z. Papadakis, U.Teomete, H. Celik, B. Turkbey, P. Choyke, D.J. Mollura, Ulas Bagci, L. Folio
    TomoGraphy, Vol 3(2), pp. 114-122 2017.
    [PDF]
  2. Brown adipose tissue detected by PET/CT imaging is associated with less central obesity.
    Aileen Green, Ulas Bagci, Sarfaraz Hussein, Patrick Kelly, Razi Muzaffar, Brent Neuschwander-Tetri, and Medhat Osman.
    Nuclear Medicine Communications, (in press), 2017.
    [PDF]
  3. Automatic Segmentation and Quantification of White and Brown Adipose Tissues from PET/CT Scans.
    Sarfaraz Hussein, Aileen Green, Arjun Watane, David Reiter, Xinjian Chen, Georgios Z Papadakis, Bradford Wood, Aaron Cypess, Medhat Osman, Ulas Bagci
    IEEE Transactions on Medical Imaging, 36(3), p. 734-744, 2017. http://ieeexplore.ieee.org/document/7775001
    [PDF]
  4. Single-channel Sparse Nonnegative Blind Source Separation Method for Automatic 3D Delineation of Lung Tumor in PET Images.
    Ivica Kopriva, Wei Ju, Bin Zhang, Fei Shi, Dehui Xiang, Kai Yu, Ximing Wang, Ulas Bagci, Xinjian Chen.
    IEEE Journal of Biomedical and Health Informatics, (in press), 2017. http://ieeexplore.ieee.org/abstract/document/7733134
    [PDF]
  5. Avascular Necrosis of the Hips With Increased Activity on 68Ga-DOTATATE PET/CT.
    Georgios Z Papadakis, Corina Millo, AH Karantanas, Ulas Bagci, N. Patronas
    Clinical Nuclear Medicine, 2017.
    [PDF]
  6. Application of 68Ga-DOTA-TATE PET/CT in metastatic neuroendocrine tumor of gastrointestinal origin.
    Georgios Z Papadakis, SM Sadowski, Ulas Bagci, C. Millo
    Clinical Nuclear Medicine, 2017.
    [PDF]
  7. 18F-FDG and 68Ga-DOTATATE PET/CT in von Hippel-Lindau Disease-Associated Retinal Hemangioblastoma.
    Georgios Z Papadakis, C. Millo, IS. Jassel, Ulas Bagci, SM Sadowski, AH Karantanas, N. Patronas
    Clinical Nuclear Medicine, 2017.
    [PDF]
  8. Fibrous Dysplasia Mimicking Malignancy on 68Ga-DOTATATE PET/CT.
    Georgios Z Papadakis, C. Millo, SM. Sadowski, AH Karantanas, Ulas Bagci, N. Patronas
    Clinical Nuclear Medicine, 2017.
    [PDF]
  9. Breast Fibroadenoma With Increased Activity on 68Ga DOTATATE PET/CT.
    Georgios Z Papadakis, C. Millo, SM. Sadowski, AH Karantanas, Ulas Bagci, N. Patronas
    Clinical Nuclear Medicine, 2017.
    [PDF]
  10. Kidney Tumor in a von Hippel-Lindau (VHL) Patient With Intensely Increased Activity on 68Ga-DOTA-TATE PET/CT.
    Georgios Z Papadakis, Corina Millo, Samira M Sadowski, Ulas Bagci, N. Patronas
    Clinical Nuclear Medicine, 41(12):970-971, 2016. http://journals.lww.com/nuclearmed/Citation/2016/12000/Kidney_Tumor_in_a_von_Hippel_Lindau__VHL__Patient.19.aspx
    [PDF]
  11. Computer-Aided Detection (CADx) for Plastic Deformation Fractures in Pediatric Forearm.
    Yuwei Zhou, Uygar Teomete, Ozgur Dandin, Onur Osman, Taner Dandinoglu, Ulas Bagci, Weizhao Zhao
    Computers in Biology and Medicine, 78:120-125, 2016. http://www.sciencedirect.com/science/article/pii/S0010482516302396
    [PDF]
  12. 18F-NaF and 18F-FDG PET/CT in Gorham-Stout Disease.
    Georgios Z Papadakis, Corina Millo, Ulas Bagci, Jenny Blau, Michael T Collins
    Clinical Nuclear Medicine, 41(11):884-885, 2016. http://journals.lww.com/nuclearmed/Abstract/2016/11000/18F_NaF_and_18F_FDG_PET_CT_in_Gorham_Stout_Disease.13.aspx
    [PDF]
  13. Atlas-based rib-bone detection in chest X-rays.
    Sema Candemir, Stefan Jaeger, Sameer Antani, Ulas Bagci, Les R Folio, Ziyue Xu, George Thoma
    Computerized Medical Imaging and Graphics, 51:32-39, 2016. http://www.sciencedirect.com/science/article/pii/S0895611116300337
    [PDF]
  14. Epididymal Cystadenomas in von Hippel-Lindau Disease Showing Increased Activity on 68Ga DOTATATE PET/CT.
    GZ Papadakis, C Millo, SM Sadowski, Ulas Bagci, NJ Patronas
    Clinical Nuclear Medicine, 41(10):781-782, 2016. http://journals.lww.com/nuclearmed/Abstract/publishahead/Epididymal_Cystadenomas_in_von_Hippel_Lindau.98417.aspx
    [PDF]
  15. Endolymphatic Sac Tumor Showing Increased Activity on 68Ga DOTATATE PET/CT.
    GZ Papadakis, C Millo, SM Sadowski, Ulas Bagci, NJ Patronas
    Clinical Nuclear Medicine, 41(10):783-784, 2016. http://journals.lww.com/nuclearmed/Abstract/publishahead/Endolymphatic_Sac_Tumor_Showing_Increased_Activity.98416.aspx
    [PDF]
  16. 3B11-N, a monoclonal antibody against MERS-CoV, reduces lung pathology in rhesus monkeys following intratracheal inoculation of MERS-CoV Jordan-n3/2012.
    R.F. Johnson, Ulas Bagci, et al.
    Virology, 490:49-58, March 2016. http://www.sciencedirect.com/science/article/pii/S0042682216000076
    [PDF]
  17. Evaluation of Candidate Vaccine Approaches for MERS-CoV.
    L.Wang, W.Shi, M.G. Joyce, K.Modjarrad, Y.Zhang, K.Leung, C.R. Lees, T.Zhou, H.M. Yassine, M.Kanekiyo, Z.Yang, X.Chen, M.M. Becker, M.C. Freeman, L.Vogel, J.C. Johnsson, G.Olinger, J.P.Todd, U. Bagci, J. Solomon, D.J. Mollura, L.Hansley, P. Jahriling, M.R. Denison, S.S.Rao, K.Subbarao, P.D.Kwong, J.R.Mascola, W.Kong, B.S. Graham
    Nature Communications, 6(7712), 28 July 2015. http://doi.org/10.1038/ncomms8712
    [PDF]
  18. Schmorl Nodes Can Cause Increased 68Ga DOTATATE Activity on PET/CT, Mimicking Metastasis in Patients With Neuroendocrine Malignancy
    G.Z. Papadakis, C. Millo, U. Bagci, S.M. Sadowski, and C.A. Stratakis
    Clinical Nuclear Medicine, Volume 41(3):249-250, 2015.
    [PDF]
  19. Lower Respiratory Tract Infection of the Ferret by 2009 H1N1 Pandemic Influenza A Virus Triggers Biphasic Systemic and Local Neutrophil Recruitment.
    J.V. Camp, U. Bagci, Y. Chu, B. Squier, M. Fraig, S.M. Uriarte, H. Guo, D.J. Mollura, C.B. Jonsson
    Journal of Virology, 89(17):8733-8748, 2015.
    [PDF]
  20. Computer-aided pulmonary image analysis in small animal models.
    Z. Xu*, U. Bagci, A. Mansoor, G. Kramer-Marek, B. Luna, A. Kubler, B. Dey, B. Foster, G. Z. Papadakis, J. V. Camp, C. B. Jonsson, W. R. Bishai, S. Jain, J. K. Udupa, D.J. Mollura
    Medical Physics, 42(7):3896-3910, 2015.
    [PDF]
  21. A Hybrid Method for Airway Segmentation and Automated Measurement of Bronchial Wall Thickness on CT.
    Z. Xu*, U. Bagci, B. Foster, A. Mansoor, J. K. Udupa, D. J. Mollura
    Medical Image Analysis, 24(1):1-17, August 2015.
    [PDF]
  22. Talc Pleurodesis with intense 18F-FDG activity but no 68Ga-DOTA-TATE activity on PET/CT.
    G.Z. Papadakis*, C. Millo, U. Bagci, N.J. Patronas, C.A. Stratakis
    Clinical Nuclear Medicine, 40(10):819-820, 2015.
    [PDF]
  23. Segmentation and Image Analysis of Abnormal Lungs at CT: Current Approaches, Challenges, and Future Trends.
    A.Mansoor,U. Bagci*, B.Foster, Z.Xu, G.Z. Papadakis, L. Folio, J.K. Udupa, D.J. Mollura
    Radiographics, 35(4):1056-1076, 2015.
    [PDF]
  24. Ectopic ACTH and CRH co-secreting tumor localized by 68Ga-DOTA-TATE PET/CT.
    G.Z. Papadakis*, U. Bagci, S.M. Sadowski, N.J. Patronas, C.A. Stratakis
    Clinical Nuclear Medicine, 40(7):576-578, 2015.
    [PDF]
  25. Mycobacterium tuberculosis dysregulates MMP/TIMP balance to drive rapid cavitation and unrestrained bacterial proliferation.
    A.Kubler, B.Luna, C.Larsson, N.C. Ammerman, B.B. Andrade, M. Orandle, K.W. Bock, Z. Xu, U. Bagci, D.J. Mollura, et al.
    The Journal of Pathology, 235(3):431-444, 2015.
    [PDF]
  26. In vivo Prediction of Tuberculosis Cavity Formation in Rabbits.
    B.Luna, A.Kubler, C.Larsson, B.Foster, U. Bagci, D.J. Mollura, S.Jain, W.R. Bishai
    Journal of Infectious Diseases, 211(3):481-485, 2014.
    [PDF]
  27. A Generic Approach to Pathological Lung Segmentation.
    A.Mansoor*,U. Bagci, Z. Xu, B.Foster, K. Olivier, J. Elinoff, A.F. Suffredini, J.K. Udupa, and D. J. Mollura
    IEEE Transactions on Medical Imaging, 33(12):2293-2310, 2014.
    [PDF]
  28. A Review on Image Segmentation Methods for Positron Emission Tomography.
    Foster*, B., U. Bagci, Z. Xu, A. Mansoor, and D. J. Mollura
    Computers in Biology and Medicine, 50:76-96, 2014.
    [PDF]
  29. Recombinant Human Factor VIIa for Alveolar Hemorrhage Following Allogeneic Stem Cell.
    Elinoff JM, U. Bagci, Moriyama B, Dreiling JL, Foster B, Gormley NJ, Salit RB, Cai R, Sun J, Beri A, Reda DJ, Fakhrejahani F, Battiwalla M, Baird K, Cuellar R, Rodriguez JM, Kang EM, Pavletic SZ, Fowler DH, John Barrett A, Lozier JN, Kleiner DE, Mollura DJ, Childs RW, and Suffredini AF
    Biol Blood Marrow Transplant, 20(7):969-78, 2014.
    [PDF]
  30. Segmentation of PET Images for Computer Aided Functional Quantification of Tuberculosis in Small Animal Models.
    B. Foster*, U. Bagci, Z. Xu, B. Dey, B. Luna, W. R. Bishai, S. Jain, and D. J. Mollura
    IEEE Transactions on Biomedical Engineering, 61(3):711-724, 2014.
    [PDF] [CODE]
  31. Introducing Willmore Flow into Level Set Segmentation of Spinal Vertebrae.
    Lim*, P., U. Bagci, and L. Bai
    IEEE Transactions on Biomedical Engineering, 60(1):115-122, 2013.
    [PDF]
  32. A computational pipeline for quantification of pulmonary infections in small animal models using serial PET-CT imaging.
    U. Bagci, B. Foster, K. Miller-Jaster, B. Luna, B. Dey, W. R. Bishai, C. B. Jonsson, S. Jain, and D. J. Mollura
    EJNMMI Res, 3(55):1-20, 2013.
    [PDF]
  33. Automated Computer Quantification of Breast Cancer in Small Animal Models from PET/MRI Dual Modality Images with 18F-ZHER2-Affibody Radiotracer: A Comparison with Radiologist-derived Quantification and Conventional 18F-FDG-PET Imaging.
    U. Bagci, G. Kramer-Marek, and D. Mollura
    EJNMMI Res, 3(49):1-13, 2013.
    [PDF]
  34. Synergistic combination of clinical and imaging features predicts abnormal imaging patterns of pulmonary infections.
    U. Bagci, K. Miller-Jaster, J.Yao, and D. Mollura
    Computers in Biology and Medicine, 43(9):1241-1251, 2013.
    [PDF]
  35. Joint Segmentation of Anatomical and Functional Images: Applications in Quantification of Lesions from PET, PET-CT, MRI-PET, and MRI-PET-CT Images.
    U. Bagci, J. K. Udupa, N. Mendhiratta, B. Foster, Z. Xu, J. Yao, X. Chen, and D. Mollura
    Medical Image Analysis, 17(8):929-945, 2013.
    [PDF]
  36. Predicting Future Morphological Changes of Lesions from Radiotracer Uptake in 18F-FDG-PET Images.
    U. Bagci, J. Yao, K. Miller, X. Chen, and D. Mollura
    Plos One, 8(2):e57105, 2013.
    [PDF]
  37. Computer-aided detection and quantification of cavitary tuberculosis from CT scans.
    Z.Xu*, U. Bagci, A. Kubler, B. Luna, S. Jain, W. Bishai, and D. Mollura
    Medical Physics, 40(11), 113701:1-14, 2013.
    [PDF]
  38. An Automatic Method for Renal Cortex Segmentation on CT images: Evaluation on Kidney Donors.
    Chen, X., R. Summers, M. Cho, U. Bagci, and J. Yao
    Academic Radiology, 19(5):562-570, 2012.
    [PDF]
  39. Medical Image Segmentation by Combining Graph Cut and Oriented Active Appearance Models.
    Chen, X., J. K. Udupa, U. Bagci, Y. Zhuge, and J. Yao
    IEEE Transactions on Image Processing, 21(4):2035-2046, 2012.
    [PDF]
  40. PET Imaging of HER2+ Pulmonary Metastases with 18F-ZHER2:342-Affibody in a Mouse Model; Comparison with 18F-Fluorodeoxyglucose (18F-FDG).
    Kramer-Marek, G., M. Bernardo, D. O. Kiesewetter, U. Bagci, M. Kuban, A. Omer, R. Zielinski, J. Seidel, P. Choyke, and J. Capala
    Journal of Nuclear Medicine, 53(6):936-946, 2012.
    [PDF]
  41. Computer-Assisted Detection of Respiratory Tract Infections: A Review.
    U. Bagci, M. Bray, J. Caban, J. Yao, and D. Mollura
    Computerized Medical Imaging and Graphics, 36(1):72-84, 2012.
    [PDF]
  42. Hierarchical Scale-Based Multi-Object Recognition of 3D Anatomical Structures.
    U. Bagci, X. Chen, J. K. Udupa
    IEEE Transactions on Medical Imaging, 31(3):777-789, 2012.
    [PDF]
  43. Detection and Quantification of Tree-in-Bud (TIB) Opacities from CT Scans.
    U. Bagci, J. Yao, A. Wu, J. Caban, A. Suffredini, T. Palmore, O. Aras, and D. J. Mollura
    IEEE Transactions on Biomedical Engineering, 59(6):1620-1632, 2012.
    [PDF]
  44. 3D Automatic Anatomy Segmentation Based on Iterative Graph- Cut-ASM.
    X. Chen, U. Bagci
    Medical Physics, 38(8):4610-4622, 2011.
    [PDF]
  45. Automatic Best Reference Slice (BRS) Selection for Smooth Volume Reconstruction of a Mouse Brain From Histological Sections.
    U. Bagci, L. Bai
    IEEE Transactions on Medical Imaging, 29(9):1688-1696, 2010.
    [PDF]
  46. Determination of Onset of Failure of Rocks in Multiple Failure State Triaxial Tests Using Scale-Based Differential Geometry.
    U. Bagci, D. Mamurekli
    Arch. Min. Sci., 54(1):55-78, 2010.
    [PDF]
  47. The Role of Intensity Standardization in Medical Image Registration.
    U. Bagci, J.K. Udupa, L. Bai
    Pattern Recognition Letters, 31(4):315-323, 2009.
    [PDF]
  48. Automatic Classification of Musical Genres Using Inter-Genre Similarity.
    U. Bagci, E. Erzin
    Signal Processing Letters, 8(14):521-524, 2007.
    [PDF]

    Peer-Reviewed Conference Papers and Lecture Notes

  49. Automatic Response Assessment in Regions of Language Cortex in Epilepsy Patients Using ECoG-based Functional Mapping and Machine Learning.
    Harish RaviPrakash, Milena Korostenskaja, Eduardo Castillo, Ki Lee, James Baumgartner, and Ulas Bagci.
    IEEE International Conference on Systems, Man and Cybernetics (SMC) 2017.
    [PDF]
  50. Multi-Planar Deep Segmentation Networks for Cardiac Substructures from MRI and CT.
    AliAsghar Mortazi, Jeremy Burt and Ulas Bagci.
    MICCAI Multi-Modality Whole Heart Segmentation Challange 2017.
    [PDF]
  51. CardiacNET: Segmentation of Left Atrium and Proximal Pulmonary Veins from MRI using Multi-View CNN.
    AliAsghar Mortazi, R. Karim, K. Rhode, Jeremy Burt and Ulas Bagci.
    MICCAI 2017.
    [PDF]
  52. Risk Stratification of Lung Nodules Using 3D CNN Multi-Task Learning.
    Sarfaraz Hussein, Kunlin Cao, Qi Song, Ulas Bagci.
    Information Processing in Medical Imaging (IPMI) 2017.
    [PDF]
  53. TumorNET: Lung Nodule Characterization using Multi-View Convolutional Neural Network with Gaussian Process.
    Sarfaraz Hussein, Robert Gillies, Kunlin Cao, Qi Song, Ulas Bagci.
    IEEE ISBI 2017, Sydney, Australia, 2017.
    [PDF]
  54. Robust and Fully Automated Segmentation of Mandible from CT Scans.
    Nelisah Torosdagli, Denise Liberton, Payal Verma, Murat Sincan, Janice Lee, Sumantha Pattanaik, Ulas Bagci.
    IEEE ISBI 2017, Sydney, Australia, 2017.
    (Oral) [PDF]
  55. Characterization of Lung Nodule Malignancy using Hybrid Shape and Appearance Features.
    Buty, M., Z. Xu, M. Gao, Ulas Bagci, A. Wu, and D. Mollura.
    MICCAI 2016, Athens Greece, October 17-22, 2016.
    [PDF]
  56. Gaze2Segment: A Pilot Study for Integrating Eye-Tracking Technology into Medical Image Segmentation.
    Naji Khosravan, Haydar Celik, Baris Turkbey, Ruida Cheng, Evan McCreedy, Matthew McAuliffe, Sandra Bednarova, Elizabeth Jones, Xinjian Chen, Peter L Choyke, Bradford J Wood, Ulas Bagci
    Medical Computer Vision, MICCAI 2016, Athens Greece, October 17-22, 2016.
    [PDF]
  57. Transferability of 3D CNN features for Organ Detection.
    S. Hussein and U. Bagci
    NIPS 2015 Workshop on Machine Learning in Healthcare.
    [PDF]
  58. Holistic Classification of CT Attenuation Patterns for Interstitial Lung Diseases via Deep Convolutional Neural Networks.
    M. Gao, U. Bagci, L. Lu, A. Wu, M. Buty, H-C. Shin, H. Roth, G.Z. Papadakis, A. Depeursinge, R.M. Summers, Z. Xu, and D.J. Mollura
    Deep Learning in Medical Image Analysis, MICCAI 2015, Munich Germany, October 5-9, 2015.
    [PDF]
  59. Highly Precise Partial Volume Correction for PET Images: An Iterative Approach via Shape Consistency.
    Z.Xu*, U. Bagci, M.Gao, D.J. Mollura
    In: IEEE 10th International Symposium on Biomedical Imaging (ISBI), 2015.
    [PDF]
  60. Fuzzy Connectedness Image Co-Segmentation for Hybrid PET/MRI and PET/CT Scans.
    Z.Xu*, U. Bagci, J.K. Udupa, D.J. Mollura
    Lecture Note in Computer Vision and Biomechanics, In: MICCAI 2014-Workshop of Computational Methods for Molecular Imaging, 2015.
    [PDF]
  61. Segmentation Based Denoising of PET Images: An Iterative Approach via Regional Means and Affinity Propagation.
    Z.Xu*, U. Bagci, J. Seidel, D. Thomasson, J. Solomon, D.J. Mollura
    In: Medical Image Computing and Computer-Assisted Intervention (MICCAI), 8673:698-705, 2014.
    [PDF]
  62. Optimally Stabilized PET Image Denoising Using Trilateral Filtering.
    A. Mansoor*, U. Bagci, D.J. Mollura
    In: Medical Image Computing and Computer-Assisted Intervention (MICCAI), 8673:130-137, 2014.
    [PDF]
  63. CIDI-Lung-Seg: A Single-Click Annotation Tool for Automatic Delineation of Lungs from CT Scans.
    A.Mansoor*, U. Bagci, B.Foster, Z.Xu, D.Douglas, J. Solomon, J.K. Udupa, D.J. Mollura
    In: Conf Proc IEEE Eng Med Biol Soc, 1087-1090, 2014.
    [PDF]
  64. Near Optimal Keypoint Sampling for Fast Pathological Lung Segmentation.
    A.Mansoor*, U. Bagci, D.J. Mollura
    In: Conf Proc IEEE Eng Med Biol Soc, 6032-6035, 2014.
    [PDF]
  65. Efficient Ribcage Segmentation from CT Scans Using Shape Features.
    Z.Xu*, U. Bagci, D.J. Mollura
    In: Conf Proc IEEE Eng Med Biol Soc, 2899-2902, 2014.
    [PDF]
  66. Accurate and Efficient Separation of Left and Right Lungs from 3D CT Scans: A Generic Hysteresis Approach.
    Z.Xu*, U. Bagci, Colleen Jonsson, Sanjay Jain, D.J. Mollura
    In: Conf Proc IEEE Eng Med Biol Soc, 6036-6039, 2014.
    [PDF]
  67. QAV-PET: Quantitative Analysis and Visualization of PET Images.
    B.Foster*, U. Bagci, G.Papadakis, D.J. Mollura
    In: Conf Proc IEEE Eng Med Biol Soc, 1909-1912, 2014.
    [PDF]
  68. A Robust Segmentation Framework for Spine Trauma Diagnosis.
    Lim*, P., U. Bagci, L. Bai
    Lecture Notes in Computational Vision and Biomechanics, In: Workshop on Computational Methods and Clinical Applications for Spine Imaging-MICCAI 2013 , 17:25-33, 2014.
    [PDF]
  69. Denoising PET Images Using Singular Value Thresholding and Stein's Unbiased Risk Estimate.
    U. Bagci, D. J. Mollura
    In: Medical Image Computing and Computer-Assisted Intervention (MICCAI), 8151:115-122, 2013.
    [PDF]
  70. Spatially Constrained Random Walk Approach for Accurate Estimation of Airway Wall Surfaces.
    Z.Xu*, U. Bagci, B. Foster, A. Mansoor, D. J. Mollura
    In: Medical Image Computing and Computer-Assisted Intervention (MICCAI), 8151:559-566, 2013.
    [PDF]
  71. Robust Segmentation and Accurate Target Definition for Positron Emission Tomography Images Using Affinity Propagation.
    Foster*, B., U. Bagci, B. Luna, B. Dey, W. Bishai, S. Jain, Z. Xu, and D. J. Mollura
    In: IEEE 10th International Symposium on Biomedical Imaging (ISBI), 1461-1464, 2013.
    [PDF]
  72. A Hybrid Multi-Scale Approach to Auto- matic Airway Tree Segmentation From CT Scan.
    Z.Xu*, U. Bagci, B. Foster, D. J. Mollura
    In: IEEE 10th International Symposium on Biomedical Imaging (ISBI), 1308-1311, 2013.
    [PDF]
  73. Characterizing Non-Linear Dependencies Among Pairs of Clinical Variables and Imaging Data.
    Caban, J., U. Bagci, A. Mehari, S. Alam, J. R. Fontana, G. J. Kato, D. J. Mollura
    In: Conf Proc IEEE Eng Med Biol Soc, 2700-2703, 2012.
    [PDF]
  74. A Novel Spinal Vertebrae Segmentation Framework Combining Geometric Flow and Shape Prior with Level Set.
    Lim*, P. H., U. Bagci, O. Aras, Y. Wang, B. Li
    In: IEEE International Symposium in Biomedical Imaging (ISBI), 1703-1706, 2012.
    [PDF]
  75. Automatic Quantification of Tree-In-Bud Patterns from CT Scans.
    U. Bagci, K. Miller-Jaster, J. Yao, A. Wu, O. Aras, D. J. Mollura
    In: IEEE International Symposium in Biomedical Imaging (ISBI), 1459-1462, 2012.
    [PDF]
  76. Co-segmentation of Functional and Anatomical Images.
    U. Bagci, J. K. Udupa, J. Yao, and D. J. Mollura
    In: Medical Image Computing and Computer-Assisted Intervention (MICCAI), 7512:459-467, 2012.
    [PDF]
  77. Monitoring Pulmonary Fibrosis by Fusing Clinical, Physiological, and Computed Tomography Features.
    Caban, J., J. Yao, U. Bagci, and D. J. Mollura
    In: Conf Proc IEEE Eng Med Biol Soc, 6216-6219, 2011.
    [PDF]
  78. A Graph-Theoretic Approach for Segmentation of PET Images.
    U. Bagci, J. Yao, J. Caban, B. E. Turkbey, O. Aras, D. J. Mollura
    In: Conf Proc IEEE Eng Med Biol Soc, 6479-6482, 2011.
    [PDF]
  79. Automatic Detection of Tree-in-Bud Patterns for Computer Assisted Diagnosis of Respiratory Tract Infections.
    U. Bagci, J. Yao, J. Caban, B. E. Turkbey, O. Aras, D. J. Mollura
    In: Conf Proc IEEE Eng Med Biol Soc, 5096-5099, 2011.
    [PDF]
  80. Learning Shape and Texture Characteristics of CT Tree-in-Bud Opacities for CAD Systems.
    U. Bagci, J. Yao, J. Caban, A. F. Suffredini, T. N. Palmore, D. J. Mollura
    In: Medical Image Computing and Computer-Assisted Intervention (MICCAI), 6893:215-222, 2011.
    [PDF]
  81. Orientation Estimation of Anatomical Structures in Medical Images for Object Recognition.
    U. Bagci, J.K. Udupa, X. Chen
    In: Proc. of SPIE Medical Imaging, 7962:79622L, 2011.
    [PDF]
  82. Intensity Non-Standardness Affects Computer Recognition of Anatomical Structures.
    U. Bagci, J.K. Udupa, X. Chen
    In: Proc. of SPIE Medical Imaging, 7964:79642M, 2011.
    [PDF]
  83. Identification of Spinal Vertebrae Using Mathematical Morphology and Level Set Method.
    P.Lim*, U. Bagci, O. Aras, L.Bai
    In: Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), 3105-3107, 2011.
    [PDF]
  84. A New Prior Shape Model for Level Set Segmentation.
    P.Lim*, U. Bagci, L.Bai
    n: Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications, 7042:125-132, 2011.
    [PDF]
  85. 3-D Automatic Anatomy Segmentation Based on Iterative-Graph-Cut Active Shape Model.
    X.Chen, J.K.Udupa, U. Bagci
    In: Proc. of SPIE Medical Imaging, 7625:76251T, 2010.
    [PDF]
  86. Influences of Standardization on Medical Image Registration.
    U. Bagci, J.K. Udupa, B. Li
    In: Proc. of SPIE Medical Imaging, 7625:76251X, 2010.
    [PDF]
  87. Ball-Scale Based Multi-Object Recognition in a Hierarchical Framework.
    U. Bagci, J.K. Udupa, X. Chen
    In: Proc. of SPIE Medical Imaging, 7623:762345, 2010.
    [PDF]
  88. 3-D Automatic Anatomy Segmentation Based on Graph Cut-Oriented Active Appearance Models.
    Chen, X., J. Yao, Y. Zhuge, U. Bagci
    In: IEEE International Conference on Image Processing (ICIP), 3653-3656, 2010.
    [PDF]
  89. Fully Automatic 3D Reconstruction of Histological Images.
    U. Bagci, L. Bai
    In: IEEE International Symposium on Biomedical Imaging (ISBI), 991-994, 2008.
    [PDF]
  90. Parallel AdaBoost Algorithm for Gabor Wavelet Selection in Face Recognition.
    Chen, X., J. Yao, Y. Zhuge, U. Bagci
    In: IEEE International Conference on Image Processing (ICIP), 1640-1643, 2008.
    [PDF]
  91. Registration of histological images in feature space.
    U. Bagci, L. Bai
    In: SPIE Medical Imaging, 6914:69142V, 2008.
    [PDF]
  92. A Comparison of Daubechies and Gabor Wavelets for Classification of MR Images.
    U. Bagci, L. Bai
    In: IEEE International Conference on Signal Processing and Communications (ICSPC), 676-679, 2007.
    [PDF]
  93. Multi-resolution Elastic Medical Image Registration in Standard Intensity Scale.
    U. Bagci, L. Bai
    In: IEEE Brazilian Symposium on Computer Graphics and Image Processing (SIBGRAPI), 305-312, 2007.
    [PDF]
  94. Inter Genre Similarity Modelling for Automatic Music Genre Classification.
    U. Bagci, E. Erzin
    In: Digital Audio Effects-DAFx, 153-156, 2006.
    [PDF]
  95. Boosting Classifiers for Music Genre Classfication.
    U. Bagci, E. Erzin
    In: International Symposium on Computer and Information Sciences (ISCIS), 33:575-584, 2005.
    [PDF]

    Meeting Abstracts and Technical Reports

  96. Deep Learning for Cardiac MRI: Automatically Segmenting Left Atrium Expert Human Level Performance
    A. Mortazi, J. Burt, U. Bagci
    Radiological Society of North America (RSNA), 103rd Scientific Assembly and Annual Meeting, November 26- December 1, 2017 McCormick Place, Chicago, 2017.
  97. Deep Learning applications in Radiology, Recent Developments, Challenges and Potential Solutions
    S. Hussein, A. Mortazi, H. RaviPrakash, J. Burt, U. Bagci
    Radiological Society of North America (RSNA), 103rd Scientific Assembly and Annual Meeting, November 26- December 1, 2017 McCormick Place, Chicago, 2017.
  98. Machine Learning for Cardiac MRI: Automated Mapping of Left Atrium and Pulmonary Veins at Human Level Performance,
    A. Mortazi, J. Burt, Raul Roya, Maria Marquez U. Bagci
    NASCI (North American Society for Cardiovascular Imaging), October 7-10, 2017 San Antonio, TX, 2017 (Young Investigator Finalist).
  99. Eye Tracking System for Prostate Cancer Diagnosis Using Multi-Parametric MRI
    H. Celik, B. Turkbey, P. Choyke, R. Cheng, E. McCreedy, M. McAuliffe, N. Khosravan, U. Bagci , B. Wood
    25th Annual Conference on ISMRM, Honolulu, Hawai'i, USA 2017.
  100. Deep Learning in Radiology: Recent Advances, Challenges and Future Trends.
    S. Hussein, H. RaviPrakash, U. Teomete, and U. Bagci
    Radiological Society of North America (RSNA), 102nd Scientific Assembly and Annual Meeting, November 27 - December 2, 2016, McCormick Place, Chicago, 2016.
  101. Value of 18F-NaF PET/CT imaging in the assessment of Gorham-Stout disease activity
    G. Z. Papadakis, C. Millo, U. Bagci , N. J. Patronas, M. T. Collins
    29th Annual Conference on European Association of Nuclear Medicine (EANM), European Journal of Nuclear Medicine and Molecular Imaging Supplement 1, Barcelona, Spain 2016.
  102. Plastic Bowing Fractures of the Pediatric Forearm: Evaluation of a Novel Computer Aided Method for Detection.
    U. Teomete, Y. Zhou, O. Dandin, W. Zhao, T. Dandinoglu, O. Osman, and U. Bagci
    Radiological Society of North America (RSNA), 101st Scientific Assembly and Annual Meeting, November 29 - December 4, 2015, McCormick Place, Chicago, 2015.
  103. A New Saliency Metric for Precise Denoising PET Images for Better Visualization and Accurate Segmentation.
    N. Souly, G.Z. Papadakis, U. Teomete, and U. Bagci
    Radiological Society of North America (RSNA), 101st Scientific Assembly and Annual Meeting, November 29 - December 4, 2015, McCormick Place, Chicago, 2015.
  104. From Signal to Screen: The Science Behind Radiologic Images.
    U. Teomete, G.Z. Papadakis, O. Osman, O. Dandin, and U. Bagci
    Radiological Society of North America (RSNA), 101st Scientific Assembly and Annual Meeting, November 29 - December 4, 2015, McCormick Place, Chicago, 2015.
  105. Recent Advances in Techniques for PET Image Denoising and Partial Volume Correction.
    Z. Xu, M. Gao, U. Bagci, and D.J. Mollura
    Radiological Society of North America (RSNA), 101st Scientific Assembly and Annual Meeting, November 29 - December 4, 2015, McCormick Place, Chicago, 2015.
  106. Nuclear Medicine Meets Computer Vision: Increasing Role of Computerized Detection, Tracking, Diagnosis, and Quantification of PET/CT and PET/MRI Studies.
    U. Bagci, GZ Papadakis, Z.Xu, A. Green, M. Osman, M. Shah.
    SNMMI (Society of Nuclear Medicine and Molecular Imaging), 2015.
  107. Brown adipose tissue detected by FDG PET/CT is associated with less central obesity compared to body mass index matched controls.
    Aileen Green, U. Bagci, Patrick V. Kelly, Medhat Osman.
    SNMMI (Society of Nuclear Medicine and Molecular Imaging), 2015.
  108. Brown Adipose Tissue Detected by FDG PET/CT is Associated with Less Visceral Fat.
    Aileen Green, U. Bagci, Patrick V. Kelly, Medhat Osman.
    SNMMI (Society of Nuclear Medicine and Molecular Imaging), 2015.
  109. Improved PET image quantification via iterative denoising and partial volume correction. Z.Xu*, U. Bagci, M. Gao, DJ Mollura.
    SNMMI (Society of Nuclear Medicine and Molecular Imaging), 2015.
  110. The Use of Radiolabelled 18-F-2-Deoxy-2-Fluro-Glucose (18-FDG) in Combined Positron Emission Tomography-Computed Tomography (PET-CT) to Evaluate Infection: Lessons Learned from a Case Series of 23 Patients with Chronic Granulomatous Disease (CGD)
    Amanda K Rudman Spergel, Clara C Chen, Cheryl Ann Beegle, Patricia Littel, Mary Garofalo, Sandra Anaya-O'Brien, Martha Marquesen, U. Bagci, Daniel J Mollura, John I Gallin, Harry L Malech.
    The Journal of Allergy and Clinical Immunology, Volume 2, Issue 135, pages AB98.
  111. Detection and Quantification of Brown Fat Tissue using PET-CT Scans: A Novel Computer Aided Detection System.
    Papadakis, G., U. Bagci, Z.Xu, K.A. Kissell, C.A. Stratakis , DJ Mollura.
    EANM, 2014.
  112. The State-of-the-Art and Recent Advances in Pulmonary Image Analysis Techniques.
    Xu, Z., U. Bagci, A. Mansoor, B.Foster,G.Papadakis, J.K. Udupa, DJ Mollura.
    RSNA, 2014.
  113. Computerized Detection and Classification of Pulmonary Pathologies from CT Images: Current Approaches, Challenges, and Future Trends.
    Mansoor,A., U. Bagci, Z.Xu, B.Foster,G.Papadakis, K.Olivier, J. Elinoff, A, Suffredini, DJ Mollura.
    RSNA, 2014.
  114. Lung Lobe Volumetry as a Reliable Biomarker: Methods for Automatic Extraction of Lobes from CT Scans, and Fissure Integrity Scoring.
    Mansoor,A., U. Bagci, Z.Xu, B.Foster,G.Papadakis, DJ Mollura.
    RSNA, 2014.
  115. Automated Computer-derived SUV and Metabolic Tumor Volume Measurements of biopsy Proven Lesions: Comparison with Radiologist-derived PET-CT Imaging.
    Papadakis, G., U. Bagci, B. Foster, Z.Xu, A.Mansoor, NJ Patronas, C.Stratakis, DJ Mollura.
    RSNA, 2014.
  116. Evaluation of MERS CoV Induced Disease in the Rhesus Macaque by Computed Tomography.
    Johnsson, R.F., U. Bagci, D. J. Mollura, C. J. Bartos, N. Oberlander, M. R. Holbrook, D. Thomas- son, G. G. Olinger, P. B. Jahrling, and L. E. Hensley.
    In ASM Biodefence, 2014.
  117. Evaluation of MERS CoV Induced Disease in Two Species of Nonhuman Primate the Common Marmoset and Rhesus Monkey by Computed Tomography.
    Johnson, R.F., D. J. Mollura, L. E. Via, U. Bagci, N. Oberlande, C. J. Bartos, J. Solomon, J. Johnson, M. R. Holbrook, D. Thomasson, G. G. Olinger, L. E. Hensley, and P. B. Jahrling.
    In 13th International Nidovirus Symposium, 2014.
  118. Multi-focal neutrophil infiltration and inflammation in lungs of ferrets infected with 2009 H1N1 Influenza A virus clinical isolate.
    Camp, JV., U. Bagci, M. Fraigb, H. Guoc, S. M. Uriarte, D. J. Mollura, and C. B. Jonsson.
    In Annual Meeting of American Society for Virology, 2014.
  119. Noise Adaptive Multi-resolution technique to accurately denoise PET,MRI-PET, and PET-CT images.
    A.Mansoor*, U. Bagci, and D. Mollura.
    SNM, 2014.
  120. Recent Advances in PET, PET-CT, and MRI-PET Image Segmentation Techniques.
    U. Bagci, Z.Xu, and D. Mollura.
    SNM, 2014.
  121. Diffusion based enhancement of PET images for improved diagnostic measurements in clinical nuclear medicine.
    Z.Xu*, U. Bagci, and D. Mollura.
    SNM, 2014.
  122. Use of Imaging for development of animal models of Biosafety Level (BSL) 3 and 4 agents.
    G.G. Ollinger, R.F. Johnson, U. Bagci, L. Via, J.Solomon, D.Hammoud, D.J. Mollura, R.C. Reba, N.Oberlander, C. Bartos, D.Douglas, K. Cooper, M.R. Holbrook, L.E. Hensley, P.B. Jahrling.
    World Molecular Imaging Congress, 2014.
  123. Challenges, Techniques, and Advancements for State-of-the-Art PET Image Segmentation.
    Foster*, B., U. Bagci, A. Mansoor, Z. Xu, and D. Mollura.
    RSNA, 2013.
  124. Affinity Propagation Clustering Determines Distributed Uptake Regions in PET Images: A Computer-Aided Approach for Quantification of Pulmonary Infections in Small Animals.
    Foster*, B., U. Bagci, Z. Xu, B. Dey, B. Luna, W. Bishai, S. Jain, and D. Mollura.
    SNM, 2013.
  125. Quantitative Analysis of Infectious Lung Disease from Serial PET-CTScans in Small Animal Models.
    Foster*, B., U. Bagci, Z. Xu, A. Mansoor, B. Luna, B. Dey, W. BIshai, C. Jonnson, S. Jain, and D. Mollura.
    RSNA, 2013.
  126. A Method for Segmenting Multi-Focal Radiotracer Uptake in PET Images to Quantify Tuberculosis in Rabbits.
    Foster*, B., U. Bagci, X. Zu, A. Mansoor, B. Dey, B. Luna, W. Bishai, S. Jain, and D. Mollura.
    RSNA, 2013.
  127. How to Correctly Denoise PET and MRI-PET Images: Current Approaches, Constraints, and Future Trends.
    Mansoor*, A., U. Bagci, B. Foster, Z. Xu, and D. Mollura.
    RSNA, 2013.
  128. A Robust Pathological Lung Segmentation Platform Using Fuzzy-Connectedness with Patient-specific Modeling.
    Mansoor*, A., U. Bagci, B. Foster, Z. Xu, J. Udupa, and D. Mollura.
    RSNA, 2013.
  129. Pathological Lung Segmentation in Computed Tomography (CT) Images.
    Mansoor*, A., U. Bagci, B. Foster, Z. Xu, J. Udupa, and D. Mollura.
    RSNA, 2013.
  130. Accurate Quantification of Brown Adipose Tissue through PET-guided CT Image Segmentation.
    Sandouk*, A., U. Bagci, Z. Xu, A. Mansoor, B. Foster, and D. Mollura.
    SNM, 2013.
  131. A Computational Platform for Quantification of Infectious Lung Disease Using PET-CT Imaging.
    U. Bagci, B. Foster, Z. Xu, B. Luna, B. Dey, W. Bishai, C. Jonsson, S. Jain, and D. Mollura.
    SNM, 2013.
  132. Simultaneous Segmentation from Hybrid MRI-PET and PET-CT Images Using Fuzzy Connectedness Image Co-segmentation.
    Xu*, Z., U. Bagci, J. Udupa, and D. Mollura.
    RSNA, 2013.
  133. Qualitative and Quantitative Analysis of Inflammation in Pulmonary Tuberculosis in Rabbit using F18-FDG-PET/CT Imaging: A multi-Parametric Approach.
    Luna, B. B., K.Miller-Jaster, B. Foster, U. Bagci, D. Mollura, S. Jain, and W. Bishai.
    In: Molecular Imaging of Infectious Diseases: Current Status and Future Challenges, 2012.
  134. Accurate and Robust Quantification of Hybrid MRI-PET and PET-CT Images through a Novel Joint-Segmentation Method.
    N.Mendhiratta*, Z. Xu*, B. Foster*, U. Bagci, and D. Mollura.
    In: Molecular Imaging of Infectious Diseases: Current Status and Future Challenges (BEST POSTER PRIZE), 2012.
  135. Correlation of Anatomical and Functional Information from PET-CT Images.
    U. Bagci, O. Aras, and D. Mollura.
    SNM, 2012.
  136. Automatic Segmentation Methods for Abnormal Activities from PET, PET-CT, and MRI-PET Images.
    U. Bagci, J. Udupa, K. Jaster-Miller, D. Mollura.
    RSNA,, 2012.
  137. Simultaneous Segmentation of Abnormal Activities from Hybrid MRI-PET.
    U. Bagci, J. Udupa, K.Jaster-Miller, D. Mollura.
    RSNA (highlighted at AuntMinnie), 2012.
  138. Computer-based Quantitative Modeling of Chest CT findings in Pulmonary Hypertension and its Association with Physiologic and Clinical Variables.
    Caban, J., J. Yao, U. Bagci, and D. J. Mollura.
    RSNA, 2011.
  139. Quantitative Measurements of Chest CT Using Texture Analysis (RSNA MERIT AWARD).
    Caban, J., J. Yao, U. Bagci, and D. J. Mollura.
    RSNA, 2011.
  140. Registration, Reconstruction, and Analysis of Serial Histological Sections.
    U. Bagci, X. Chen, L. Bai, D. Mollura, B. Turkbey, and O. Aras.
    RSNA, 2011.
  141. Model Based Segmentation Methods: Multi-Organ Segmentation Platform.
    U. Bagci, X. Chen, J. K. Udupa, L. Bai, D. J. Mollura, B. Turkbey, and O. Aras.
    RSNA, 2011.
  142. Quantitative Assessment of Multiple Sclerosis (MS) Lesions in Longitudinal MRI Studies.
    U. Bagci, X. Chen, J. K. Udupa, B. Li, S. Messian, B. Turkbey, and O. Aras.
    RSNA, 2011.
  143. Automated Analysis of Multi-detector CT images for Preoperative Assessment of Living Renal Donors.
    U. Bagci, X. Chen, J. Udupa, S. Histed, S.Perez-Pujol, B. Turkbey, and O. Aras.
    RSNA, 2011.
  144. Is There a Reliable Correlation Between computer-aided diagnosis (CAD) Results from CT Images and Information from PET Images in Longitudinal Studies: An Example Study in Interstitial Lung Disease.
    U. Bagci, B. Turkbey, S. Perez-Pujol, D. Mollura, and O. Aras.
    RSNA, 2011.
  145. Characteristics of Shape Functional in Iterative Graph Cut Active Shape Model Segmentation (IGCASM).
    U. Bagci and X.Chen.
    Tech. rep. NIH, Technical Report, 2011.
  146. CAD for Pulmonary Infections: Automatic Detection of Tree-in-Bud Opacities.
    U. Bagci, J. Yao, J. Caban, T. N. Palmore, A. F. Suffredini, and D. J. Mollura.
    RSNA, 2011.
  147. Quantification of Small Airway Pulmonary Infections: Subjective Visual Grading versus Objective Quantification Through a CAD System.
    U. Bagci, J. Yao, J. Caban, T. Palmore, A. Suffredini, A. Wu, and D. Mollura.
    RSNA, 2011.
  148. Automatic Anatomy Recognition and Registration.
    U. Bagci.
    PhD thesis. University of Nottingham, 2010.
  149. The Role of Standardization in Medical Image Registration.
    U. Bagci and J. K. Udupa.
    Tech. rep. MIPG Technical Report-341, 2008.
  150. Towards Efficient Medical Image Registration Methods.
    U. Bagci and J. K. Udupa.
    In: Marie Curie Workshop-Barcelona, 2008.
  151. Fundamental Issues of Registration: Applications for change analysis in health and disease.
    U. Bagci (2007).
    Tech. rep. CMIAG Technical Report, 2007.
  152. Boosting Classifiers for Automatic Music Genre Classification.
    U. Bagci
    Tech. rep. MSc Thesis, Koc, University, 2005.

Contact

[Ulas Bagci in 2015]
Ulas Bagci in 2009
Name: Ulas Bagci
Email:
URL: http://www.cs.ucf.edu/~bagci
Work number: (+1) 407-823-1047
Fax number: (+1) 407-823-0594
CRCV Assistant: Tonya LaPrarie
Mailing address: Dr. Ulas Bagci
Center for Research in Computer Vision (CRCV)
4328 Scorpius Street, HEC 221, UCF

Orlando, Florida 32816, USA.

Last updated February, 2017 by Ulas Bagci.