Journal papers

  1. X Zhang, RD Badawi, SR Cherry, J Qi, “Theoretical study of the benefit of long axial field-of-view PET on region of interest quantification,” Physics in Medicine and Biology, 2018
  2. K Gong, J Cheng-Liao, G Wang, K Chen, C Catana, and J Qi, “Direct Patlak reconstruction from dynamic PET data using the kernel method with MRI information based on structural similarity,” IEEE Transactions on Medical Imaging, 37(4), 955-965, 2018.
  3. E Berg, X Zhang, J Bec, MS Judenhofer, B Patel, Q Peng, M Kapusta, M Schmand, M Casey, AF Tarantal, J Qi, RD Badawi, and SR Cherry, “Development and evaluation of mini-EXPLORER: a long axial field-of-view PET scanner for non-human primate imaging,” J Nucl Med, 2018.
  4. X Zhang, Q Peng, J Zhou, J Huber, WW Moses, and J Qi, “Lesion detection and quantification performance of the Tachyon-I time-of-flight PET scanner: phantom and human studies,” Physics in Medicine and Biology, 63(6):065010, 2018
  5. G Wang, J Zhou, Z Yu, W Wang and J Qi, “Hybrid pre-log and post-log image reconstruction for computed tomography,” IEEE Transactions on Medical Imaging, 36(12):2457-2465, 2017
  6. K Gong, J Zhou, M Tohme, M Judenhofer, Y Yang, J Qi,”Sinogram Blurring Matrix Estimation from Point sources Measurements with Rank-One Approximation for Fully 3D PET“, IEEE TMI, 2017
  7. M Zhang, J Zhou, X Niu, E Asma, W Wang and J Qi,”Regularization parameter selection for penalized-likelihood list-mode image reconstruction in PET“,Physics in medicine and biology, 62(12), 5114.
  8. AZ Kyme, M Judenhofer, K Gong, J Bec, A Selfridge, J Du, J Qi, S Cherry, S Meikle, “Open-field mouse brain PET: design optimisation and detector characterisation“, Physics in medicine and biology, 62(15), 6207.
  9. X Zhang,  J Zhou, SR Cherry, RD Badawi and J Qi, “Quantitative image reconstruction for total-body PET imaging using the 2-meter long EXPLORER scanner“, Physics in medicine and biology, 62(6), 2465.
  10. W Hutchcroft, G Wang, K T Chen, C Catana and Jinyi Qi,”Anatomically-aided PET reconstruction using the kernel method“, Physics in Medicine and Biology, 2016, 61(18): 6668.
  11. E Berg, E Roncali, W Hutchcroft, J Qi and Simon Cherry,”Improving depth, energy and timing estimation in PET detectors with deconvolution and maximum likelihood pulse shape discrimination“,  IEEE transactions on medical imaging, 2016, 35(11): 2436-2446.
  12. Y Yang, J Bec, J Zhou, M Zhang, M S Judenhofer, X Bai, K Di, Y Wu, M Rodriguez, P Dokhale, K S Shah, R Farrell, J Qi, S R Cherry, “A Prototype High-Resolution Small-Animal PET Scanner Dedicated to Mouse Brain Imaging,” Journal of Nuclear Medicine, 2016, 57(7): 1130-1135.
  13. K Gong, S Majewski, P E Kinahan, R L Harrison, B F Elston, R Manjeshwar, S Dolinsky, A V Stolin, J A Brefczynski-Lewis and J Qi, “Designing a compact high performance brain PET scanner—simulation study”, Physics in medicine and biology, 2016, 61(10): 3681.
  14. L Yang, G Wang, J Qi, “Theoretical Analysis of Penalized Maximum-Likelihood Patlak Parametric Image Reconstruction in Dynamic PET for Lesion Detection,” IEEE transactions on medical imaging, 2016, 35(4): 947-956.
  15. K Gong,S R Cherry , J Qi, “On the assessment of spatial resolution of PET systems with iterative image reconstruction,” Physics in medicine and biology, 2016, 61(5): N193.
  16. M Zhang, J Zhou,Y Yang, M R Villafuerte, J Qi, “Efficient system modeling for a small animal PET scanner with tapered DOI detectors,” Physics in medicine and biology, 2015, 61(2): 461.
  17. G Wang, J Qi, “Edge-preserving PET image reconstruction using trust optimization transfer,” IEEE transactions on medical imaging, 2015, 34(4): 930-939.
  18. Q Peng, W S Choong, C Vu , JS Huber, M Janecek, D Wilson, RH Huesman, J Qi, J Zhou, WW Moses, “Performance of the tachyon time-of-flight PET camera,” IEEE transactions on nuclear science, 2015, 62(1): 111-119.
  19. J K Poon, M L Dahlbom, M E Casey, J Qi, S R Cherry, R D Badawi, “Validation of the SimSET simulation package for modeling the Siemens Biograph mCT PET scanner,” Physics in medicine and biology, 2015, 60(3): N35.
  20. D Gorpas, H Fatakdawala, J Bec, D Ma, D R Yankelevich, J Qi, L Marcu,”Fluorescence lifetime imaging and intravascular ultrasound: co-registration study using ex vivo human coronaries,” IEEE transactions on medical imaging, 2015, 34(1): 156-166.
  21. Wang G, Qi J, “PET image reconstruction using kernel method, ” IEEE transactions on medical imaging, 2015, 34(1): 61-71.
  22. L Yang, A Ferrero, R J Hagge, R D Badawi and J Qi, “Evaluation of penalty design in penalized maximum-likelihood image reconstruction for lesion detection,” Journal of Medical Imaging, 1(3): 035501-1–7, 2014
  23. L Yang, J Zhou, A Ferrero, R D Badawi and J Qi, “Regularization design in penalized maximum-likelihood image reconstruction for lesion detection in 3D PET,” Physics in Medicine and Biology, 59:403-419, 2014.
  24. G Wang and J Qi, “Direct Estimation of Kinetic Parametric Images for Dynamic PET,” Theranostics 2013; doi:10.7150/thno.5130 (invited review)
  25. A Rahmim, J Qi, and V Sossi, “Resolution modeling in PET imaging: Theory, practice, benefits, and pitfalls,” Medical Physics, 40(5):064301 (15 pages), 2013.
  26. G Wang and J Qi, “An optimization transfer algorithm for nonlinear parametric image reconstruction from dynamic PET data,” IEEE Transactions on Medical Imaging, 31(10):1977-1988, 2012.
  27. G Wang and J Qi, “Penalized likelihood PET image reconstruction using patch-based edge-preserving regularization,” IEEE Transactions on Medical Imaging, 31(12):2194-2204, 2012.
  28. J Liu, Y Sun, J Qi, and L Marcu, “A novel method for fast and robust estimation of fluorescence decay dynamics using constrained least-square deconvolution with Laguerre expansion,” Physics in Medicine and Biology, Physics in Medicine and Biology, 57:843-865, 2012.
  29. J. Qi, Y. Yang, J. Zhou, Y. Wu, S. R. Cherry, “Experimental Assessment of Resolution Improvement of a Zoom-in PET,” Physics in Medicine and Biology, 56:N165-N174, 2011.
  30. J Zhou and J Qi, “Fast and efficient fully 3D PET image reconstruction using sparse system matrix factorization with GPU acceleration,” Physics in Medicine and Biology, 56:6739-6757, 2011.
  31. J Cheng-Liao and J Qi, “PET image reconstruction with anatomical edge guided level set prior,” Physics in Medicine and Biology, 56:6899-6918, 2011.
  32. Y Yang, S St James, Y Wu, H Du, J Qi, R Farrell, PA Dokhale, KS Shah, K Vaigneur, and SR Cherry, “Tapered LSO Arrays for Small Animal PET,” Physics in Medicine and Biology, 56:139-154, 2011.
  33. J Zhou and J Qi, “Adaptive imaging for lesion detection using a zoom-in PET system,” IEEE Transactions on Medical Imaging, 30:119-130,2011.
  34. MS Tohme and J Qi, “Iterative reconstruction of Fourier-rebinned PET data using sinogram blurring function estimated from point source scans,” Medical Physics, 37:5530-5540, 2010.
  35. L Fu and J Qi, “A Residual Correction Method for High-Resolution PET Reconstruction with Application to On-the-fly Monte Carlo-Based Model of Positron Range,” Medical Physics, 37(2):704-713, 2010.
  36. G Wang and J Qi, “Acceleration of direct reconstruction of linear parametric images using nested algorithms,” Physics in Medicine and Biology, 55:1505-1517, 2010.
  37. J Cheng-Liao and J Qi, “Dynamic PET image segmentation using a multiphase level set method,” Physics in Medicine and Biology, 55:6549-6569, 2010.
  38. N Cao, RH Huesman, WW Moses, and J Qi, “Detection Performance Analysis for Time-of-Flight PET,” Physics in Medicine and Biology, 55:6931-6950, 2010.
  39. S St James, Y Yang, SL Bowen, J Qi and SR Cherry, “Simulation study of spatial resolution and sensitivity for the tapered depth of interaction PET detectors for small animal imaging,” Physics in Medicine and Biology, 55:N63-N74, 2010.
  40. S. Qin, JW Seo, H. Zhang, J Qi, FE Curry, and KW Ferrara, “An imaging-driven model for liposomal stability and circulation,” Molecular Pharmaceutics, 7(1):12-21, 2010.
  41. J Zhou and J Qi, “Theoretical analysis and simulation study of a high-resolution zoom-in PET system,” Physics in Medicine and Biology, 54:5193-5208, 2009.
  42. G Wang and J Qi, “Generalized algorithms for direct reconstruction of parametric images from dynamic PET data,” IEEE Transactions on Medical Imaging, 28(11):1717-1726, 2009.
  43. C Li, G Wang, J Qi, and SR Cherry, “PET Guided Three-Dimensional Fluorescence Optical Tomography in Small Animal Imaging,” Optics Letters, 34(19):2933-2035, 2009.
  44. S. Qin, JW Seo, H. Zhang, J Qi, FE Curry, and KW Ferrara, “An imaging-driven model for liposomal stability and circulation,” Molecular Pharmaceutics, 2009, in press.
  45. SL Bowen, Y Wu, AJ Chaudhari, L Fu, NJ Packard, GW. Burkett, K Yang, KK Lindfors, DK Shelton, AD Borowsky, SR Martinez, J Qi, JM Boone, SR Cherry, and RD Badawi, “Initial Characterization of a Combined and Dedicated Breast PET/CT,” Journal of Nuclear Medicine, 50(9):1401-1408, 2009.
  46. G Wang, L Schultz, and J Qi, “Statistical image reconstruction for muon tomography using a Gaussian scale mixture model,” IEEE Transactions on Nuclear Science, 56(4):2480-2486, 2009.
  47. Y Wu, C Catana, R Farrell, PA Dokhale, KS Shah, J Qi, and SR Cherry, “PET Performance Evaluation of an MR-Compatible PET Insert,” IEEE Transactions on Nuclear Science, 56(3):574-580, 2009.
  48. Michel Tohme and J Qi, “Iterative image reconstruction for positron emission tomography based on detector response function estimated from point source measurements,” Physics in Medicine and Biology, 54 (12):3709-3725, 2009.
  49. Y Yang, J. Qi, Y. Wu, S St. James, R Farrell, PA Dokhale, KS Shah, and SR Cherry, “Depth of interaction calibration for PET detectors with dual-ended readout by PSAPDs,” Physics in Medicine and Biology, vol. 54, pp. 433-445, 2009.
  50. L Fu, JR Stickel, R Badawi, and J Qi, “Quantitative Accuracy of Penalized-Likelihood Reconstruction for ROI Activity Estimation,” IEEE Transactions on Nuclear Science, 56 (1):167-172, 2009
  51. G Wang and J Qi, “Analysis of Penalized Likelihood Image Reconstruction for Dynamic PET Quantification,” IEEE Transactions on Medical Imaging, 28 (4):608-620, 2009.
  52. G Wang, L Schultz, and J Qi, “Bayesian Image Reconstruction for Improving Detection Performance of Muon Tomography,” IEEE Transactions on Image Processing, 18 (5):1080-1089, 2009.
  53. Y Wu, SL Bowen, K Yang, N Packard, L Fu, G Burkett Jr, J Qi, JM Boone, SR Cherry and RD Badawi, “PET characteristics of a dedicated breast PET/CT scanner prototype,” Physics in Medicine and Biology, 54 (13):4273-4287, 2009.
  54. H Zhang, J Kusunose, A Kheirolomoom, JW Seo, J Qi, K Watson, H Lindfors, E Ruoslahti, JL Sutcliffe, KW Ferrara, “Dynamic imaging of arginine-rich heart-targeted vehicles in a mouse model,” Biomaterials, Vol. 29, pp. 1976-1988, 2008.
  55. C Catana, Y Wu, MS Judenhofer, J Qi, BJ Pichler and SR Cherry, “Simultaneous in vivo Imaging with Positron Emission Tomography and Magnetic Resonance Imaging,” PNAS, Vol. 105, pp. 3705-3710, 2008.
  56. Y Yang, Y Wu, J Qi, S St. James, H Du, PA Dokhale, KS Shah, R Farrell and SR Cherry, “A Prototype PET Scanner with DOI-Encoding Detectors,” Journal of Nuclear Medicine, Vol. 49, pp. 1132-1140, 2008.
  57. G. Wang, L. Fu, and J. Qi, ” Maximum a posteriori reconstruction of Patlak parametric image from sinograms in dynamic PET,” Physics in Medicine and Biology, Vol. 53, pp. 593-604, 2008.
  58. J. R. Stickel, J. Qi, and S. R. Cherry, ” Fabrication and characterization of a 0.5 mm LSO detector array for high resolution PET applications,” Journal of Nuclear Medicine, Vol. 48, pp. 115-121, 2007.
  59. J. Qi and R. M. Leahy, “Iterative reconstruction techniques in emission computed tomography,” Physics in Medicine and Biology, Vol. 51, pp. R541-R578, 2006 (invited).
  60. C. Catana, Y. Wu, M. S. Judenhofer, J. Qi, B. J. Pichler, and S. R. Cherry, ” Simultaneous Acquisition of MultiSlice PET and MR Images – Initial Results with a MR-Compatible PET Scanner, ” Journal of Nuclear Medicine, Vol. 47, pp. 1968-1976, 2006.
  61. J. S. Huber, W. S. Choong, W. W. Moses, J. Qi, J. Hu, G. C. Wang, D. Wilson, S. Oh, R. H. Huesman, S. E. Derenzo, and T. F. Budinger, “Initial Results of a Positron Tomograph for Prostate Imaging,” IEEE Transactions on Nuclear Science, Vol. 53, pp. 2653-2659, 2006.
  62. J. Qi, “Calculation of the sensitivity image for list mode reconstruction,” IEEE Transactions on Nuclear Science, Vol. 53, pp. 2746-2751, 2006.
  63. J. Qi and R. H. Huesman. “Penalized maximum-likelihood image reconstruction for lesion detection,” Physics in Medicine and Biology, Vol. 51, pp. 4017-4029, 2006.
  64. J. Qi, “Investigation of Lesion Detection in MAP Reconstruction with Non-Gaussian Priors,” International Journal on Biomedical Imaging, vol. 2006, Article ID 87567, 2006.
  65. J. Qi and R. H. Huesman, “Theoretical study of penalized-likelihood image reconstruction for region of interest quantification,” IEEE Transactions on Medical Imaging, Vol. 25, pp. 640-648, 2006.
  66. R. Namba, L. Young, C. Abbey, L. Kim, A. Borowsky, J. Qi, S. Cherry, C.Tepper, R. Cardiff, and J. Gregg, “Rapamycin inhibits growth of premalignant and malignant mammary lesions in a mouse model of DCIS,” Clinical Cancer Research, Vol. 12, No. 8, pp. 2613-2621, 2006.
  67. G-C Wang, J. S. Huber, W. W. Moses, J. Qi, and W-S Choong, “Characterization of the LBNL PEM camera,” IEEE Transactions on Nuclear Science, Vol. 53, pp. 1129-1135, 2006.
  68. J. Qi, “Comparison of statistical reconstructions with isotropic and anisotropic resolution,” IEEE Transactions on Nuclear Science, Vol. 53, pp. 147-151, 2006.
  69. J. Qi and R. H. Huesman, “Effect of errors in the system matrix on iterative image reconstruction,” Physics in Medicine and Biology, Vol. 50, pp. 3297-3312, 2005.
  70. J. Hu, K. Tam, and J. Qi, “An approximate short scan helical FDK cone beam algorithm based on nutating curved surfaces satisfying the Tuy’s condition,” Medical Physics, Vol. 32, No. 6, pp. 1527-1536, 2005.
  71. J. Qi, “Noise propagation in iterative image reconstruction with line searches,” IEEE Transactions on Nuclear Science, Vol. 52, No. 1, pp. 57-62, 2005.
  72. J. Qi, J. S. Huber, R. H. Huesman, W. W. Moses, S. E. Derenzo, and T. F. Budinger, “Septa design for a prostate specific PET camera,” IEEE Transactions on Nuclear Science, Vol. 52, No. 1, pp. 107-113, 2005.
  73. J. Qi and R. H. Huesman, “Propagation of errors from the efficiency image in list mode reconstruction,” IEEE Transactions on Medical Imaging, Vol. 23, No. 9, pp. 1094-1099, 2004.
  74. Q. Li, E. Asma, J. Qi, and R. M. Leahy, “Accurate estimation of Fisher information matrix in MAP reconstruction,” IEEE Transactions on Medical Imaging, Vol. 23, No. 9, pp. 1057-1064, 2004.
  75. W. W. Moses and J. Qi, “Instrumentation optimization for positron emission mammography,” Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 527, No. 1-2, pp. 76-82, 2004.
  76. J. Qi and R. H. Huesman, “Wavelet crosstalk matrix and its application to assessment of shift-variant imaging systems,” IEEE Transactions on Nuclear Science, Vol. 51, No.1, pp. 123-129, 2004.
  77. J. Qi, “Analysis of Lesion Detectability in Bayesian Emission Reconstruction with Non-stationary Object Variability,” IEEE Transactions on Medical Imaging, Vol. 23, No. 3, pp. 321-329, 2004.
  78. J. Qi, “A Unified Noise Analysis for Iterative Image Estimation,” Physics in Medicine and Biology, Vol. 48, pp. 3505-3519, 2003.
  79. J. S. Huber, W. S. Choong, J. Wang, J. S. Maltz, J. Qi, E. Mandelli, and W. W. Moses, “Development of the LBNL positron emission mammography camera,” IEEE Transactions on Nuclear Science, Vol. 50, No. 5, pp. 1650-1653, 2003.
  80. W. W. Moses and J. Qi, “Fundamental limits of positron emission mammography,” Nuclear Instruments and Methods in Physics Research Section A, Vol. 497, No. 1, pp. 82-89, 2003.
  81. J. Qi, R. H. Huesman, G. J. Klein, C. Kuo, W. W. Moses, and B. W. Reutter, “Comparison of Rectangular and Planar Positron Emission Mammography Scanners,” IEEE Transactions on Nuclear Science, Vol. 49, No. 5, pp. 2089-2096, 2002.
  82. J. Qi and R. H. Huesman, “Scatter Correction for Positron Emission Mammography,” Physics in Medicine and Biology, Vol. 47, No. 15, pp. 2759-2772, 2002.
  83. D. Shattuck, J. Rapela, E. Asma, A. Chatziioannou, J. Qi, and R. Leahy, “Internet2-based 3D PET Image Reconstruction using A PC Cluster,” Physics in Medicine and Biology, Vol. 47, No. 15, pp. 2785-2796, 2002.
  84. T. E. Nichols, J. Qi, E Asma, and R. M. Leahy, “Spatiotemporal reconstruction of list mode PET data,” IEEE Transactions on Medical Imaging, Vol. 21, No. 4, pp. 396-404, 2002.
  85. J. Qi and R. H. Huesman, “Theoretical study of lesion detectability of MAP reconstruction using computer observers,” IEEE Transactions on Medical Imaging, Vol. 20, No. 8, pp. 815-822, 2001.
  86. P. R. G. Virador, W. W. Moses, R. H. Huesman, and J. Qi, “3D Reconstruction in PET Cameras with Irregular Sampling and Depth of Interaction,” IEEE Transactions on Nuclear Science, Vol. 48, No. 4, pp. 1524-1529, 2001.
  87. J. S. Huber, S. E. Derenzo, J. Qi, W. W. Moses, R. H. Huesman, and T. F. Budinger, “Conceptual Design of a Compact Positron Tomograph for Prostate Imaging,” IEEE Transactions on Nuclear Science, Vol. 48, No. 4, pp. 1506-1511, 2001.
  88. J. Qi, G. J. Klein, and R. H. Huesman, “Image Properties of List Mode Likelihood Reconstruction for a Rectangular Positron Emission Mammography with DOI Measurements,” IEEE Transactions on Nuclear Science, Vol. 48, No. 4, pp. 1343-1349, 2001.
  89. J. Qi, “Optimization of PET System Design for Lesion Detection,” IEEE Transactions on Nuclear Science, Vol. 48, No. 4, pp. 1470-1476, 2001.
  90. P. Bonetto, J. Qi and R. M. Leahy, “Covariance approximation for fast and accurate computation of Channelized Hotelling Observer Statistics,” IEEE Transactions on Nuclear Science, Vol. 47, No. 4, pp. 1567-1572, 2000.
  91. R. H. Huesman, G. J. Klein, W. W. Moses, J. Qi, B.W. Reutter, and P. R. G. Virador, “List mode maximum likelihood reconstruction applied to positron emission mammography with irregular sampling,” IEEE Transactions on Medical Imaging, Vol. 19, No. 5, pp. 532-537, 2000.
  92. A. Chatziioannou, J. Qi, A. Annala, A. Moore, R. M. Leahy, and S. R. Cherry, “Comparison of 3D MAP and FBP algorithms for image reconstruction in microPET,” IEEE Transactions on Medical Imaging, Vol. 19, No. 5, pp. 507-512, 2000.
  93. J. Qi and R. M. Leahy, “Resolution and noise properties MAP reconstruction for fully 3D PET,” IEEE Transactions on Medical Imaging, Vol. 19, No. 5, pp. 493-506, 2000.
  94. R. M. Leahy and J. Qi, “Statistical approaches in quantitative positron emission tomography,” Statistics and Computing, invited paper, Vol. 10, No. 2, pp. 147-165, 2000.
  95. T. H. Farquhar, J. Llacer, C. K. Hoh, J. Czernin, S. S. Gambhir, M. A. Seltzer, D. H. S. Silverman, J. Qi, C. Hsu, and E. J. Hoffman, “ROC and localization ROC analyses of lesion detection in whole-body FDG PET: effects of acquisition mode, attenuation correction and reconstruction algorithm,” Journal of Nuclear Medicine, Vol. 40, No. 12, pp. 2043-2052, 1999.
  96. J. Qi and R. M. Leahy, “A theoretical study of the contrast recovery and variance of MAP reconstructions from PET data,” IEEE Transactions on Medical Imaging, Vol. 18, No. 4, pp. 293-305, 1999.
  97. J. Qi, R. M. Leahy, C-H Hsu, T. H. Farquhar, and S. R. Cherry, “Fully 3D Bayesian image reconstruction for the ECAT EXACT HR+,” IEEE Transactions on Nuclear Science, Vol. 45, No. 3, pp. 1096-1103, 1998.
  98. J. Qi, R. M. Leahy, S. R. Cherry, A. Chatziioannou, and T. H. Farquhar, “High resolution 3D Bayesian image reconstruction using the microPET small animal scanner,” Physics in Medicine and Biology, Vol. 43, No. 4, pp. 1001-1013, 1998.
  99. Z. Zhou, R. M. Leahy, and J. Qi, “Approximate maximum likelihood hyperparameter estimation for Gibbs priors,” IEEE Transactions on Image Processing, Vol. 6, pp. 844-861, 1997.
  100. J. Qi, S. Gao, and F. Yang, “An assessment on the wideband and narrowband methods for ultrasonic blood flow measurements,” Chinese Journal of Acoustics. Vol. 16, No. 1, pp. 59-70, 1997. (in English)
  101. Y. An, Y. Huang, J. Qi, Y. Chao, M. Li, and S. Gao, “A new digital scan converter with high performance cost ratio,” Chinese Journal of Ultrasound in Medicine, Vol. 9, No. 3, pp. 189-191, 1993.

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