Jim Gee

Jim's major area of interest is biomedical image analysis and computing, with active research in all of the quantitative methods represented, including segmentation, registration, morphometry and shape statistics, as applied to a variety of organ systems and all of the major and emerging modalities in biological/biomaterials imaging and in vivo medical imaging.


publications

Select Articles
  1. B. B. Avants, C. L. Epstein, M. Grossman, and J. C. Gee, "Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain," Medical Image Analysis, vol. 12, iss. 1, pp. 26–41, 2008.
  2. J. C. Gee, "Digital Brain Atlases for Biomedicine," IEEE Signal Processing Magazine, vol. 25, iss. 1, pp. 138–141, 2008.
  3. J. Kim, B. B. Avants, S. Patel, J. Whyte, B. H. Coslett, J. Pluta, J. A. Detre, and J. C. Gee, "Structural consequences of diffuse traumatic brain injury: a large deformation tensor-based morphometry study," NeuroImage, vol. 39, iss. 3, pp. 1014–1026, 2008.
  4. S. Kiryu, T. Sundaram, S. Kubo, K. Ohtomo, T. Asakura, J. C. Gee, H. Hatabu, and M. Takahashi, "MRI assessment of lung parenchymal motion in normal mice and transgenic mice with sickle cell disease," Journal of Magnetic Resonance Imaging, vol. 27, iss. 1, pp. 49–56, 2008.
  5. M. Siqueira, L. J. Latecki, N. J. Tustison, J. Gallier, and J. C. Gee, "Topological Repairing of 3D Digital Images," Journal of Mathematical Imaging and Vision, vol. 30, iss. 3, pp. 249–274, 2008.
  6. P. A. Yushkevich, H. Zhang, T. J. Simon, and J. C. Gee, "Structure-specific statistical mapping of white matter tracts," NeuroImage, vol. 41, iss. 2, pp. 448–461, 2008.
  7. G. K. Aguirre, A. Komáromy, A. V. Cideciyan, D. H. Brainard, T. S. Aleman, A. J. Roman, B. B. Avants, J. C. Gee, M. Korczykowski, W. W. Hauswirth, G. M. Acland, and G. D. Aguirre, "Canine and human visual cortex intact and responsive despite early retinal blindness from RPE65 mutation," PLoS Medicine, vol. 4, iss. 6, p. 230, 2007.
  8. B. B. Avants, C. Anderson, M. Grossman, and J. C. Gee, "Spatiotemporal normalization for longitudinal analysis of gray matter atrophy in frontotemporal dementia," in Proc. Medical Image Computing and Computer-Assisted Intervention, Heidelberg, 2007, pp. 303–310.
  9. B. B. Avants, H. Hurt, J. M. Giannetta, C. L. Epstein, D. M. Shera, H. Rao, J. Wang, and J. C. Gee, "Effects of heavy in utero cocaine exposure on adolescent caudate morphology," Pediatric Neurology, vol. 37, iss. 4, pp. 275–279, 2007.
  10. S. P. Awate and J. C. Gee, "A fuzzy, nonparametric segmentation framework for DTI and MRI analysis," in Proc. Information Processing in Medical Imaging, Heidelberg, 2007, pp. 296–307.
  11. S. P. Awate, H. Zhang, and J. C. Gee, "Fuzzy nonparametric DTI segmentation for robust cingulum-tract extraction," in Proc. Medical Image Computing and Computer-Assisted Intervention, Heidelberg, 2007, pp. 294–301.
  12. S. P. Awate, H. Zhang, and J. C. Gee, "A fuzzy, nonparametric segmentation framework for DTI and MRI analysis: with applications to DTI-tract extraction," IEEE Transactions on Medical Imaging, vol. 26, iss. 11, pp. 1525–1536, 2007.
  13. Y. Fan, H. Rao, H. Hurt, J. M. Giannetta, M. Korczykowski, D. M. Shera, B. B. Avants, J. C. Gee, J. Wang, and D. Shen, "Multivariate examination of brain abnormality using both structural and functional MRI," NeuroImage, vol. 36, iss. 4, pp. 1189–1199, 2007.
  14. J. C. Gee and P. M. Thompson, "Guest editorial: Special Issue on Computational Neuroanatomy," IEEE Transactions on Medical Imaging, vol. 26, iss. 4, pp. 425–426, 2007.
  15. A. M. C. Machado, T. J. Simon, V. Nguyen, D. M. McDonald-McGinn, E. H. Zackai, and J. C. Gee, "Corpus callosum morphology and ventricular size in chromosome 22q11.2 deletion syndrome," Brain Research, vol. 1131, iss. 1, pp. 197–210, 2007.
  16. L. Ng, S. Pathak, C. Kuan, C. Lau, H. Dong, A. Sodt, C. Dang, B. B. Avants, P. A. Yushkevich, J. C. Gee, D. R. Haynor, E. Lein, A. Jones, and M. Hawrylycz, "Neuroinformatics for genome-wide 3D gene expression mapping in the mouse brain," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4, iss. 3, pp. 382–393, 2007.
  17. S. Novais-Santos, J. C. Gee, M. Shah, V. Troiani, M. Work, and M. Grossman, "Resolving sentence ambiguity with planning and working memory resources: Evidence from fMRI," NeuroImage, vol. 37, iss. 1, pp. 361–378, 2007.
  18. H. Rao, J. Wang, J. M. Giannetta, M. Korczykowski, D. M. Shera, B. B. Avants, J. C. Gee, J. A. Detre, and H. Hurt, "Altered resting cerebral blood flow in adolescents with in utero cocaine exposure revealed by perfusion functional MRI," Pediatrics, vol. 120, iss. 5, p. e1245–e1254, 2007.
  19. T. P. Schoenemann, J. C. Gee, B. B. Avants, R. L. Holloway, J. Monge, and J. E. Lewis, "Validation of plaster endocast morphology through 3D CT image analysis," American Journal of Physical Anthropology, vol. 132, iss. 2, pp. 183–192, 2007.
  20. H. Sun, P. A. Yushkevich, H. Zhang, P. A. Cook, J. T. Duda, T. J. Simon, and J. C. Gee, "Shape-based normalization of the corpus callosum for (DTI) connectivity analysis," IEEE Transactions on Medical Imaging, vol. 26, iss. 9, pp. 1166–1178, 2007.
  21. M. Takahashi, S. Kubo, S. Kiryu, J. C. Gee, and H. Hatabu, "MR microscopy of the lung in small rodents," European Journal of Radiology, vol. 64, iss. 3, pp. 367–374, 2007.
  22. N. J. Tustison, B. B. Avants, and J. C. Gee, "Gridding Graphic Graticules," Insight Journal, vol. 1, p. i, 2007. [url]
  23. P. A. Yushkevich, J. A. Detre, D. Mechanic-Hamilton, M. A. Fernández-Seara, K. Z. Tang, A. Hoang, M. Korczykowski, H. Zhang, and J. C. Gee, "Hippocampus-specific fMRI group activation analysis using the continuous medial representation," NeuroImage, vol. 35, iss. 4, pp. 1516–1530, 2007.
  24. H. Zhang, B. B. Avants, P. A. Yushkevich, J. Woo, S. Wang, L. F. McCluskey, L. B. Elman, E. R. Melhem, and J. C. Gee, "High-dimensional spatial normalization of diffusion tensor images improves the detection of white matter differences: an example study using amyotrophic lateral sclerosis," IEEE Transactions on Medical Imaging, vol. 26, iss. 11, pp. 1585–1597, 2007.
  25. H. Zhang, P. A. Yushkevich, D. Rueckert, and J. C. Gee, "Unbiased white matter atlas construction using diffusion tensor images," in Proc. Medical Image Computing and Computer-Assisted Intervention, Heidelberg, 2007, pp. 211–218.
  26. B. B. Avants, T. P. Schoenemann, and J. C. Gee, "Lagrangian frame diffeomorphic image registration: Morphometric comparison of human and chimpanzee cortex," Medical Image Analysis, vol. 10, iss. 3, pp. 397–412, 2006.
  27. A. Cooke, M. Grossman, C. DeVita, J. Gonzalez-Atavales, P. N. Moore, W. Chen, J. C. Gee, and J. A. Detre, "Large-scale neural network for sentence processing," Brain and Language, vol. 96, iss. 1, pp. 14–36, 2006.
  28. S. Matsumoto, H. L. Kundel, J. C. Gee, W. B. Gefter, and H. Hatabu, "Pulmonary nodule detection in CT images with quantized convergence index filter," Medical Image Understanding, vol. 10, iss. 3, pp. 343–352, 2006.
  29. Z. Song, N. J. Tustison, B. B. Avants, and J. C. Gee, "Integrated graph cuts for brain MRI segmentation," in Proc. Medical Image Computing and Computer-Assisted Intervention, Heidelberg, 2006, pp. 831–838.
  30. N. J. Tustison, M. Siqueira, and J. C. Gee, "N-D Linear Time Exact Signed Euclidean Distance Transform," Insight Journal, vol. 1, p. i, 2006. [url]
  31. P. A. Yushkevich, J. Piven, H. Hazlett, R. Smith, S. Ho, J. C. Gee, and G. Gerig, "User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability," NeuroImage, vol. 31, iss. 3, pp. 1116–1128, 2006.
  32. P. A. Yushkevich, H. Zhang, and J. C. Gee, "Continuous medial representation for anatomical structures," IEEE Transactions on Medical Imaging, vol. 25, iss. 12, pp. 1547–1564, 2006.
  33. H. Zhang, P. A. Yushkevich, D. C. Alexander, and J. C. Gee, "Deformable registration of diffusion tensor MR images with explicit orientation optimization," Medical Image Analysis, vol. 10, iss. 5, pp. 764–785, 2006.
  34. J. C. Gee, A. J. B. Maintz, and M. W. Vannier, Biomedical Image Registration, ser. Lecture Notes in Computer Science, G. Goos, J. Hartmanis, and J. vanLeeuwen, Eds. Heidelberg: Springer-Verlag, 2003, vol. 2717.

degrees

  • Postdoc in Computer and Information Science and Neurology, University of Pennsylvania, Philadelphia, 1997
  • Ph.D. in Computer and Information Science, University of Pennsylvania, Philadelphia, 1996
  • Visiting Scholar, Faculte de Medecine, Universite de Rennes I, Rennes, France, 1995
  • M.S. in Electrical Engineering, University of Washingon, Seattle, 1989
  • Dual B.S. in Computer Science and Electrical Engineering, University of Washington, Seattle, 1987

current position

  • Associate Professor of Radiologic Science and Computer and Information Science
  • Co-Director, HHMI-NIBIB Integrated Graduate Training Program in Clinical Imaging and Informational Sciences

member since

1998

research interests

  • computational and statistical anatomy
  • biomedical image analysis
  • image registration and segmentation

contact information

PICSL, Department of Radiology
University of Pennsylvania School of Medicine
3600 Market Street, Suite 370
Philadelphia, PA 19104-2644
TEL: +1 215
FAX: +1 215 615 3681
email