Publications

Journal Articles and Book Chapters

1. A. Ozturk, S.A. Smith, E.M. Gordon-Lipkin, D.M. Harrison, N. Shiee, D.L. Pham, B.S. Caffo, P.A. Calabresi, D.S. Reich, "MRI of the Corpus Callosum in Multiple Sclerosis: Association with Disability " Multiple Sclerosis, in press.
   
   
2. N. Shiee, P.-L. Bazin, A. Ozturk, P.A. Calabresi, D.S. Reich, D.L. Pham, "A Topology-Preserving Approach to the Segmentation of Brain Images with Multiple Sclerosis Lesions" NeuroImage, in press.
   
   
3. V. Rao, C.A. Munro, P. Rosenberg,J. Ward, M. Bertrand, M. Degoankar, A Horska, D.L Pham, D.M. Yousem, P.B. Barker, "Neuroanatomical Correlates of Depression in Post Traumatic Brain Injury: Preliminary Results of a Pilot Study," The Journal of Neuropsychiatry and Clinical Neurosciences, in press.
   
   
4. D.L. Pham, P.-L. Bazin, "Unsupervised Tissue Classification," Handbook of Medical Image Processing and Analysis, 2nd Edition, Isaac Bankman (ed.), Elsevier, Burlington, MA, pp. 209-221, 2008.
   
   
5. C. Krishnan, A.I. Kaplin, R.A. Brodsky, D.B. Drachman, R.J. Jones, D.L. Pham, N.D. Richert, C.A. Pardo, D.M. Yousem, E. Hammond, M. Quigg, C. Trecker, J.C. McArthur, A. Nath, B.M. Greenberg, P.A. Calabresi, D.A. Kerr, "Reduction of Disease Activity and Disability With High-Dose Cyclophosphamide in Patients With Aggressive Multiple Sclerosis," Archives of Neurology, 65(8):1044-1051, 2008.
   
   
6. P.-L. Bazin, D.L. Pham, "Homeomorphic Brain Image Segmentation with Topological and Statistical Atlases," Medical Image Analysis, 12(5):616-625, 2008.
   
   
7. J.C. Carter, D.C. Lanham, D.L. Pham, G. Bibat, S. Naidu, W.E. Kaufmann, "Selective Cerebral Volume Reduction in Rett Syndrome: a Multiple Approach MRI Study," American Journal of Neuroradiology, 29(3): 436-441, American Journal of Neuroradiology, March 2008.
   
   
8. P.-L. Bazin, D.L. Pham, "Topology Correction of Segmented Medical Images using a Fast Marching Algorithm," Computer Methods and Programs in Biomedicine, 88(2): 182-290, Nov 2007.
   
   
9. P.-L. Bazin, J.L. Cuzzocreo, M.A. Yassa, W. Gandler, M.J. McAuliffe, S.S. Bassett, D.L. Pham, "Volumetric neuroimage analysis extensions for the MIPAV software package," Journal of Neuroscience Methods 165(1): 111-121, Sept 2007.
   
   
10. P.-L. Bazin, D.L. Pham, "Topology-Preserving Tissue Classification of Magnetic Resonance Brain Images," IEEE Transactions on Medical Imaging, 26(4): 487-496, April 2007.
    
    
11. D. Tosun, M.E. Rettmann, X. Han, X. Tao, C. Xu, S.M. Resnick, D. Pham, and J.L. Prince, " Cortical Surface Segmentation and Mapping," NeuroImage, 23: S108-S118, 2004.
    
    
12. X. Han, D. Pham, D. Tosun, M.E. Rettmann, C. Xu, and J.L. Prince, " CRUISE: Cortical Reconstruction Using Implicit Surface Evolution," NeuroImage, 23: 997-1012, 2004.
    
    
13. S.M. Resnick, D.L. Pham, M.A. Kraut, A.B. Zonderman, C. Davatzikos, "Longitudinal MRI Studies of Older Adults: A Shrinking Brain," Journal of Neuroscience, 23(8):3295-3301, 2003. [.pdf (0.5MB)]
    
    
14. R. Leigh, J. Ostuni, D.L. Pham, B.K. Lewis, T. Howard, H. McFarland, J.A. Frank, ``Comparison of Various MRI Pulse Sequences in Estimating Cerebral Atrophy in MS and Normal Patients with Intensity Based Segmentation,'' Multiple Sclerosis, 8(5):420-429, 2002.
    
    
15. D.L. Pham, ``Spatial Models for Fuzzy Clustering,'' Computer Vision and Image Understanding, 84(2): 285-297, 2001. [.pdf (0.5MB)]
    
    
16. C. Xu, D. L. Pham, J. L. Prince, "Medical Image Segmentation Using Deformable Models," SPIE Handbook on Medical Imaging -- Volume II: Medical Image Processing and Analysis, M. Sonka and J.M. Fitzpatrick (eds.), pp. 129-174, SPIE Press, Bellingham, WA, 2000. [.pdf (5.6MB)]
    
    
17. A.F. Goldszal, D.L. Pham, ``Volumetric Segmentation of Magnetic Resonance Images of the Brain,'' Handbook of Medical Image Processing, Academic Press, I. Bankman (ed.), pp. 185-194, Academic Press, San Diego, CA, 2000.
    
    
18. D.L. Pham, C. Xu, J.L. Prince, ``Current Methods in Medical Image Segmentation,'' Annual Review of Biomedical Engineering, Annual Reviews, vol. 2, pp. 315-337, Annual Reviews, Palo Alto, CA, 2000. [Technical report version: .ps (2.3MB) .ps.gz (0.4MB) .pdf (0.7MB)]
    
    
19. D.L. Pham, J.L. Prince, ``Adaptive Fuzzy Segmentation of Magnetic Resonance Images,'' IEEE Transactions on Medical Imaging, 18(9):737-752, 1999. [.ps (3.8MB), .ps.gz (0.7MB), .pdf (0.9MB)]
    
    
20. C. Xu, D.L. Pham, M.E. Rettmann, D. Yu, J.L. Prince, ``Reconstruction of the Central Layer of the Human Cerebral Cortex from MR Images,'' IEEE Transactions on Medical Imaging, 18(6):467-480, 1999. [.pdf (0.9MB)]
    
    
21. D.L. Pham, J.L. Prince, ``An Adaptive Fuzzy C-Means Algorithm for Image Segmentation in the Presence of Intensity Inhomogeneities,'' Pattern Recognition Letters, 20(1):57-68, 1999. [.ps (2.7MB), .ps.gz (0.5MB)]
    
    
22. A.F. Goldszal, C. Davatzikos, D.L. Pham, M.X.H. Yan, R.N. Bryan, and S.M. Resnick, ``An Image Processing System for Qualitative and Quantitative Volumetric Analysis of Brain Images,'' Journal of Computer Assisted Tomography, 22(5):827-837, 1998. [.pdf (0.3MB)]
    
    
23. D.L. Pham, J.L. Prince, A.P. Dagher, and C. Xu, ``An Automated Technique for Statistical Characterization of Brain Tissues in Magnetic Resonance Imaging,'' International Journal of Pattern Recognition and Artificial Intelligence, 11(8): 1189-1211, 1997. [.ps (6.8MB), .ps.gz (1.6MB)]
    
    
24. J.L. Prince, Q. Tan, and D. Pham, ``Optimization of MR Pulse Sequences for Bayesian Image Segmentation,'' Medical Physics, 22(10):1651-1656, Oct. 1995. [.ps (1.8MB), .ps.gz (0.15MB)]
    
    

Conference Articles

1. P.-L. Bazin, J. Bogovic, D. Reich, J.L. Prince, D.L. Pham, "Efficient MRF Segmentation of DTI White Matter Tracts using an Overlapping Fiber Model," to be presented at the 12th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Workshop on Diffusion Modelling and the Fibre Cup, in London, UK, Sep. 24, 2009.
   
   
2. P.-L. Bazin, J. Bogovic, D. Reich, J.L. Prince, D.L. Pham, "Belief Propagation Based Segmentation of White Matter Tracts in DTI," to be presented at the 12th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), in London, UK, Sep. 20-24, 2009.
   
   
3. N. Shiee, P.-L. Bazin, D.S. Reich, D.L. Pham, "Automated Reconstruction of the Cerebral Cortex in Multiple Sclerosis Patients," Proceedings of the 6th International Symposium on Biomedical Imaging: From Macro to Nano, pp. 1334-1337, in Boston, Massachusetts, June, 2009.
   
   
4. B. Kishore, P.-L. Bazin, D.L. Pham, "BrainIACS : A System for Web-based Medical Image Processing," presented at SPIE Medical Imaging: Advance PACS-based Imaging Informatics and Therapeutic Applications in Orlando, FL, Feb. 7-12, 2009.
   
   
5. N. Shiee, P.-L. Bazin, D.L. Pham, "Multiple Sclerosis Lesion Segmentation Using Statistical and Topological Atlases," presented at the 11th International Conference on Medical Image Computing and Computer Assisted Intervention Workshop on 3D Segmentation in the Clinic: A Grand Challenge, in New York, NY, Sept 6-10, published in the Midas Journal, 2008.
   
   
6. N. Shiee, P.-L. Bazin, J.L. Cuzzocreo, D.S. Reich, P.A. Calabresi, D.L. Pham, "Topologically Constrained Segmentation of Brain Images with Multiple Sclerosis Lesions," presented at the 11th International Conference on Medical Image Computing and Computer Assisted Intervention Workshop on Medical Image Analysis on Multiple Sclerosis, in New York, NY, Sept 6-10, Proceedings pp. 71-81, 2008.
   
   
7. S. Roy, H. Agarwal, A. Carass, Y. Bai, D.L. Pham, J.L. Prince, "Fuzzy c-means with Variable Compactness", Proceedings of the 5th International Symposium on Biomedical Imaging: From Macro to Nano, pp. 452-455, in Paris, France, May, 2008.
   
   
8. P.-L. Bazin and D.L. Pham, "Statistical and Topological Atlas Based Brain Image Segmentation", presented at the 10th International Conference on Medical Image Computing and Computer Assisted Intervention, in Brisbane, Australia, Oct 2007, LNCS 4791, pp. 94-101, 2007.
   
   
9. P.-L. Bazin, L.M. Ellingsen and D.L. Pham, "Digital Homeomorphisms in Deformable Registration", presented at the 20th International Conference on Information Processing in Medical Imaging, in Kerkrade, NL, July 2007, LNCS 4584, pp. 211-222, 2007.
   
   
10. D.L. Pham and P.-L. Bazin , ``Simultaneous registration and tissue classification using clustering algorithms,'' Proceedings of the The 3rd IEEE International Symposium on Biomedical Imaging: Macro to Nano, pp. 650-653, in Arlington, VA, Apr. 6-9, 2006.
    
    
11. P.-L. Bazin and D.L. Pham, ``TOADS: Topology-preserving, anatomy-driven segmentation,'' Proceedings of the 3rd IEEE International Symposium on Biomedical Imaging: Macro to Nano, pp. 327-330, in Arlington, VA, Apr. 6-9, 2006.
    
    
12. P.-L. Bazin and D.L. Pham, ``Topology Correction using Fast Marching Methods and its Application to Brain Segmentation,'' , LNCS 3750, pp. 484-491, in Palm Springs, CA, October 26-29, 2005.
    
    
13. P.-L. Bazin and D.L. Pham, ``Topology Preserving Tissue Classification with Fast Marching and Topology Templates,'' Proceedings of the 19th International Conference on Information Processing in Medical Imaging, LNCS 3565, pp. 234-245, in Glenwood Springs, CO, July 11-15, 2005.
    
    
14. P.-L. Bazin, W. Gandler, M. McAuliffe, D.L. Pham, ``A Software Tool for Atlas-based Volumetric Neuroimage Analysis,'' presented at SPIE Medical Imaging 2005: Image Processing vol. 5747, pp. 1824-1833, in San Diego, CA, Feb. 12-17, 2005.
    
    
15. Y. Bai, X. Han, D.L. Pham, J.L. Prince, ``Super-resolved Multi-channel Fuzzy Segmentation of MR Brain Images,'' presented at SPIE Medical Imaging 2005: Image Processing vol. 5747, pp. 580-589, in San Diego, CA, Feb. 12-17, 2005.
    
    
16. P.-L. Bazin and D.L. Pham, ``Topology Smoothing for Segmentation and Surface Reconstruction,'' Proceedings of the 7th International Conference on Medical Image Computing and Computer Assisted Intervention, LNCS 3216, pp. 111-118, in Saint-Malo, France, September 26-30, 2004.
    
    
17. D.L. Pham, P.-L. Bazin, ``Simultaneous Boundary and Partial Volume Estimation in Medical Images,'' Proceedings of the 7th International Conference on Medical Image Computing and Computer Assisted Intervention, LNCS 3216, pp. 111-118, in Saint-Malo, France, September 26-30, 2004.
    
    
18. D.L. Pham, ``Integrating Intensity and Boundary Information for Tissue Classification'', Proceedings of the 2004 Conference on Computer-Based Medical Systems, pp. 216-220, in Bethesda, MD, June 24-25, 2004. [.pdf (0.3MB)]
    
    
19. D.L. Pham, J.L. Prince, ``Robust Unsupervised Tissue Classification in MR Images'', Proceedings of the 2004 IEEE International Symposium on Biomedical Imaging: Macro to Nano,pp. 109-112, in Arlington, VA, April 15-18, 2004.
    
    
20. D.L. Pham, ``Unsupervised Tissue Classification in Medical Images using Edge-Adaptive Clustering,'' Proceedings of the 25th International Conference of the IEEE Engineering in Medicine and Biology Society, vol. 1, pp. 17-21, in Cancun, Mexico, Sept. 17-21, 2003. [.pdf (0.6MB)]
    
    
21. K.J. Behnke, M.E. Rettmann, D.L. Pham, D. Shen, S.M. Resnick, J.L. Prince, ``Automatic Classification of Sulcal Regions of the Human Brain Cortex Using Pattern Recognition,'' Proceedings of SPIE Medical Imaging 2003: Image Processing vol. 5032, pp. 1499-1510, in San Diego, CA, Feb. 15-20, 2003.
    
    
22. D.L. Pham, ``Fuzzy Clustering with Spatial Constraints,'' Proceedings of the 2002 IEEE International Conference on Image Processing (ICIP2002), Vol. 2, pp. 65-68, in Rochester, NY, Sept. 22-25, 2002.
    
    
23. S. Yu, D.L. Pham, D. Shen, E.H. Herskovitz, S.M. Resnick, C. Davatzikos, ``Automatic Segmentation of White Matter Lesions in T1-weighted Brain MR Images,'' Proceedings of the 2002 IEEE International Symposium on Biomedical Imaging (ISBI2002), pp. 253-256, in Washington, DC, July 7-10, 2002.
    
    
24. D.L. Pham, X. Han, M.E. Rettmann, C. Xu,, D. Tosun, S.M. Resnick,, J.L. Prince, ``New Approaches for Measuring Changes in the Cortical Surface Using an Automatic Reconstruction Algorithm,'' to be presented at SPIE Medical Imaging 2002, in San Diego, CA, Feb. 23-28, 2002.
    
    
25. D.L. Pham, ``Robust Fuzzy Segmentation of Magnetic Resonance Images,'' Proceedings of the Fourteenth IEEE Symposium on Computer-Based Medical Systems (CBMS2001), pp. 127-131, in Bethesda, MD, July 26-27, 2001. [.pdf (0.3MB)]
    
    
26. D.L. Pham, ``Edge--Adaptive Clustering for Unsupervised Image Segmentation'', Proceedings of the 2000 International Conference on Image Processing, in Vancouver, Canada, September 10-13, 2000.
    
    
27. D.L. Pham, J.L. Prince, ``Unsupervised Partial Volume Estimation in Single-Channel Image Data'', Proceedings of the IEEE Workshop on Mathematical Methods in Biomedical Image Analysis, pp. 170-177, in Hilton Head, SC, June 11-12, 2000.
    
    
28. D.N. Yu, C. Xu, M.E. Rettmann, D.L. Pham,J.L. Prince, ``Quantitative Validation of a Deformable Cortical Surface Model,'' SPIE Medical Imaging: Image Processing, San Diego, CA, Feb. 19-25, Proceedings of SPIE vol. 3979: 1593-1604, 2000.
    
    
29. M.E. Rettmann, C. Xu, D.L. Pham, J.L. Prince. Automated Segmentation of Sulcal Regions, 2nd International Conference on Medical Image Computing and Computer-Assisted Interventions (MICCAI99), Springer-Verlag, September 1999.
    
    
30. D.L. Pham, J.L. Prince, ``An Adaptive Fuzzy Segmentation Algorithm for Three-dimensional Magnetic Resonance Images,'' Presented at XVIth Conference on Information Processing in Medical Imaging (IPMI99), June 28 - July 2 1999. [.ps (2.0MB), .ps.gz (0.4MB)]
    
    
31. D.L. Pham, J.L. Prince, ``A Generalized EM Algorithm for Robust Segmentation of Magnetic Resonance Images,'' Proceedings of the 33rd Annual Conference on Information Sciences and Systems (CISS99), pp. 558-563, in Baltimore, MD, Mar. 17-19, 1999. [.ps (1.4MB), .ps.gz (0.2MB)]
    
    
32. D.L. Pham, J.L. Prince, ``Partial Volume Estimation and the Fuzzy C-means Algorithm,'' International Conference on Image Processing (ICIP98) , Chicago, IL, Oct. 4-7, IEEE Signal Processing Society, Proceedings vol. III: pp. 819-822, 1998. [.ps (1.4MB), .ps.gz (0.3MB) , poster.ps.gz (0.6MB) ]
    
    
33. C. Xu, D.L. Pham, J.L. Prince, M.E. Etemad, D. Yu, "Reconstruction of the Central Layer of the Human Cerebral Cortex from MR images", to appear in the First International Conference on Medical Image Computing and Computer Assisted Interventions, Massachusetts Institute of Technology, Boston MA, USA, October 11-13, Springer, Lecture Notes in Computer Science vol. 1496: 399-404, 1998.
    
    
34. D.L. Pham, J.L. Prince, ``An Adaptive Fuzzy C-Means Algorithm for Image Segmentation in the Presence of Intensity Inhomogeneities,'' SPIE Medical Imaging: Image Processing, San Diego, CA, Feb. 21-27, Proceedings of SPIE vol. 3338: 555-563, 1998. [.ps (1.4MB), .ps.gz (0.3MB) , slides.ps.gz (0.6MB) ]
    
    
35. D.L. Pham, J.L. Prince, and A.P. Dagher, ``Estimation of Joint Probability Density Functions in Magnetic Resonance Imaging,'' Proceedings of The Ninth Workshop on Image and Multidimensional Signal Processing (IMDSP), pp. 148-149, 1996. [.ps (1.0MB), .ps.gz (0.06MB)]
    
    
36. C. Xu, D.L. Pham, and J.L. Prince, "Finding the Brain Cortex Using Fuzzy Segmentation, Isosurfaces, and Deformable Surface Models," Proceedings of the XVth International Conference on Information Processing in Medical Imaging, pp.399-404, 1997. [.ps (1.3MB), .ps.gz (0.37MB)]
    
    

Abstracts

1. N. Shiee, P.L. Bazin, D.L. Pham, "An Automated Pipeline for Cortical Reconstruction of Brains with MS," presented at the 14th Annual Meeting of the Organization of Human Brain Mapping, in Melbourne, Austrailia, June 18-23, 2009.
   
   
2. M.E. Richardson, D. Crocetti, J. Wan, D.L. Pham, J.L. Prince, K. Subramaniam, B. Fischl, W.E. Kaufmann, S.H. Mostofsky, "Automated MRI Parcellation of the Frontal Lobe," presented at the 14th Annual Meeting of the Organization of Human Brain Mapping, in Melbourne, Austrailia, June 18-23, 2009.
   
   
3. Susan S. Bassett, P.-L. Bazin, C. Cristinzioa and D.L. Pham, "Changes in cortical thickness in asymptomatic individuals at genetic risk for Alzheimer's disease," Alzheimer's Association International Conference on Alzheimer's Disease, in Vienna, Austria, July 11-16, 2009.
   
   
4. D. Nguyen, N.Nguyen, P.-L. Bazin, T. Tran, D.L. Pham, "JPEG 2000 Image Compression Tool for the MIPAV Software Package," presented at the 14th Annual Meeting of the Organization of Human Brain Mapping, in Melbourne, Austrailia, June 15-19, 2008.
   
   
5. B. Lucas, B. Landman, J. Prince, D.L. Pham, "MAPS: A Free Medical Image Processing Pipeline," presented at the 14th Annual Meeting of the Organization of Human Brain Mapping, in Melbourne, Austrailia, June 15-19, 2008.
   
   
6. V. Rao, J. Spiro, C. Munro, D.L. Pham, A. Horska, D.M. Yousem, P.B. Barker, "Neuroanatomical Correlates of Post-TBI Depression," presented at the 19th Anuual Meeting of the American Neuropsychiatric Association (ANPA), in Savannah, GA, Mar.1-4, 2008.
   
   
7. J.C. Carter, D.C. Lanham, D.L. Pham, G. Bibat, S. Naidu, W.E. Kaufmann, "Selective Cerebral Volume Reductions in Rett Syndrome: a Multiple Approach MRI Study," presented at Neuroscience 2007, in San Diego, CA, November 3-7, 2007.
   
   
8. V.J. Rodrigues, A. Ozturk, P.-L.Bazin, D.L. Pham, M. McAuliffe, D.D. Lin, "Semiautomated Quantitative Software Tool for Atlas-based Volumetric Lobar Brain Analysis Made Easy for Neuroradiologists," presented at the 45th Annual Meeting of the American Society of Neuroradiology (ASNR), Chicago, IL, June 9-14, 2007.
   
   
9. P.-L. Bazin, X. Han, D. Tosun, J.L. Prince, D.L. Pham, "Cortical Reconstruction using Topology Preserving Tissue Classification," presented at the 12th Annual Meeting of the Organization of Human Brain Mapping, in Florence, Italy, June 11-15, 2006.
   
   
10. P.-L. Bazin, M. McAuliffe, D.L. Pham, "Free Software Tools for Structural Neuroimage Analysis," presented at the 11th Annual Meeting of the Organization of Human Brain Mapping, in Toronto, Canada, June 12-16, 2005.
    
    
11. S.M. Resnick, S.D. Moffat, D.L. Pham, ``Free Testosterone Concentration is Associated with Regional Cerebral Patterns in Elderly Men,'' presented at the Annual Meeting of the American College of Neuropsychopharmacology (ACNP), in San Juan, Puerto Rico, December 8-12, 2002.
    
    
12. S.M. Resnick, D.L. Pham, C. Davatzikos, M.A. Kraut, ``Sex Differences in Regional Cerebral Blood Flow: Clinical Implications for Alzheimer's Disease,'' presented at the 8th International Conference on Alzheimer's Disease and Related Disorders, in Stockholm, Sweden, July 20-25, 2002.
    
    
13. J. Varga, D.L. Pham, Y. Wang, K. Huang, and Z. Szabo, ``Comparison of MRI Brain Segmentation Methods for the Partial Volume Correction of Coregistered PET,'' European Association of Nuclear Medicine Congress, Vienna, Austria, August 31 - September 4, published in European Journal of Nuclear Medicine 29(S1): S157, 2002.
    
    
14. M.E. Rettmann, X. Han, D.L. Pham. J.L. Prince, ``Geodesics for Sulcal Segmentation and Depth Measurements,'' Sixth International Conference on Functional Mapping of the Human Brain (HBM), in San Antonio, TX, June 12-16, published in Neuroimage 11(5), Part 2, page S667, 2000.
    
    
15. M.E. Etemad, C. Xu, D.L. Pham, D. Yu, & J.L. Prince, "On Automated Segmentation of Buried Gyri," 5th International Conference on Functional Mapping of the Human Brain (HBM), in Dusseldorf, Germany, June 22-26, published in Neuroimage 9(6), Part 2, page S143, 1999.
    
    
16. C. Xu, D.L. Pham, J.L. Prince, M.E. Etemad, D. Yu, "A Spherical Map for Cortical Geometry", 4th International conference on Functional Mapping of the Human Brain, June 7-12, 1998, Montreal, Quebec, Canada; NeuroImage 7(4):734, May 1998. [.ps (1.6MB), .ps.gz (0.3MB)]
    
    
17. C. Xu, D.L. Pham, J.L. Prince , "Reconstruction of the Human Cortical Surface from MR Images", 4th International conference on Functional Mapping of the Human Brain, June 7-12, 1998, Montreal, Quebec, Canada; NeuroImage 7(4):715, May 1998. [.ps (2.7MB), .ps.gz (0.5MB)]