Publications

For a full description of the work associated with these publications, see my projects or curriculum vitae. You can also find my papers in these databases: PubMed, Google Scholar, SMARTech, SPL, DBLP.

“Aseptic Bone Resorption Following Cranioplasty: A Systematic Review of Overall Incidence And Risk Factors.” Malcolm, Rindler, Ahmad. Georgia Neurological Surgeons Annual Fall Meeting. December 2015. [slides]

“Cirrhosis: A red flag when treating cellulitis.” Malcolm, Webster, and Langah. American College of Physicians, Georgia Chapter Conference. October 2015. [abstract, poster]

“Processing and Visualization of Diffusion MRI”, Malcolm, Rathi, Westin, Recent Advances in Biomedical Image Processing and Analysis, T. Deserno (Editor), Chapter 16, pages 387-410, 2011. [bib]

@incollection{malcolm2011pv,
  author = "J. G. Malcolm and Y. Rathi and C.-F. Westin",
  title = "Processing and Visualization of Diffusion {MRI}",
  booktitle = "Recent Advances in Biomedical Image Processing and Analysis",
  editor = "T. Deserno",
  publisher = "Springer",
  chapter = 16,
  pages = "387--410",
  year = 2011,
  isbn = "978-3-642-15815-5"
}

“Jacket: GPU Powered MATLAB Acceleration”, Larsen, Pryor, Malcolm, GPU Gems, Hwu (Editor), Chapter 28, pages 387-398, 2011. [bib]

@incollection{larsen,
  author = "Larsen, Pryor, Malcolm",
  title = "Jacket: GPU Powered MATLAB Acceleration",
  booktitle = "GPU Gems - Jade Edition",
  editor = "Hwu",
  publisher = "Morgan Kaufmann",
  chapter = 28,
  pages = "387--298",
  year = 2011,
  isbn = "9780123859631"
}

“Filtered multi-tensor tractography”, Malcolm, Shenton, Rathi, IEEE Trans. in Medical Imaging (TMI), 29(9), pages 1664-1675, 2010. [bib]

@article{malcolm2010tmi,
  author = "J. G. Malcolm and M. E. Shenton and Y. Rathi",
  title = "Filtered multi-tensor tractography",
  journal = "IEEE Trans. on Medical Imaging",
  volume = 29,
  issue = 9,
  pages = {1664-1675},
  year = 2010,
  doi = {10.1109/TMI.2010.2048121}
}

“Filtered tractography”, Malcolm, (PhD dissertation), October 2010. [slides, bib]

@phdthesis{malcolm2010diss,
  author = "J. G. Malcolm",
  title = "Filtered tractography",
  school = "Georgia Institute of Technology",
  address = "Atlanta, GA",
  month = October,
  year = 2010,
}

“Quantitative Evaluation of 10 Tractography Algorithms on a Realistic Diffusion MR Phantom”, Fillard, Descoteaux, Goh, Gouttard, Jeurissen, Malcolm, Ramirez, Reisert, Sakaie, Tensaouti, Yo, Mangin,Poupon, NeuroImage, 56(1):220-234,

[bib]

@article{fillard2011fc,
  title = "Quantitative Evaluation of 10 Tractography Algorithms on a Realistic Diffusion {MR} Phantom",
  author = "P. Fillard and M. Descoteaux and A. Goh and S. Gouttard and B. Jeurissen and J. Malcolm and A. Ramirez and M. Reisert and K Sakaie and F. Tensaouti and T. Yo and J.-F. Mangin and C. Poupon",
  journal = "NeuroImage",
  volume = 56,
  number = 1,
  pages = "220--234",
  year = 2011
}

“A Full Bi-tensor Neural Tractography Algorithm Using the Unscented Kalman Filter”, Lienhard, Malcolm, Westin, Rathi, J. of Advances in Signal Processing, 77,

[bib]

@article{lienhard2011bitensor,
  title = "A Full Bi-tensor Neural Tractography Algorithm Using the Unscented {Kalman} Filter",
  author = "S. Lienhard and J. Malcolm and C.-F. Westin and Y. Rathi",
  journal = "J of Advances in Signal Processing",
  year = 2011,
  volume = 77,
  doi = {10.1186/1687-6180-2011-77}
}

“Biomarkers for identifying first-episode schizophrenia patients using diffusion weighted imaging”, Rathi, Malcolm, Michailovich, Goldstein, Seidman, McCarley, Westin, Shenton, Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 657-665, 2010. [bib]

@conference{rathi2010miccai,
  title = "Biomarkers for identifying first-episode schizophrenia patients using diffusion weighted imaging",
  author = "Y. Rathi and J. Malcolm and O. Michailovich and J. Goldstein and L. Seidman and R. W. McCarley and C.-F. Westin and M. E. Shenton",
  booktitle = "Medical Image Computing and Computer Assisted Intervention ({MICCAI})",
  volume = 6361,
  pages = "657--665",
  year = 2010
}

“A geometry-based particle filtering approach to white matter tractography”, Savadjiev, Rathi, Malcolm, Shenton, Westin, Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 233-240, 2010. [bib]

@conference{savadjiev2010miccai,
  title = "A geometry-based particle filtering approach to white matter tractography",
  author = "P. Savadjiev and Y. Rathi and J. G. Malcolm and M. E. Shenton and C.-F. Westin",
  booktitle = "Medical Image Computing and Computer Assisted Intervention ({MICCAI})",
  volume = 6362,
  pages = "233-240",
  year = 2010
}

“Imaging of Meningioma Progression by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry”, Agar, Malcolm, Mohan, Yang, Johnson, Tannenbaum, Agar, Black, Analytic Chemistry, 82(7), pages 2621-5, 2010. [bib]

@article{agar2010ac,
  author = "N. Y. R. Agar and J. G. Malcolm and V. Mohan and H. W. Yang and M. D. Johnson and A. Tannenbaum and J. N. Agar and P. M. Black",
  title = "Imaging of Meningioma Progression by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry",
  journal = "Analytic Chemistry",
  year = 2010,
  month = "Apr",
  volume = 82,
  number = 7,
  pages = "2621-5",
  doi = "10.1021/ac100113w",
  pubmed = 20196536,
}

“A filtered approach to neural tractography using the Watson directional function”, Malcolm, Michailovich, Bouix, Westin, Shenton, Rathi, Medical Image Analysis (MedIA), 14(1), pages 58-69, 2010. [bib]

@article{Malcolm2010watson,
  author = "J. G. Malcolm and O. Michailovich and S. Bouix and C.-F. Westin and M. E. Shenton and Y. Rathi",
  title = "A filtered approach to neural tractography using the {Watson} directional function",
  journal = "Medical Image Analysis",
  volume = 14,
  issue = 1,
  year = 2010,
  pages = "58--69"
}

“Tensor-kernels for simultaneous fiber model estimation and tractography”, Rathi, Malcolm, Michailovich, Westin, Shenton, Bouix, Magnetic Resonance in Medicine (MRM), 64(1), pages 138-148, 2010. [bib]

@article{rathi2010mrm,
  author = "Y. Rathi and J. G. Malcolm and O. Michailovich and C.-F. Westin and M. E. Shenton and S. Bouix",
  title = "Tensor-kernels for simultaneous fiber model estimation and tractography",
  journal = "Magnetic Resonance in Medicine",
  volume = 64,
  number = 1,
  pages = "138--148",
  pubmed = 20572129,
  year = 2010,
  doi = {10.1002/mrm.22292},
}

“Affine registration of label maps in Label Space”, Rathi, Malcolm, Bouix, Tannenbaum, Shenton, J. of Computing, 2(4), pages 1-11, 2010. [bib]

@article{Rathi2010affine,
  title = {Affine registration of label maps in {Label Space}},
  author = {Y. Rathi and J. Malcolm and S. Bouix and A. Tannenbaum and M. E. Shenton},
  journal = "J. of Computing",
  volume = 2,
  number = 4,
  pages = "1--11",
  year = 2010
}

“Disease classification: A probabilistic approach”, Rathi, Malcolm, Bouix, McCarley, Seidman, Goldstein, Westin, Shenton, Int. Symp. on Biomedical Imaging (ISBI), pages 1345-1348, 2010. [bib]

@conference{rathi2010isbi,
  author = {Y. Rathi and J. G. Malcolm and S. Bouix and R. W. McCarley and L. J. Seidman and J. M. Goldstein and C.-F. Westin and M. Shenton},
  title = {Disease classification: A probabilistic approach},
  booktitle = "Int. Symp. on Biomedical Imaging (ISBI)",
  year = 2010,
  pages = {1345-1348}
}

“Two-Tensor Tractography Using a Constrained Filter”, Malcolm, Shenton, Rathi, Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 894-902, 2009. [poster, bib]

@conference{Malcolm2009miccai,
  author = "J. G. Malcolm and M. E. Shenton and Y. Rathi",
  title = "Two-Tensor Tractography Using a Constrained Filter",
  booktitle = "Medical Image Computing and Computer Assisted Intervention ({MICCAI})",
  pages = "894--902",
  year = 2009
}

“Vision-Based Range Regulation of a Leader-Follower Formation”, Vela, Betser, Malcolm, Tannenbaum, IEEE Transactions on Control Systems Technology, 17(2):442-448, 2009

“Filtered Tractography: State estimation in a constrained subspace”, Malcolm, Shenton, Rathi, Diffusion Modeling and Fiber Cup (in MICCAI), 2009. [poster, bib]

@conference{Malcolm2009dmfc,
  author = "J. G. Malcolm and M. E. Shenton and Y. Rathi",
  title = "Filtered Tractography: State estimation in a constrained subspace",
  booktitle = "Diffusion Modeling and Fiber Cup (in {MICCAI})",
  pages = "122-133",
  year = 2009
}

“Filtered Tractography: Validation on a Physical Phantom”, Malcolm, Shenton, Rathi, Fiber Cup (in MICCAI), 2009. [slides,submission, bib]

@conference{Malcolm2009fc,
  author = "J. G. Malcolm and M. E. Shenton and Y. Rathi",
  title = "Filtered Tractography: Validation on a Physical Phantom",
  booktitle = "Fiber Cup (in {MICCAI})",
  pages = "220-223",
  year = 2009
}

“The Effect of Local Fiber Model On Population Studies”, Malcolm, Kubicki, Shenton, Rathi, Diffusion Modeling and Fiber Cup (in MICCAI), 2009. [poster, bib]

@conference{Malcolm2009study,
  author = "J. G. Malcolm and M. Kubicki and M. E. Shenton and Y. Rathi",
  title = "The Effect of Local Fiber Model On Population Studies",
  booktitle = "Diffusion Modeling and Fiber Cup (in {MICCAI})",
  pages = "33-40",
  year = 2009
}

“Neural Tractography Using An Unscented Kalman Filter”, Malcolm, Shenton, Rathi, Information Processing in Medical Imaging (IPMI), pages 126-138, 2009. [slides, bib]

@conference{Malcolm2009ipmi,
  author = {J. G. Malcolm and M. E. Shenton and Y. Rathi},
  title = {Neural Tractography using an unscented {Kalman} filter},
  booktitle = {Information Processing in Medical Imaging (IPMI)},
  pages = {126--138},
  year = 2009
}

“Mixture Model for estimating fiber ODF and multi-directional Tractography”, Rathi, Malcolm, Bouix, Kindlmann, Westin, Kubicki, Shenton, Intl. Soc. of Magnetic Resonance in Medicine (ISMRM),

[slides, bib]

 @conference{Rathi2009ismrm,
  author = {Y. Rathi and J. Malcolm and S. Bouix and C-F. Westin and
            M. Kubicki and M.E. Shenton},
  title = {Mixture Model for estimating fiber {ODF} and multi-directional Tractography},
  booktitle = {Int. Symp. on Magnetic Resonance in Medicine (ISMRM)},
  pages = 3548,
  year = 2009
}

“Label Space: A Coupled Multi-Shape Representation”, Malcolm, Rathi, Shenton, Tannenbaum, Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 416-424, 2008. Runner-Up, MICCAI Young Scientist Award [slides, bib]

@conference{Malcolm2008lss,
  author = {J. Malcolm and Y. Rathi and M. E. Shenton and A. Tannenbaum},
  title = {Label Space: A Coupled Multi-Shape Representation},
  booktitle = {Medical Image Computing and Computer Assisted Intervention (MICCAI)},
  pages = {416--424},
  year = 2008
}

“Kernel-Based High-Dimensional Histogram Estimation For Visual Tracking”, Karasev, Malcolm, Tannenbaum, Int. Conf. on Image Processing (ICIP), 2008.

“Tracking Through Changes in Scale”, Lankton, Malcolm, Nakhmani, Tannenbaum, Int. Conf. on Image Processing (ICIP), 2008. [poster]

“Localized statistics for DW-MRI fiber bundle segmentation”, Lankton, Melonakos, Malcolm, Dambreville, Tannenbaum, MMBIA, 2008. [poster]

“Label Space: A Multi-Object Shape Representation”, Malcolm, Rathi, Tannenbaum, Combinatorial Image Analysis, 2008. [bib]

@conference{Malcolm2008ls,
  author = {J. Malcolm and Y. Rathi and A. Tannenbaum},
  title = {Label Space: A Multi-Object Shape Representation},
  booktitle = {Combinatorial Image Analysis},
  pages = {185--196},
  year = 2008
}

“Fast Approximate Surface Evolution in Arbitrary Dimension”, James, Rathi, Yezzi, Tannenbaum, IS&T/SPIE Symposium on Medical Imaging, 2008. [slides, poster]

“Segmenting Images Analytically in Shape Space”, Rathi, Dambreville, Niethammer, Malcolm, Levitt, Shenton, Tannenbaum, IS&T/SPIE Symposium on Medical Imaging, 2008. [bib]

 @conference{Rathi2008mi,
  author = {Y. Rathi and S. Dambreville and M. Niethammer and
            J. Malcolm and J. Levitt and M. E. Shenton and A. Tannenbaum},
  title = {Segmenting images analytically in shape space},
  booktitle = {SPIE Medical Imaging},
  volume = 6914,
  year = 2008
}

“Tracking with Graph Cuts: Treating Clutter with Adaptive Penalties”, Malcolm, Rathi, Tannenbaum. (unpublished)

“Distribution metrics and image segmentation”, Georgiou, Michailovich, Rathi, Malcolm, Tannenbaum. Linear Algebra and Its Applications, 2(425):663-672, 2007.

“A Graph Cut Approach to Image Segmentation in Tensor Space”, Malcolm, Rathi, Tannenbaum. Workshop on Component Analysis Methods (in CVPR), 2007. [slides]

“Multi-Object Tracking Through Clutter Using Graph Cuts”, Malcolm, Rathi, Tannenbaum, Workshop on Non-rigid Registration and Tracking through Learning (in ICCV), 2007. [slides].

“Quantum error correction”, Malcolm (unpublished, final report for Math4782).

“Tracking Through Clutter Using Graph Cuts”, Malcolm, Rathi, Tannenbaum, British Machine Vision Conference (BMVC), 2007. [poster].

“Graph cut segmentation with nonlinear shape priors”, Malcolm, Rathi, Tannenbaum, Int. Conf. on Image Processing (ICIP), 2007. [poster].

“Seeing the Unseen: Segmenting with Distributions”, Rathi, Michailovich, Malcolm, Tannenbaum, Intl. Conference on Signal and Image Processing (SIP), 2006.

“Closed Loop Visual Tracking Using Observer-Based Dynamic Active Contours”, Vela, Niethammer, Malcolm, Tannenbaum, Conf. on Guidance, Navigation, and Control, 2005.

Friends and colleagues

Matt Might - systems, languages, compilers

Shawn Lankton - active contour image segmentation, stereo vision

John Melonakos and Gallagher Pryor - image processing, co-founded ArrayFire with me

Patent

“System for Improving Utilization of GPU Resources”, Pryor, Malcolm, Melonakos, Rehman. U.S. App No. 12/323,572, filed 29 Nov 2007, granted 25 Dec 2012.