Brian B. Avants

Curriculum Vitae
Cell: 215-870-0787
Email:
Web-Resume: link, CV: (pdf)
H-index: 29 (click to get most current value)

I develop analysis systems for multidimensional medical datasets that include imaging. While most of my work focuses on the human brain, I have also contributed to the Allen Brain Atlas, Waxholm space, non-human primate studies and studies of other organ systems such as the heart and lung. This WordCloud summarizes my topics of research. I achieve my research goals with open-source projects, ANTs and ANTsR (answer), which allow others to benefit from my work. Some consider ANTs the premier medical image registration toolkit in the world. ANTsR is an emerging tool supporting standardized multimodality image analysis. I am also a founder and lead developer of the Insight ToolKit (ITK), a medical image processing library used throughout academia and industry.

Education

PhD, University of Pennsylvania2005

Bioengineering, Philadelphia, PA

MS, University of Pennsylvania2002

Computer Science, Philadelphia, PA

BA, New College of Florida1998

Physics, Sarasota, FL

Professional Appointments

Assistant Professor of Radiology2012
University of Pennsylvania

Research Scientist, Radiology 2010
University of Pennsylvania

Post-Doctoral Scientist, Radiology2006
University of Pennsylvania

Awards and Honors

Advanced Normalization Tools (ANTs) Software Determined as "Standard Setting" Registration for MICCAI 2013 Multi-Atlas Segmentation Challenge2013

ANTs finished 1st overall in an unbiased EMPIRE10 intl. lung mapping competition2010

ANTs finished in 1st rank in an unbiased Klein 2009 intl. brain mapping competition2009

Young Investigator Award, General Medical Computing, MICCAI2007

Best Poster Award SPIE Medical Imaging2003

Future Healthcare Researcher Scholarship, Humana Health Care1995

National Merit Scholarship, New College of Florida, Sarasota, FL1994

Current Grants

IARPA KRNS multi-center proposal pending

Continued Development and Maintenance of ITKSNAP 3D Image Segmentation Software - % effort2012

TDP-43 Proteinopathies in ALS-Dementia - % effort2010

Fundamental Refactoring of Deformable Image Registration in ITK with Distributed Computing and GPU Acceleration - Co-PI2010

Past Grants and Fellowships

Traumatic Brain Injury: A Pilot Study - Sub-contract PI2011

Pediatric Template Of Brain Perfusion - Sub-contract PI2009

Tract-Specific Analysis of Brain White Matter - % effort2009

Advanced Neuroimages Registration Methods: Effects of Prenatal Cocaine Exposure - % effort2008

The Longitudinal Effect of Neurodegeneration on Language-Network Neuroanatomy and Cognition, University of Pennsylvania, Institute of Aging2008

Long Term Effects of Prenatal Cocaine Exposure - % effort2007

Shape Optimizing Diffeomorphisms for Computational Biology (based on my PhD thesis) - % effort2006

Surface-based Cortical Analysis in ITK: Segmentation, Conformal Flattening and Statistics - % effort2004

Bioengineering Training in Cardiovascular Pathophysiology - Institute for Medicine and Engineering Training Grant, University of Pennsylvania2002

Invited Talks

"A Unified Image Registration Framework for ITKv4," National Library of Medicine, Bethesda, MD2012

"Eigenanatomy Methods for Multivariate Brain Mapping," University of California, San Francisco2012

"Multivariate Methods for Integrating Multiple Modalities in Brain Mapping," Incheon National University, Incheon, South Korea2012

"Early Home Environment Impacts Cortical Thickness in Young Adulthood," Chinese Academy of Sciences, Beijing, China2012

"Modern analytics for neuroimaging," University of California, Los Angeles2011

"Multivariate methods and applications in neuroimaging," Washington Univ. at St. Louis2011

"Democratizing Hippocampus Labeling with Open-Source Software," Columbia University, NY, NY 2009

"Multivariate Methods and software for Neuroimaging," SRI, Menlo Park, CA 2009

"Template-based Brain Mapping with Diffeomorphisms," Janelia Farm, Ashburn, Virginia 2008

Selected Conference Participation

Leading an R tutorial on statistical methods in medical imaging at MICCAI, Nagoya, JapanSept 2013

My student Ben Kandel's paper accepted for oral presentation at Information Processing in Medical Imaging, Asilomar, CAJuly 2013

Session Chair, 3rd Intl. Workshop on Pattern Recognition in Neuroimaging (PRNI), Philadelphia, PAJune 2013

My student Paramveer Dhillon's paper accepted for oral presentation at PRNI 2013June 2013

Eigenanatomy research first presented at MICCAIOct. 2012

Media and poster presentation at Society for Neuroscience meeting, New Orleans, LAOct. 2012

Oral presentation at the Workshop on Biomedical Image Registration, Vanderbilt University, Nashville, TNJuly 2012

Co-Chair with Simon Warfield, Image Analysis Session, ISMRM, Melbourne, AustraliaMay 2012

Oral presentation: "Multivariate analyses improve detection power for cortical longitudinal change in dementia" at Society for Neuroscience meeting, Washington D.C.Nov. 2011

Conducted ITKv4 image registration tutorial with Kitware, Inc. at MICCAI, Toronto, CanadaSept. 2011

Oral presentation at MICCAI, Beijing China. (45 of 786 submissions accepted for oral presentation)Sept. 2010

Oral presentation "Grammatical comprehension and longitudinal adolescent brain development: a multivariate DTI and T1 analysis," Human Brain Mapping, San Francisco, CA. Jun 2009

Teaching Experience

Advising Ben Kandel, Doctoral student, BioengineeringCurrent

Co-advising Paramveer Dhillon, Doctoral student, Computer Science with Professor Lyle UngarCurrent

Doctoral committee member for Efstathios D GennatasCurrent

Other Research Experience

Insight ToolKit Version 4 Development Leader 2010 - present

Experience working with large-scale software development teams that include both academia and industry 2002 - present

Service to Profession

Grant Reviewer - Alzheimer's Association2013

Consultant, American College of Radiology Head Injury Institute Information Technology Committee2013

Topic Editor - Frontiers in Neuroinformatics: ITK topic2012-present

International Neuroinformatics Coordinating Facility Registration and Atlasing Task Force Member (youtube video)2011-present

Spatial Transformations Informatics Technology Initiative (SIFTI) member2006

Neuroimaging Informatics Tools and Resources Clearinghouse member2006

Ad hoc Reviewer - Medical Image Analysis

Ad hoc Reviewer - Neuroimage

Ad hoc Reviewer - IEEE Transaction on Medical Imaging

Ad hoc Reviewer - Pediatrics

Ad hoc Reviewer - Medical Physics

Ad hoc Reviewer - Human Brain Mapping

Ad hoc Reviewer - IEEE Pattern Analysis Machine Intelligence

Ad hoc Reviewer - Nature Neuroscience

Campus Service

"Multi-Modality Analysis" talk @ CMROI Workshop, University of Pennsylvania2013

Organizer of Provost-sponsored Penn Interdisciplinary Seminar Series on multi-modality brain mapping: invited speakers and related activities2012-2013

Hosted Moriah Thomason for talk on Fetal Connectome2013

Hosted Mert Sabuncu for talk on Relevance Vector Machines2013

Hosted David Van Essen for talk on Human Connectome Project2012

See brainomics link for full list of activities.

Delivered "The Longitudinal Effect of Neurodegeneration on Language Network Neuroanatomy and Cognition," talk @ Pendergrass Symposium 2008

Media Coverage

Daily Mail UK article on SFN 2012 presentation2012

Washington post article on SFN 2012 presentation2012

PENN medicine press publicity for our MICCAI 2012 segmentation competition win: article2012

Professional Skills

Human Subjects Research Training University of Pennsylvania2013

Software Engineering & Programming - C++, CMake, R, Bash, Rst, LaTeX, Git, Gerrit, others as needed2000 - present

Visualization: e.g. a gource of ANTs development

Presentations: e.g. a Prezi about ANTs (WIP)

Reproducible science as a teaching tool: e.g. ANTs tutorial (WIP)

Other examples slideshow

Languages

SpanishConversational

Professional Memberships

The Organization for Human Brain Mapping (OHBM)2011-present

The International Society for Magnetic Resonance in Medicine (ISMRM) 2011-present

Web Links to Publications

Search Google Scholar

Search Pubmed

Journal Publications
  1. W. D. Hopkins & B. B. Avants,
    "Regional and Hemispheric Variation in Cortical Thickness in Chimpanzees (Pan troglodytes)",
    JOURNAL OF NEUROSCIENCE 33, 5241-5248 (2013)

  2. J. Kim, B. Avants, J. Whyte & J. C. Gee,
    "Methodological considerations in longitudinal morphometry of traumatic brain injury",
    FRONTIERS IN HUMAN NEUROSCIENCE 7, (2013)

  3. C. T. McMillan, B. Avants, D. J. Irwin, J. B. Toledo, D. A. Wolk, V. M. Van Deerlin, L. M. Shaw, J. Q. Trojanoswki & M. Grossman,
    "Can MRI screen for CSF biomarkers in neurodegenerative disease?",
    NEUROLOGY 80, 132-138 (2013)

  4. C. T. McMillan, D. J. Irwin, B. B. Avants, J. Powers, P. A. Cook, J. B. Toledo, E. McCarty Wood, V. M. Van Deerlin, V. M.-Y. Lee, J. Q. Trojanowski & M. Grossman,
    "White matter imaging helps dissociate tau from TDP-43 in frontotemporal lobar degeneration.",
    J Neurol Neurosurg Psychiatry , (2013)  PDF

  5. M. J. Weber, J. A. Detre, S. L. Thompson-Schill & B. B. Avants,
    "Reproducibility of functional network metrics and network structure: A comparison of task-related BOLD, resting ASL with BOLD contrast, and resting cerebral blood flow",
    Cognitive, Affective, & Behavioral Neuroscience accepted, (2013)

  6. A. Badea, S. Gewalt, B. B. Avants, J. J. Cook & G. A. Johnson,
    "Quantitative mouse brain phenotyping based on single and multispectral MR protocols",
    NEUROIMAGE 63, 1633-1645 (2012)

  7. S. R. Das, B. B. Avants, J. Pluta, H. Wang, J. W. Suh, M. W. Weiner, S. G. Mueller & P. A. Yushkevich,
    "Measuring longitudinal change in the hippocampal formation from in vivo high-resolution T2-weighted MRI",
    NEUROIMAGE 60, 1266-1279 (2012)

  8. R. Datta, J. Lee, J. Duda, B. B. Avants, C. H. Vite, B. Tseng, J. C. Gee, G. D. Aguirre & G. K. Aguirre,
    "A Digital Atlas of the Dog Brain",
    PLOS ONE 7, (2012)

  9. S. S. Ghosh, A. Klein, B. Avants & K. J. Millman,
    "Learning from open source software projects to improve scientific review",
    FRONTIERS IN COMPUTATIONAL NEUROSCIENCE 6, (2012)

  10. R. G. Gross, C. T. McMillan, K. Chandrasekaran, M. Dreyfuss, S. Ash, B. Avants, P. Cook, P. Moore, D. J. Libon, A. Siderowf & M. Grossman,
    "Sentence processing in Lewy body spectrum disorder: The role of working memory",
    BRAIN AND COGNITION 78, 85-93 (2012)

  11. J. L. Hanson, M. K. Chung, B. B. Avants, K. D. Rudolph, E. A. Shirtcliff, J. C. Gee, R. J. Davidson & S. D. Pollak,
    "Structural Variations in Prefrontal Cortex Mediate the Relationship between Early Childhood Stress and Spatial Working Memory",
    JOURNAL OF NEUROSCIENCE 32, 7917-7925 (2012)

  12. J. L. Hanson, J. W. Suh, B. M. Nacewicz, M. J. Sutterer, A. A. Cayo, D. E. Stodola, C. A. Burghy, H. Wang, B. B. Avants, P. A. Yushkevich, M. J. Essex, S. D. Pollak & R. J. Davidson,
    "Robust Automated Amygdala Segmentation via Multi-Atlas Diffeomorphic Registration.",
    Front Neurosci 6, 166 (2012)  PDF

  13. D. R. Hurst, P. T. Schoenemann, M. M. Loyet, B. B. Avants & J. C. Gee,
    "How well does endocranial morphology predict behavioral differences in primates?",
    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 147, 171 (2012)

  14. V. Jain, J. Duda, B. Avants, M. Giannetta, S. X. Xie, T. Roberts, J. A. Detre, H. Hurt, F. W. Wehrli & D. J. J. Wang,
    "Longitudinal Reproducibility and Accuracy of Pseudo-Continuous Arterial Spin-labeled Perfusion MR Imaging in Typically Developing Children",
    RADIOLOGY 263, 527-536 (2012)

  15. D. J. Libon, C. McMillan, B. Avants, A. Boller, B. Morgan, L. Burkholder, K. Chandrasekaran, L. Elman, L. McCluskey & M. Grossman,
    "Deficits in Concept Formation in Amyotrophic Lateral Sclerosis",
    NEUROPSYCHOLOGY 26, 422-429 (2012)

  16. M. M. Loyet, P. T. Schoenemann, B. B. Avants & J. C. Gee,
    "Associations between localized variation in brain anatomy and social behavior in healthy human subjects.",
    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 147, 196 (2012)

  17. T. Rohlfing & B. Avants,
    ""Nonparametric Local Smoothing" is not image registration.",
    BMC Res Notes 5, 610 (2012)  PDF

  18. N. J. Tustison, B. B. Avants, P. A. Cook, J. Kim, J. Whyte, J. C. Gee & J. R. Stone,
    "Logical circularity in voxel-based analysis: Normalization strategy may induce statistical bias.",
    Hum Brain Mapp , (2012)  PDF

  19. M. Ashtari, B. Avants, L. Cyckowski, K. L. Cervellione, D. Roofeh, P. Cook, J. Gee, S. Sevy & S. Kumra,
    "Medial temporal structures and memory functions in adolescents with heavy cannabis use",
    JOURNAL OF PSYCHIATRIC RESEARCH 45, 1055-1066 (2011)

  20. B. B. Avants, N. J. Tustison, J. Wu, P. A. Cook & J. C. Gee,
    "An Open Source Multivariate Framework for n-Tissue Segmentation with Evaluation on Public Data",
    NEUROINFORMATICS 9, 381-400 (2011)

  21. B. B. Avants, N. J. Tustison, G. Song, P. A. Cook, A. Klein & J. C. Gee,
    "A reproducible evaluation of ANTs similarity metric performance in brain image registration",
    NEUROIMAGE 54, 2033-2044 (2011)

  22. A. Boller, D. Libon, K. Rascovsky, R. G. Gross, M. Dreyfuss, B. Avants, L. Massimo, P. Moore, J. Kitain, H. Coslett, A. Chatterjee & M. Grossman,
    "Philadelphia Brief Assessment of Cognition (PBAC): A Validated Screening Measure for Dementia",
    NEUROLOGY 76, A511 (2011)

  23. S. R. Das, D. Mechanic-Hamilton, J. Pluta, M. Korczykowski, J. A. Detre & P. A. Yushkevich,
    "Heterogeneity of functional activation during memory encoding across hippocampal subfields in temporal lobe epilepsy.",
    Neuroimage 58, 1121-1130 (2011)  PDF

  24. B. Morgan, R. G. Gross, R. Clark, M. Dreyfuss, A. Boller, E. Camp, T.-W. Liang, B. Avants, C. T. McMillan & M. Grossman,
    "Some is not enough: Quantifier comprehension in corticobasal syndrome and behavioral variant frontotemporal dementia",
    NEUROPSYCHOLOGIA 49, 3532-3541 (2011)

  25. K. Murphy, B. van Ginneken, J. M. Reinhardt, S. Kabus, K. Ding, X. Deng, K. Cao, K. Du, G. E. Christensen, V. Garcia, T. Vercauteren, N. Ayache, O. Commowick, G. Malandain, B. Glocker, N. Paragios, N. Navab, V. Gorbunova, J. Sporring, M. de Bruijne, X. Han, M. P. Heinrich, J. A. Schnabel, M. Jenkinson, C. Lorenz, M. Modat, J. R. McClelland, S. Ourselin, S. E. A. Muenzing, M. A. Viergever, D. De Nigris, D. L. Collins, T. Arbel, M. Peroni, R. Li, G. C. Sharp, A. Schmidt-Richberg, J. Ehrhardt, R. Werner, D. Smeets, D. Loeckx, G. Song, N. Tustison, B. Avants, J. C. Gee, M. Staring, S. Klein, B. C. Stoel, M. Urschler, M. Werlberger, J. Vandemeulebroucke, S. Rit, D. Sarrut & J. P. W. Pluim,
    "Evaluation of Registration Methods on Thoracic CT: The EMPIRE10 Challenge",
    IEEE TRANSACTIONS ON MEDICAL IMAGING 30, 1901-1920 (2011)

  26. P. T. Schoenemann, R. Holloway, J. Monge, B. Avants & J. Gee,
    "Differences in endocranial shape between Homo and Pongids assessed through non-rigid deformation analysis of high-resolution CT images.",
    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 144, 265-266 (2011)

  27. N. J. Tustison, B. B. Avants, L. Flors, T. A. Altes, E. E. de lange, J. P. Mugler, III & J. C. Gee,
    "Ventilation-Based Segmentation of the Lungs Using Hyperpolarized He-3 MRI",
    JOURNAL OF MAGNETIC RESONANCE IMAGING 34, 831-841 (2011)

  28. N. Tustison, B. Avants, P. Cook, J. Kim, J. Whyte, J. Gee, S. Ahlers & J. Stone,
    "MULTIVARIATE ANALYSIS OF DIFFUSION TENSOR IMAGING AND CORTICAL THICKNESS MAPS IN A TRAUMATIC BRAIN INJURY (TBI) COHORT USING ADVANCED NORMALIZATION TOOLS (ANTS)",
    JOURNAL OF NEUROTRAUMA 28, A111 (2011)

  29. N. J. Tustison, B. B. Avants, M. Siqueira & J. C. Gee,
    "Topological Well-Composedness and Glamorous Glue: A Digital Gluing Algorithm for Topologically Constrained Front Propagation",
    IEEE TRANSACTIONS ON IMAGE PROCESSING 20, 1756-1761 (2011)

  30. H. Wang, S. R. Das, J. W. Suh, M. Altinay, J. Pluta, C. Craige, B. Avants, P. A. Yushkevich & A. D. N. Initia,
    "A learning-based wrapper method to correct systematic errors in automatic image segmentation: Consistently improved performance in hippocampus, cortex and brain segmentation",
    NEUROIMAGE 55, 968-985 (2011)

  31. S. Ash, C. McMillan, D. Gunawardena, B. Avants, B. Morgan, A. Khan, P. Moore, J. Gee & M. Grossman,
    "Speech errors in progressive non-fluent aphasia",
    BRAIN AND LANGUAGE 113, 13-20 (2010)

  32. B. B. Avants, P. A. Cook, L. Ungar, J. C. Gee & M. Grossman,
    "Dementia induces correlated reductions in white matter integrity and cortical thickness: A multivariate neuroimaging study with sparse canonical correlation analysis",
    NEUROIMAGE 50, 1004-1016 (2010)

  33. B. B. Avants, P. Yushkevich, J. Pluta, D. Minkoff, M. Korczykowski, J. Detre & J. C. Gee,
    "The optimal template effect in hippocampus studies of diseased populations",
    NEUROIMAGE 49, 2457-2466 (2010)

  34. C. Farag, V. Troiani, M. Bonner, C. Powers, B. Avants, J. Gee & M. Grossman,
    "Hierarchical Organization of Scripts: Converging Evidence from fMRI and Frontotemporal Degeneration",
    CEREBRAL CORTEX 20, 2453-2463 (2010)

  35. M. Grossman, P. J. Eslinger, V. Troiani, C. Anderson, B. Avants, J. C. Gee, C. McMillan, L. Massimo, A. Khan & S. Antani,
    "The role of ventral medial prefrontal cortex in social decisions Converging evidence from fMRI and frontotemporal lobar degeneration",
    NEUROPSYCHOLOGIA 48, 3505-3512 (2010)

  36. D. Gunawardena, S. Ash, C. McMillan, B. Avants, J. Gee & M. Grossman,
    "Why are patients with progressive nonfluent aphasia nonfluent?",
    NEUROLOGY 75, 588-594 (2010)

  37. J. L. Hanson, M. K. Chung, B. B. Avants, E. A. Shirtcliff, J. C. Gee, R. J. Davidson & S. D. Pollak,
    "Early Stress Is Associated with Alterations in the Orbitofrontal Cortex: A Tensor-Based Morphometry Investigation of Brain Structure and Behavioral Risk",
    JOURNAL OF NEUROSCIENCE 30, 7466-7472 (2010)

  38. J. Kim, J. Whyte, S. Patel, B. Avants, E. Europa, J. Wang, J. Slattery, J. C. Gee, H. B. Coslett & J. A. Detre,
    "Resting Cerebral Blood Flow Alterations in Chronic Traumatic Brain Injury: An Arterial Spin Labeling Perfusion fMRI Study",
    JOURNAL OF NEUROTRAUMA 27, 1399-1411 (2010)

  39. A. Klein, S. S. Ghosh, B. Avants, B. T. T. Yeo, B. Fischl, B. Ardekani, J. C. Gee, J. J. Mann & R. V. Parsey,
    "Evaluation of volume-based and surface-based brain image registration methods",
    NEUROIMAGE 51, 214-220 (2010)

  40. H. Rao, L. Betancourt, J. M. Giannetta, N. L. Brodsky, M. Korczykowski, B. B. Avants, J. C. Gee, J. Wang, H. Hurt, J. A. Detre & M. J. Farah,
    "Early parental care is important for hippocampal maturation: Evidence from brain morphology in humans",
    NEUROIMAGE 49, 1144-1150 (2010)

  41. P. T. Schoenemann, J. Monge, R. L. Holloway, B. B. Avants & J. C. Gee,
    "Creating statistical atlases of modern primate endocranial morphology rising non-rigid deformation analysis of high-resolution CT images.",
    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY , 208-209 (2010)

  42. N. J. Tustison, B. B. Avants, P. A. Cook, Y. Zheng, A. Egan, P. A. Yushkevich & J. C. Gee,
    "N4ITK: Improved N3 Bias Correction",
    IEEE TRANSACTIONS ON MEDICAL IMAGING 29, 1310-1320 (2010)

  43. D. J. J. Wang, X. Bi, B. B. Avants, T. Meng, S. Zuehlsdorff & J. A. Detre,
    "Estimation of Perfusion and Arterial Transit Time in Myocardium Using Free-Breathing Myocardial Arterial Spin Labeling With Navigator-Echo",
    MAGNETIC RESONANCE IN MEDICINE 64, 1289-1295 (2010)

  44. P. A. Yushkevich, H. Wang, J. Pluta, S. R. Das, C. Craige, B. B. Avants, M. W. Weiner & S. Mueller,
    "Nearly automatic segmentation of hippocampal subfields in in vivo focal T2-weighted MRI",
    NEUROIMAGE 53, 1208-1224 (2010)

  45. P. A. Yushkevich, B. B. Avants, S. R. Das, J. Pluta, M. Altinay, C. Craige & A. D. N. Initi,
    "Bias in estimation of hippocampal atrophy using deformation-based morphometry arises from asymmetric global normalization: An illustration in ADNI 3 T MRI data",
    NEUROIMAGE 50, 434-445 (2010)

  46. S. Ash, P. Moore, L. Vesely, D. Gunawardena, C. McMillan, C. Anderson, B. Avants & M. Grossman,
    "Non-fluent speech in frontotemporal lobar degeneration",
    JOURNAL OF NEUROLINGUISTICS 22, 370-383 (2009)

  47. B. Avants, A. Khan, L. McCluskey, L. Elman & M. Grossman,
    "Longitudinal Cortical Atrophy in Amyotrophic Lateral Sclerosis With Frontotemporal Dementia",
    ARCHIVES OF NEUROLOGY 66, 138-139 (2009)

  48. M. F. Bonner, L. Vesely, C. Price, C. Anderson, L. Richmond, C. Farag, B. Avants & M. Grossman,
    "Reversal of the concreteness effect in semantic dementia",
    COGNITIVE NEUROPSYCHOLOGY 26, 568-579 (2009)

  49. S. R. Das, B. B. Avants, M. Grossman & J. C. Gee,
    "Registration based cortical thickness measurement",
    NEUROIMAGE 45, 867-879 (2009)

  50. S. R. Das, D. Mechanic-Hamilton, M. Korczykowski, J. Pluta, S. Glynn, B. B. Avants, J. A. Detre & P. A. Yushkevich,
    "Structure Specific Analysis of the Hippocampus in Temporal Lobe Epilepsy",
    HIPPOCAMPUS 19, 517-525 (2009)

  51. A. Klein, J. Andersson, B. A. Ardekani, J. Ashburner, B. Avants, M.-C. Chiang, G. E. Christensen, D. L. Collins, J. Gee, P. Hellier, J. H. Song, M. Jenkinson, C. Lepage, D. Rueckert, P. Thompson, T. Vercauteren, R. P. Woods, J. J. Mann & R. V. Parsey,
    "Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration",
    NEUROIMAGE 46, 786-802 (2009)

  52. L. Massimo, C. Powers, P. Moore, L. Vesely, B. Avants, J. Gee, D. J. Libon & M. Grossman,
    "Neuroanatomy of Apathy and Disinhibition in Frontotemporal Lobar Degeneration",
    DEMENTIA AND GERIATRIC COGNITIVE DISORDERS 27, 96-104 (2009)

  53. J. Pluta, B. B. Avants, S. Glynn, S. Awate, J. C. Gee & J. A. Detre,
    "Appearance and Incomplete Label Matching for Diffeomorphic Template Based Hippocampus Segmentation",
    HIPPOCAMPUS 19, 565-571 (2009)

  54. P. T. Schoenemann, J. Monge, B. B. Avants & J. C. Gee,
    "An atlas of modern human cranial morpbology constructed via non-rigid deformation analysis of high-resolution CT images.",
    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY , 231 (2009)

  55. N. J. Tustison, B. B. Avants & J. C. Gee,
    "Directly Manipulated Free-Form Deformation Image Registration",
    IEEE TRANSACTIONS ON IMAGE PROCESSING 18, 624-635 (2009)

  56. P. A. Yushkevich, B. B. Avants, J. Pluta, S. Das, D. Minkoff, D. Mechanic-Hamilton, S. Glynn, S. Pickup, W. Liu, J. C. Gee, M. Grossman & J. A. Detre,
    "A high-resolution computational atlas of the human hippocampus from postmortem magnetic resonance imaging at 9.4 T",
    NEUROIMAGE 44, 385-398 (2009)

  57. B. Avants, J. T. Duda, J. Kim, H. Zhang, J. Pluta, J. C. Gee & J. Whyte,
    "Multivariate Analysis of Structural and Diffusion Imaging in Traumatic Brain Injury",
    ACADEMIC RADIOLOGY 15, 1360-1375 (2008)

  58. B. B. Avants, C. L. Epstein, M. Grossman & J. C. Gee,
    "Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain",
    MEDICAL IMAGE ANALYSIS 12, 26-41 (2008)

  59. M. Grossman, C. Anderson, A. Khan, B. Avants, L. Elman & L. McCluskey,
    "Impaired action knowledge in amyotrophic lateral sclerosis",
    NEUROLOGY 71, 1396-1401 (2008)

  60. M. Grossman, C. Anderson, A. Khan, B. Avants, L. Elman & L. McCluskey,
    "Neural basis for impaired action knowledge in amyotrophic lateral sclerosis",
    NEUROLOGY 70, A248 (2008)

  61. J. Kim, B. Avants, S. Patel, J. Whyte, B. H. Coslett, J. Pluta, J. A. Detre & J. C. Gee,
    "Structural consequences of diffuse traumatic brain injury: A large deformation tensor-based morphometry study",
    NEUROIMAGE 39, 1014-1026 (2008)

  62. L. M. Massimo, C. Anderson, P. Moore, B. Avants, D. Libon, B. Cynwyd & M. Grossman,
    "Neuroanatomical correlates of apathy and disinhibition in frontotemporal dementia",
    NEUROLOGY 70, A443 (2008)

  63. P. T. Schoenemann, R. L. Holloway, B. B. Avants & J. C. Gee,
    "Endocast asymmetry in pongids assessed via non-rigid deformation analysis of high-resolution CT images.",
    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY , 188 (2008)

  64. P. T. Schoenemann, R. L. Holloway, B. B. Avants & J. C. Gee,
    "The role of micro-morphological stress markers in the differential diagnosis of infectious bone diseases.",
    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY , 188-189 (2008)

  65. T. J. Simon, Z. Wu, B. Avants, H. Zhang, J. C. Gee & G. T. Stebbins,
    "Atypical cortical connectivity and visuospatial cognitive impairments are related in children with chromosome 22q11.2 deletion syndrome",
    BEHAVIORAL AND BRAIN FUNCTIONS 4, (2008)

  66. T. J. Simon, Z. Wu, B. Avants, H. Zhang, J. C. Gee & G. T. Stebbins,
    "Atypical cortical connectivity and visuospatial cognitive impairments are related in children with chromosome 22q11.2 deletion syndrome.",
    Behav Brain Funct 4, 25 (2008)  PDF

  67. G. K. Aguirre, A. M. Komaromy, 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, G. D. Aguirre & S. G. Jacobson,
    "Canine and human visual cortex intact and responsive despite early retinal blindness from RPE65 mutation",
    PLOS MEDICINE 4, 1117-1128 (2007)

  68. B. B. Avants, H. Hurt, J. M. Giannetta, C. L. Epstein, D. M. Shera, H. Rao, J. Wang & J. C. Gee,
    "Effects of heavy in utero cocaine exposure on adolescent caudate morphology",
    PEDIATRIC NEUROLOGY 37, 275-279 (2007)

  69. B. Avants, C. Anderson, M. Grossman & J. C. Gee,
    "Spatiotemporal normalization for longitudinal analysis of gray matter atrophy in frontotemporal dementia.",
    Med Image Comput Comput Assist Interv 10, 303-310 (2007)

  70. Y. Fan, H. Rao, H. Hurt, J. Giannetta, M. Korczykowski, D. Shera, B. B. Avants, J. C. Gee, J. Wang & D. Shen,
    "Multivariate examination of brain abnormality using both structural and functional MRI",
    NEUROIMAGE 36, 1189-1199 (2007)

  71. L. Ng, S. D. Pathak, C. Kuan, C. Lau, H. Dong, A. Sodt, C. Dang, B. Avants, P. Yushkevich, J. C. Gee, D. Haynor, E. Lein, A. Jones & M. Hawrylycz,
    "Neuroinformatics for genome-wide 3D gene expression mapping in the mouse brain",
    IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 4, 382-393 (2007)

  72. H. Rao, J. Wang, J. Giannetta, M. Korczykowski, D. Shera, B. B. Avants, J. Gee, J. A. Detre & H. Hurt,
    "Altered resting cerebral blood flow in adolescents with in utero cocaine exposure revealed by perfusion functional MRI",
    PEDIATRICS 120, E1245-E1254 (2007)

  73. P. T. Schoenemann, J. Gee, B. Avants, R. L. Holloway, J. Monge & J. Lewis,
    "Validation of plaster endocast morphology through 3D CT image analysis",
    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 132, 183-192 (2007)

  74. P. T. Schoenemann, J. Monge, B. B. Avants, D. Glotzer & J. C. Gee,
    "Sex differences in cranial form assessed via non-rigid deformation analysis of high-resolution CT images.",
    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY , 209 (2007)

  75. H. Zhang, B. B. Avants, P. A. Yushkevich, J. H. Woo, S. Wang, L. F. McCluskey, L. B. Elman, E. R. Melhem & J. C. Gee,
    "Differences: An example study using amyotrophic lateral sclerosis",
    IEEE TRANSACTIONS ON MEDICAL IMAGING 26, 1585-1597 (2007)

  76. H. Zhang, B. B. Avants, P. A. Yushkevich, J. H. Woo, S. Wang, L. F. McCluskey, L. B. Elman, E. R. Melhem & 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 Trans Med Imaging 26, 1585-1597 (2007)  PDF

  77. B. B. Avants, P. T. Schoenemann & J. C. Gee,
    "Lagrangian frame diffeomorphic image registration: Morphometric comparison of human and chimpanzee cortex",
    MEDICAL IMAGE ANALYSIS 10, 397-412 (2006)

  78. B. Avants, M. Grossman & J. Gee,
    "The correlation of cognitive decline with frontotemporal dementia induced annualized gray matter loss using diffeomorphic morphometry",
    ALZHEIMER DISEASE & ASSOCIATED DISORDERS 19, S25-S28 (2005)

  79. B. Avants, J. Gee, P. Schoenemann, J. Monge, J. Lewis & R. Holloway,
    "A new method for assessing endbcast morphology: calculating local curvature from 3D CT images.",
    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY , 67 (2005)

  80. B. Avants, J. Gee, P. T. Schoenemann, J. Monge, J. E. Lewis & R. L. Holloway,
    "Validation of plaster endocast morphology through 3D CT image analysis",
    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY , 56 (2004)

  81. B. Avants & J. Gee,
    "Geodesic estimation for large deformation anatomical shape averaging and interpolation",
    NEUROIMAGE 23, S139-S150 (2004)

  82. P. T. Schoenemann, B. B. Avants, J. C. Gee, L. D. Glotzer & M. J. Sheehan,
    "Analysis of chimp-human brain differences via non-rigid deformation of 3D MR images",
    AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY , 174-175 (2004)

  83. A. Dubb, R. Gur, B. Avants & J. Gee,
    "Characterization of sexual dimorphism in the human corpus callosum",
    NEUROIMAGE 20, 512-519 (2003)

  84. B. Avants, D. Soodak & G. Ruppeiner,
    "Measuring the electrical conductivity of the earth",
    AMERICAN JOURNAL OF PHYSICS 67, 593-598 (1999)

Conference Publications
  1. P. Dhillon, B. M. Kandel, D. Wolk, J. C. Gee & B. Avants,
    "Prior-based Eigenanatomy for Classification of Autism Spectrum Disorder",
    PRNI , (2013)

  2. B. M. Kandel, D. Wolk, J. C. Gee & B. Avants,
    "Predicting Cognitive Data From Medical Images Using Sparse Linear Regression ",
    Inf. Process. Med. Imaging , (2013)

  3. B. Avants, P. Dhillon, B. M. Kandel, P. A. Cook, C. T. McMillan, M. Grossman & J. C. Gee,
    "Eigenanatomy improves detection power for longitudinal cortical change.",
    Med Image Comput Comput Assist Interv 15, 206-213 (2012)

  4. P. A. Cook, B. B. Avants, C. T. McMillan, J. Powers, J. C. Gee & M. Grossman,
    "Multimodal neuroimaging reveals gray and white matter associations with verbal fluency in frontotemporal degeneration",
    DEMENTIA AND GERIATRIC COGNITIVE DISORDERS 33, 154-155 (2012)

  5. B. Avants, P. A. Cook, C. McMillan, M. Grossman, N. J. Tustison, Y. Zheng & J. C. Gee,
    "Sparse unbiased analysis of anatomical variance in longitudinal imaging.",
    Med Image Comput Comput Assist Interv 13, 324-331 (2010)

  6. H. Wang, S. Das, J. Pluta, C. Craige, M. Altinay, B. Avants, M. Weiner, S. Mueller & P. Yushkevich,
    "Standing on the shoulders of giants: improving medical image segmentation via bias correction.",
    Med Image Comput Comput Assist Interv 13, 105-112 (2010)

  7. H. Sun, B. B. Avants, A. F. Frangi, F. Sukno, J. C. Geel & P. A. Yushkevich,
    "Cardiac medial modeling and time-course heart wall thickness analysis.",
    Med Image Comput Comput Assist Interv 11, 766-773 (2008)

  8. P. A. Yushkevich, B. B. Avants, J. Pluta, D. Minkoff, J. A. Detre, M. Grossman & J. C. Gee,
    "Shape-based alignment of hippocampal subfields: evaluation in postmortem MRI.",
    Med Image Comput Comput Assist Interv 11, 510-517 (2008)

  9. B. B. Avants, M. Grossman & J. C. Gee,
    "Symmetric diffeomorphic image registration: Evaluating automated labeling of elderly and neurodegenerative cortex and frontal lobe",
    4057, 50-57 (2006)

  10. B. B. Avants, C. L. Epstein & J. C. Gee,
    "Geodesic image normalization and temporal parameterization in the space of diffeomorphisms",
    4091, 9-16 (2006)

  11. Z. Song, N. Tustison, B. Avants & J. C. Gee,
    "Integrated graph cuts for brain MRI segmentation",
    4191, 831-838 (2006)

  12. Z. Song, N. Tustison, B. Avants & J. C. Gee,
    "Integrated graph cuts for brain MRI segmentation.",
    Med Image Comput Comput Assist Interv 9, 831-838 (2006)

  13. N. J. Tustison, B. B. Avants, T. A. Sundaram, J. T. Duda & J. C. Gee,
    "A generalization of Free-Form Deformation image registration within the ITK finite element framework",
    4057, 238-246 (2006)

  14. P. A. Yushkevich, B. B. Avants, L. Ng, M. Hawrylycz, P. D. Burstein, H. Zhang & J. C. Gee,
    "3D mouse brain reconstruction from histology using a coarse-to-fine approach",
    4057, 230-237 (2006)

  15. B. Avants, C. Epstein & J. Gee,
    "Geodesic image interpolation: Parameterizing and interpolating spatiotemporal images",
    3752, 247-258 (2005)

  16. P. Cook, H. Zhang, B. Avants, P. Yushkevich, D. Alexander, J. Gee, O. Ciccarelli & A. Thompson,
    "An automated approach to connectivity-based partitioning of brain structures",
    3749, 164-171 (2005)

  17. T. Sundaram, B. Avants & J. Gee,
    "Towards a dynamic model of pulmonary parenchymal deformation: Evaluation of methods for temporal reparameterization of lung data",
    3750, 328-335 (2005)

  18. T. A. Sundaram, B. B. Avants & J. C. Gee,
    "Towards a dynamic model of pulmonary parenchymal deformation: evaluation of methods for temporal reparameterization of lung data.",
    Med Image Comput Comput Assist Interv 8, 328-335 (2005)

  19. B. Avants & J. Gee,
    "Symmetric geodesic shape averaging and shape interpolation",
    3117, 99-110 (2004)

  20. T. Sundaram, B. Avants & J. Gee,
    "A dynamic model of average lung deformation using capacity-based reparameterization and shape averaging of lung MR images",
    3217, 1000-1007 (2004)

  21. B. Avants & J. Gee,
    "Formulation and evaluation of variational curve matching with prior constraints",
    2717, 21-30 (2003)

  22. B. Avants & J. Gee,
    "The shape operator for differential analysis of images",
    2732, 101-113 (2003)

  23. B. Avants & J. Gee,
    "Continuous curve matching with scale-space curvature and extrema-based scale selection",
    2695, 798-813 (2003)

  24. B. Avants & J. Williams,
    "An adaptive minimal path generation technique for vessel tracking in CTA/CE-MRA volume images",
    1935, 707-716 (2000)