open source, neuro, learning, collaboration, sound theory, solid results

Publications

Some links to papers (or refs to papers) below:

My papers as listed in pubmed.

ANTs paper 2010 (pdf)

Atropos tech report (pdf)

SCCA applied to FTD and AD (pdf)

Glamorous Glue topologically constrained segmentation (pdf)

a slender selection of references

Avants, B. B.; Tustison, N. J.; Song, G.; Cook, P. A.; Klein, A. & Gee, J. C. (2011), ‘A reproducible evaluation of ANTs similarity metric performance in brain image registration.’, Neuroimage 54(3), 2033–2044.

Ash, S.; McMillan, C.; Gunawardena, D.; Avants, B.; Morgan, B.; Khan, A.; Moore, P.; Gee, J. & Grossman, M. (2010), ‘Speech errors in progressive non-fluent aphasia.’, Brain Lang 113(1), 13–20.

Avants, B. B.; Cook, P. A.; Ungar, L.; Gee, J. C. & Grossman, M. (2010), ‘Dementia induces correlated reductions in white matter integrity and cortical thickness: A multivariate neuroimaging study with sparse canonical correlation analysis.’, Neuroimage 50(3), 1004–1016.

Avants, B.; Cook, P. A.; McMillan, C.; Grossman, M.; Tustison, N. J.; Zheng, Y. & Gee, J. C. (2010), ‘Sparse unbiased analysis of anatomical variance in longitudinal imaging.’, Med Image Comput Comput Assist Interv 13(Pt 1), 324–331.

Avants, B. B.; Yushkevich, P.; Pluta, J.; Minkoff, D.; Korczykowski, M.; Detre, J. & Gee, J. C. (2010), ‘The optimal template effect in hippocampus studies of diseased populations.’, Neuroimage 49(3), 2457–2466.

Avants, B. B.; Tustison, N. J.; Song, G.; Cook, P. A.; Klein, A. & Gee, J. C. (2010), ‘A reproducible evaluation of ANTs similarity metric performance in brain image registration.’, Neuroimage.

Farag, C.; Troiani, V.; Bonner, M.; Powers, C.; Avants, B.; Gee, J. & Grossman, M. (2010), ‘Hierarchical organization of scripts: converging evidence from FMRI and frontotemporal degeneration.’, Cereb Cortex 20(10), 2453–2463.

Grossman, M.; Eslinger, P. J.; Troiani, V.; Anderson, C.; Avants, B.; Gee, J. C.; McMillan, C.; Massimo, L.; Khan, A. & Antani, S. (2010), ‘The role of ventral medial prefrontal cortex in social decisions: Converging evidence from fMRI and frontotemporal lobar degeneration.’, Neuropsychologia 48(12), 3505–3512.

Hanson, J. L.; Chung, M. K.; Avants, B. B.; Shirtcliff, E. A.; Gee, J. C.; Davidson, R. J. & Pollak, S. D. (2010), ‘Early stress is associated with alterations in the orbitofrontal cortex: a tensor-based morphometry investigation of brain structure and behavioral risk.’, J Neurosci 30(22), 7466–7472.

Kim, J.; Whyte, J.; Patel, S.; Avants, B.; Europa, E.; Wang, J.; Slattery, J.; Gee, J. C.; Coslett, H. B. & Detre, J. A. (2010), ‘Resting cerebral blood flow alterations in chronic traumatic brain injury: an arterial spin labeling perfusion FMRI study.’, J Neurotrauma 27(8), 1399–1411.

Klein, A.; Ghosh, S. S.; Avants, B.; Yeo, B. T. T.; Fischl, B.; Ardekani, B.; Gee, J. C.; Mann, J. J. & Parsey, R. V. (2010), ‘Evaluation of volume-based and surface-based brain image registration methods.’, Neuroimage 51(1), 214–220.

Rao, H.; Betancourt, L.; Giannetta, J. M.; Brodsky, N. L.; Korczykowski, M.; Avants, B. B.; Gee, J. C.; Wang, J.; Hurt, H.; Detre, J. A. & Farah, M. J. (2010), ‘Early parental care is important for hippocampal maturation: evidence from brain morphology in humans.’, Neuroimage 49(1), 1144–1150.

Tustison, N. J.; Avants, B. B.; Cook, P. A.; Zheng, Y.; Egan, A.; Yushkevich, P. A. & Gee, J. C. (2010), ‘N4ITK: improved N3 bias correction.’, IEEE Trans Med Imaging 29(6), 1310–1320.

Tustison, N.; Avants, B.; Siqueira, M. & Gee, J. (2010), ‘Topological Well-Composedness and Glamorous Glue: A Digital Gluing Algorithm for Topologically Constrained Front Propagation.’, IEEE Trans Image Process.

Wang, H.; Das, S.; Pluta, J.; Craige, C.; Altinay, M.; Avants, B.; Weiner, M.; Mueller, S. & Yushkevich, P. (2010), ‘Standing on the shoulders of giants: improving medical image segmentation via bias correction.’, Med Image Comput Comput Assist Interv 13(Pt 3), 105–112.

Wang, D. J. J.; Bi, X.; Avants, B. B.; Meng, T.; Zuehlsdorff, S. & Detre, J. A. (2010), ‘Estimation of perfusion and arterial transit time in myocardium using free-breathing myocardial arterial spin labeling with navigator-echo.’, Magn Reson Med 64(5), 1289–1295.

Yushkevich, P. A.; Avants, B. B.; Das, S. R.; Pluta, J.; Altinay, M.; Craige, C. & Initiative, A. D. N. (2010), ‘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(2), 434–445.

Yushkevich, P. A.; Wang, H.; Pluta, J.; Das, S. R.; Craige, C.; Avants, B. B.; Weiner, M. W. & Mueller, S. (2010), ‘Nearly automatic segmentation of hippocampal subfields in in vivo focal T2-weighted MRI.’, Neuroimage 53(4), 1208–1224.

Avants, B.; Khan, A.; McCluskey, L.; Elman, L. & Grossman, M. (2009), ‘Longitudinal cortical atrophy in amyotrophic lateral sclerosis with frontotemporal dementia.’, Arch Neurol 66(1), 138–139.

Bonner, M. F.; Vesely, L.; Price, C.; Anderson, C.; Richmond, L.; Farag, C.; Avants, B. & Grossman, M. (2009), ‘Reversal of the concreteness effect in semantic dementia.’, Cogn Neuropsychol 26(6), 568–579.

Das, S. R.; Avants, B. B.; Grossman, M. & Gee, J. C. (2009), ‘Registration based cortical thickness measurement.’, Neuroimage 45(3), 867–879.

Das, S. R.; Mechanic-Hamilton, D.; Korczykowski, M.; Pluta, J.; Glynn, S.; Avants, B. B.; Detre, J. A. & Yushkevich, P. A. (2009), ‘Structure specific analysis of the hippocampus in temporal lobe epilepsy.’, Hippocampus 19(6), 517–525.

Klein, A.; Andersson, J.; Ardekani, B. A.; Ashburner, J.; Avants, B.; Chiang, M.-C.; Christensen, G. E.; Collins, D. L.; Gee, J.; Hellier, P.; Song, J. H.; Jenkinson, M.; Lepage, C.; Rueckert, D.; Thompson, P.; Vercauteren, T.; Woods, R. P.; Mann, J. J. & Parsey, R. V. (2009), ‘Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration.’, Neuroimage 46(3), 786–802.

Massimo, L.; Powers, C.; Moore, P.; Vesely, L.; Avants, B.; Gee, J.; Libon, D. J. & Grossman, M. (2009), ‘Neuroanatomy of apathy and disinhibition in frontotemporal lobar degeneration.’, Dement Geriatr Cogn Disord 27(1), 96–104.

Pluta, J.; Avants, B. B.; Glynn, S.; Awate, S.; Gee, J. C. & Detre, J. A. (2009), ‘Appearance and incomplete label matching for diffeomorphic template based hippocampus segmentation.’, Hippocampus 19(6), 565–571.

Tustison, N. J.; Avants, B. B. & Gee, J. C. (2009), ‘Directly manipulated free-form deformation image registration.’, IEEE Trans Image Process 18(3), 624–635.

Yushkevich, P. A.; Avants, B. B.; Pluta, J.; Das, S.; Minkoff, D.; Mechanic-Hamilton, D.; Glynn, S.; Pickup, S.; Liu, W.; Gee, J. C.; Grossman, M. & Detre, J. A. (2009), ‘A high-resolution computational atlas of the human hippocampus from postmortem magnetic resonance imaging at 9.4 T.’, Neuroimage 44(2), 385–398.

Avants, B. B.; Epstein, C. L.; Grossman, M. & Gee, J. C. (2008), ‘Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain.’, Med Image Anal 12(1), 26–41.

Avants, B.; Duda, J. T.; Kim, J.; Zhang, H.; Pluta, J.; Gee, J. C. & Whyte, J. (2008), ‘Multivariate analysis of structural and diffusion imaging in traumatic brain injury.’, Acad Radiol 15(11), 1360–1375.

Grossman, M.; Anderson, C.; Khan, A.; Avants, B.; Elman, L. & McCluskey, L. (2008), ‘Impaired action knowledge in amyotrophic lateral sclerosis.’, Neurology 71(18), 1396–1401.

Kim, J.; Avants, B.; Patel, S.; Whyte, J.; Coslett, B. H.; Pluta, J.; Detre, J. A. & Gee, J. C. (2008), ‘Structural consequences of diffuse traumatic brain injury: A large deformation tensor-based morphometry study.’, Neuroimage 39(3), 1014–1026.

Simon, T. J.; Wu, Z.; Avants, B.; Zhang, H.; Gee, J. C. & Stebbins, G. T. (2008), ‘Atypical cortical connectivity and visuospatial cognitive impairments are related in children with chromosome 22q11.2 deletion syndrome.’, Behav Brain Funct 4, 25.

Sun, H.; Avants, B. B.; Frangi, A. F.; Sukno, F.; Geel, J. C. & Yushkevich, P. A. (2008), ‘Cardiac medial modeling and time-course heart wall thickness analysis.’, Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv 11(Pt 2), 766–773.

Yushkevich, P. A.; Avants, B. B.; Pluta, J.; Minkoff, D.; Detre, J. A.; Grossman, M. & Gee, J. C. (2008), ‘Shape-based alignment of hippocampal subfields: evaluation in postmortem MRI.’, Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv 11(Pt 1), 510–517.

Aguirre, G. K.; Komeromy, A. M.; Cideciyan, A. V.; Brainard, D. H.; Aleman, T. S.; Roman, A. J.; Avants, B. B.; Gee, J. C.; Korczykowski, M.; Hauswirth, W. W.; Acland, G. M.; Aguirre, G. D. & Jacobson, S. G. (2007), ‘Canine and human visual cortex intact and responsive despite early retinal blindness from RPE65 mutation.’, PLoS Med 4(6), e230.

Avants, B.; Anderson, C.; Grossman, M. & Gee, J. C. (2007), ‘Spatiotemporal normalization for longitudinal analysis of gray matter atrophy in frontotemporal dementia.’, Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv 10(Pt 2), 303–310.

Avants, B. B.; Duda, J. T.; Zhang, H. & Gee, J. C. (2007), ‘Multivariate normalization with symmetric diffeomorphisms for multivariate studies.’, Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv 10(Pt 1), 359–366.

Avants, B. B.; Hurt, H.; Giannetta, J. M.; Epstein, C. L.; Shera, D. M.; Rao, H.; Wang, J. & Gee, J. C. (2007), ‘Effects of heavy in utero cocaine exposure on adolescent caudate morphology.’, Pediatr Neurol 37(4), 275–279.

Fan, Y.; Rao, H.; Hurt, H.; Giannetta, J.; Korczykowski, M.; Shera, D.; Avants, B. B.; Gee, J. C.; Wang, J. & Shen, D. (2007), ‘Multivariate examination of brain abnormality using both structural and functional MRI.’, Neuroimage 36(4), 1189–1199.

Ng, L.; Pathak, S. D.; Kuan, C.; Lau, C.; Dong, H.; Sodt, A.; Dang, C.; Avants, B.; Yushkevich, P.; Gee, J. C.; Haynor, D.; Lein, E.; Jones, A. & Hawrylycz, M. (2007), ‘Neuroinformatics for genome-wide 3D gene expression mapping in the mouse brain.’, IEEE/ACM Trans Comput Biol Bioinform 4(3), 382–393.

Rao, H.; Wang, J.; Giannetta, J.; Korczykowski, M.; Shera, D.; Avants, B. B.; Gee, J.; Detre, J. A. & Hurt, H. (2007), ‘Altered resting cerebral blood flow in adolescents with in utero cocaine exposure revealed by perfusion functional MRI.’, Pediatrics 120(5), e1245–e1254.

Schoenemann, P. T.; Gee, J.; Avants, B.; Holloway, R. L.; Monge, J. & Lewis, J. (2007), ‘Validation of plaster endocast morphology through 3D CT image analysis.’, Am J Phys Anthropol 132(2), 183–192.

Zhang, H.; Avants, B. B.; Yushkevich, P. A.; Woo, J. H.; Wang, S.; McCluskey, L. F.; Elman, L. B.; Melhem, E. R. & Gee, J. C. (2007), ‘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(11), 1585–1597.

Avants, B.; Epstein, C. L. & Gee, J. C. (2006), ‘Geodesic image normalization in the space of diffeomorphisms’, Mathematical Foundations of Computational Anatomy, 125-133.

Avants, B.; Grossman, M. & Gee, J. C. (2006), ‘Symmetric Diffeomorphic Image Registration: Evaluating Automated Labeling of Elderly and Neurodegenerative Cortex and Frontal Lobe’, WBIR, 50-57.

Avants, B. B.; Schoenemann, P. T. & Gee, J. C. (2006), ‘Lagrangian frame diffeomorphic image registration: Morphometric comparison of human and chimpanzee cortex.’, Med Image Anal 10(3), 397–412.

Song, Z.; Tustison, N.; Avants, B. & Gee, J. C. (2006), ‘Integrated graph cuts for brain MRI segmentation.’, Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv 9(Pt 2), 831–838.

Avants, B.; Grossman, M. & Gee, J. C. (2005), ‘The correlation of cognitive decline with frontotemporal dementia induced annualized gray matter loss using diffeomorphic morphometry.’, Alzheimer Dis Assoc Disord 19 Suppl 1, S25–S28.

Cook, P. A.; Zhang, H.; Avants, B. B.; Yushkevich, P.; Alexander, D. C.; Gee, J. C.; Ciccarelli, O. & Thompson, A. J. (2005), ‘An automated approach to connectivity-based partitioning of brain structures.’, Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv 8(Pt 1), 164–171.

Sundaram, T. A.; Avants, B. B. & Gee, J. C. (2005), ‘Towards a dynamic model of pulmonary parenchymal deformation: evaluation of methods for temporal reparameterization of lung data.’, Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv 8(Pt 2), 328–335.

Avants, B. & Gee, J. (2004), ‘Symmetric Geodesic Shape Averaging and Shape Interpolation’, Computer Vision Approaches to Medical Image Analysis (CVAMIA) and Mathematical Methods in Biomedical Image Analysis (MMBIA) Workshop 2004 in conjunction with the 8th European Conference on Computer Vision, Prague, CZ., 99-110.

Avants, B. & Gee, J. C. (2004), ‘Geodesic estimation for large deformation anatomical shape averaging and interpolation.’, Neuroimage 23 Suppl 1, S139–S150.

Avants, B. & Gee, J. (2003), ‘The shape operator for differential analysis of images.’, Inf Process Med Imaging 18, 101–113.

Dubb, A.; Gur, R.; Avants, B. & Gee, J. (2003), ‘Characterization of sexual dimorphism in the human corpus callosum.’, Neuroimage 20(1), 512–519.

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