Shattuck Research Group

Journal Articles

pre-prints
  1. Kim Y, Joshi AA, Choi S, Joshi SH, Bhushan C, Varadarajan D, Haldar JP, Leahy RM, Shattuck DW (2023) BrainSuite BIDS App: Containerized Workflows for MRI Analysis. bioRxiv 2023.03.14.532686; doi: 10.1101/2023.03.14.532686 [in review at NeuroImage]
published
  1. Joshi AA, Choi S, Chong M, Sonkar G, Gonzalez-Martinez J, Nair D, Wisnowski JL, Haldar JP, Shattuck DW, Damasio H, Leahy RM (2022) A Hybrid High-Resolution Anatomical MRI Atlas with Sub-parcellation of Cortical Gyri using Resting fMRI Journal of Neuroscience Methods 374:109566.
  2. Cain JA, Visagan S, Johnson MA, Crone J, Blades R, Spivak NM, Shattuck DW, Monti MM (2021) Real Time and Delayed Effects of Subcortical Low Intensity Focused Ultrasound Scientific Reports 11(1):6100.
  3. Kuhn T, Jin Y, Huang C, Kim Y, Nir TM, Gullettc JM, Jones J, Singer EJ, Shattuck DW, Jahanshad N, Bookheimer SY, Hinkin CH, Zhu H, Thompson PM, Thames AD (2019) The Joint Effect of Aging and HIV Infection on Microstructure of White Matter Bundles Human Brain Mapping 40:4370-4380.
  4. Shattuck DW (2018) Multiuser virtual reality environment for visualising neuroimaging data Health Technology Letters, 5(5):183-188.
  5. Phillips OR, Joshi SH, Narr KL, Shattuck DW, Singh M, Di Paola M, Ploner CJ, Prüss H, Paul F, Finke C (2018) Superficial white matter damage in anti-NMDA receptor encephalitis Journal of Neurology, Neurosurgery, and Psychiatry 89(5):518-525.
  6. Chong M, Bhushan C, Joshi AA, Choi S, Haldar JP, Shattuck DW, Spreng RN, Leahy RM (2017) Individual parcellation of resting fMRI with a group functional connectivity prior. NeuroImage, 156:87-100.
  7. Wang ZI, Krishnan B, Shattuck DW, Leahy RM, Moosa ANV, Wyllie E, Burgess RC, Al-Sharif NB, Joshi AA, Alexopoulos AV, Mosher JC, Udayasankar U, the Pediatric Imaging Neurocognition and Genetics Study, Jones SE (2016) Automated MRI Volumetric Analysis in Epilepsy Patients with Rasmussen’s Syndrome. American Journal of Neuroradiology 37(12):2348-2355
  8. Phillips OR, Joshi SH, Squitieri F, Sanchez-Castaneda C, Narr K, Shattuck DW, Caltagirone C, Sabatini U, Di Paola M (2016) Major Superficial White Matter Abnormalities in Huntington Disease Frontiers in Neuroscience, 10(0197)
  9. Phillips O, Joshi S, Squitieri F, Sanchez-Castaneda C, Narr K, Shattuck D, Elifani F, Caltagirone C, Sabatini U, Di Paola M (2016) The Superficial White Matter in Alzheimer’s Disease. Human Brain Mapping, 37(4):1321–1334.
  10. Wei M, Joshi AA, Zhang M, Meid L, Manis FR, He Q, Beattie RL, Xue G, Shattuck DW, Leahy RM, Xue F, Houston SM, C Cheng, Q Dong, ZL Lu (2015) How age of acquisition influences brain architecture in bilinguals. Journal of Neurolinguistics, 36:35-55.
  11. Marusak HA, Furman DJ, Kuruvadi N, Shattuck DW, Joshi SH, Joshi AA, Etkin A, Thomason ME (2015) Amygdala responses to salient social cues vary with oxytocin receptor genotype in youth. Neuropsychologia. 2015 Oct 15. pii: S0028-3932(15)30191-3.
  12. Marusak HA, Kuruvadi N, Vila AM, Shattuck DW, Joshi S, Joshi AA, Jella PK, Thomason ME (2015) Interactive effects of BDNF Val66Met genotype and trauma on limbic brain anatomy in childhood. European Child & Adolescent Psychiatry
  13. Bhushan C, Haldar JP, Choi S, Joshi AA, Shattuck DW, and Leahy RM (2015) Co-registration and Distortion Correction of Diffusion and Anatomical Images Based on Inverse Contrast Normalization. NeuroImage 115:269-80
  14. Habibi A, Ilari B, Crimi K, Metke M, Kaplan JT, Joshi AA, Leahy RM, Shattuck DW, Choi SY, Ficek B, Haldar JP, Damasio A, Damasio H (2014) An Equal Start: Absence of Group Differences in Cognitive, Social and Neural Measures Prior to Music or Sports Training in Children. Frontiers in Human Neuroscience, 8(690)1:11.
  15. Toga AW, Clark KA, Thompson PM, Shattuck DW, Van Horn JD (2012) Mapping the Human Connectome. Neurosurgery 71(1):1-5.
  16. Toga AW, Dinov ID, Thompson PM, Woods RP, Van Horn JD, Shattuck DW, Parker DS (2012) The Center for Computational Biology: Resources, Achievements, and Challenges J Am Med Inform Assoc, 19(2):202-6.
  17. Luders E, Sanchez FJ, Tosun D, Shattuck DW, Gaser CW, Vilain E, Toga AW (2012) Increased Cortical Thickness in Male-to-Female Transsexualism.Journal of Behavioral and Brain Science 2(3):357-362.
  18. Joshi AA, Chaudhari JA, Li C, Dutta J, Cherry SR, Shattuck DW, Toga AW and Leahy RM (2010) DigiWarp: a method for deformable mouse atlas warping to surface topographic data. Physics in Medicine and Biology 55(20):6197-214.
  19. Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan MA, Schneider JE, Tomancak P, Heriche J-K (2010) Visualization of image data from cells to organisms. Nature Methods 7(3):S26-S41.
  20. O’Donoghue SI, Gavin A-C, Gehlenborg N, Goodsell DS, Jean-Karim Heriche, Cydney B, Nielsen C, North C, Olson AJ, Procter JB, Shattuck DW, Walter T (2010) Visualizing biological data – now and in the future. Nature Methods 7(3):S2-S4.
  21. Tohka J, Dinov ID, Shattuck DW, and Arthur W. Toga (2010) Brain MRI Tissue Classification Based on Local Markov Random Fields. Magnetic Resonance Imaging 28(4):557–573.
  22. Joshi AA, Pantazis D, Li Q, Damasio H, Shattuck D, Toga A, Leahy RM (2010) Sulcal set optimization for cortical surface registration. NeuroImage, 2010 Jan 4.
  23. Pantazis D, Joshi AA, Jintao J, Shattuck DW, Bernstein LE, Damasio H, and Leahy RM (2010) Comparison of landmark-based and automatic methods for cortical surface registration. NeuroImage 49(3):2479-93.
  24. Eckstein I, Shattuck DW, Stein JL, McMahon KL, de Zubicaray GI, Wright MJ, Thompson PM, and Toga AW (2009) Active Fibers: Matching Deformable Tract Templates to Diffusion Tensor Images. NeuroImage 47(Suppl 2):T82-9.
  25. Joshi AA, Shattuck DW, Thompson PM, and Leahy RM (2009) A Parameterization-based Numerical Method for Isotropic and Anisotropic Diffusion Smoothing on Non-Flat Surfaces IEEE Trans. on Image Processing 18(6):1358-1365.
  26. Hageman NS, Toga AW, Narr KL, Shattuck DW (2009) A Diffusion Tensor Imaging Tractography Algorithm Based on Navier-Stokes Fluid Mechanics IEEE Trans. on Medical Imaging 28(3):348-360
  27. Shattuck DW, Joshi AA, Pantazis D, Kan E, Dutton RA, Sowell ER, Thompson PM, Toga AW, Leahy RM (2009) Semi-automated Method for Delineation of Landmarks on Models of the Cerebral Cortex. Journal of Neuroscience Methods 178(2):385-392.
  28. Shattuck DW, Prasad G, Mirza M, Narr KL, and Toga AW (2009) Online Resource for Validation of Brain Segmentation Algorithms. NeuroImage 45(2):431-439.
  29. Chiang MC, Barysheva M, Shattuck DW, Lee AD, Madsen S, Avedissian C, Klunder AD, Toga AW, McMahon KL, de Zubicaray GI, Wright MJ, Srivastava A, Balov N, and Thompson PM (2009) Genetics of Brain Fiber Architecture and Intellectual Performance. Journal of Neuroscience 29(7):2212-2224.
  30. Narr KL, Hageman N, Woods RP, Hamilton LS, Clark K, Phillips O, Shattuck DW, Asarnow RF, Toga AW (2009) Mean diffusivity: A biomarker for CSF-related disease and genetic liability effects in schizophrenia Psychiatric Research: NeuroImaging 171(1):20-32.
  31. de Zubicaray G, Chiang MC, McMahon KL Shattuck DW, Toga AW, Martin NG, Wright MJ, and Thompson PM (2008) Meeting the challenges of neuroimaging geneticsBrain Imaging and Behavior 2(4):258-263
  32. Shattuck DW, Mirza M, Adisetiyo V, Hojatkashani C, Salamon G, Narr KL, Poldrack RA, Bilder RM, Toga AW (2008) Construction of a 3D Probabilistic Atlas of Human Brain Structures NeuroImage 39(3):1064-1080.
  33. Joshi AA, Shattuck DW, Thompson PM, and Richard M. Leahy (2007) Surface-Constrained Volumetric Brain Registration Using Harmonic Mappings IEEE Trans. on Medical Imaging 26(12):1657-1669
  34. Tohka J, Krestyannikov E, Dinov ID, MacKenzie-Graham A, Shattuck DW, Ruotsalainen U, Toga AW (2007) Genetic Algorithms for Finite Mixture Model Based Voxel Classification in Neuroimaging. IEEE Trans. on Medical Imaging, 26(5):696-711
  35. Sicotte NL, Giesser BS, Tandon V, Klutch R, Steiner B, Drain AE, Shattuck DW, Hull L, Wang HJ, Elashoff RM, Swerdloff RS, Voskuhl RR (2007) Testosterone Treatment in Multiple Sclerosis: A Pilot Study. Arch Neurol 64(5):683-8
  36. MacKenzie-Graham A, Tinsley MR, Shaha KP, Aguilar C, Strickland LV, Boline J, Martin M, Morales L, Shattuck DW , Jacob RE, Voskuhl RR and Toga AW (2006) Cerebellar cortical atrophy in experimental autoimmune encephalomyelitis. NeuroImage 32(3):1016-1023.
  37. Sicotte NL, Salamon G, Shattuck DW, Hageman N, Rub U, Salamon N, Drain AE, Demer JL, Engle EC, Alger JR, Baloh RW, Deller T, Jen JC (2006) Diffusion tensor MRI shows abnormal brainstem crossing fibers associated with ROBO3 mutations. Neurology 67(3):519-21.
  38. Dinov ID, Valentino D, Shin BC, Konstantinidis F, Hu G, MacKenzie-Graham A, Lee E-F, Shattuck D, Ma J, Schwartz C, and Toga AW (2006) LONI Visualization Environment Journal of Digital Imaging 19(2):148-158.
  39. Fennema-Notestine C, Ozyurt IB, Clark CP, Morris S, Bischoff-Grethe A, Bondi MW, Jernigan TL, Fischl B, Segonne F, Shattuck DW, Leahy RM, Rex DE, Toga AW, Zou KH, the Morphometry BIRN, and Brown GG (2006) Quantitative Evaluation of Automated Skull-Stripping Methods Applied to Contemporary and Legacy Images: Effects of Diagnosis, Bias Correction, and Slice Location Human Brain Mapping 27(2):99-113.
  40. Salamon N, Sicotte N, Mongkolwat P, Shattuck D, Salamon G (2005) The human cerebral cortex on MRI: value of the coronal plane Surg Radiol Anat 27(5):431-43
  41. Salamon N, Sicotte N, Alger J, Shattuck D, Perlman S, Sinha U, Schultze-Haakh H, Salamon G (2005) Analysis of the brain-stem white-matter tracts with diffusion tensor imaging Neuroradiology 47(12):895-902
  42. Dogdas B, Shattuck DW, and Leahy RM (2005) Segmentation of Skull and Scalp in 3D Human MRI Using Mathematical Morphology Human Brain Mapping26(4):273-85
  43. Rex DE, Shattuck DW, Woods RP, Narr KL, Luders E, Rehm K, Stolzner SE, Rottenberg DA & Toga AW (2004) A meta-algorithm for brain extraction in MRI, NeuroImage 23(2):625-637
  44. Jen JC, Chan WM, Bosley TM, Wan J, Carr JR, Rub U, Shattuck D, Salamon G, Kudo LC, Ou J, Lin DD, Salih MA, Kansu T, Al Dhalaan H, Al Zayed Z, MacDonald DB, Stigsby B, Plaitakis A, Dretakis EK, Gottlob I, Pieh C, Traboulsi EI, Wang Q, Wang L, Andrews C, Yamada K, Demer JL, Karim S, Alger JR, Geschwind DH, Deller T, Sicotte NL, Nelson SF, Baloh RW, Engle EC (2004) Mutations in a human ROBO gene disrupt hindbrain axon pathway crossing and morphogenesis. Science. 2004 Jun 4;304(5676):1509-13 PMCID: PMC1618874.
  45. MacKenzie-Graham A, Lee E-F, Dinov ID, Bota M, Shattuck DW, Ruffins S, Yuan H, Konstantinidis F, Pitiot A, Ding Y, Hu G, Jacobs RE, and Toga AW (2003) A multimodal, multidimensional atlas of the C57BL/6J mouse brain Journal of Anatomy 204(2):93-102
  46. MacKenzie-Graham A, Jones ES, Shattuck DW, Dinov ID, Bota M, and Toga AW (2003) The Informatics of a C57BL/6J Mouse Brain Atlas Neuroinformatics 1(4):397-410
  47. Asma E, Shattuck DW, Leahy RM (2003) Lossless Compression of Dynamic PET Data, IEEE Transactions on Nuclear Science 50(1):9-16.
  48. Shattuck DW, Rapela J, Asma E, Chatzioannou A, Qi J, Leahy RM. (2002) Internet2-based 3D PET image reconstruction using a PC cluster. Phys Med Biol47(15):2785-95
  49. Shattuck DW and Leahy RM (2002) BrainSuite: An Automated Cortical Surface Identification Tool Medical Image Analysis, 8(2):129-142.
  50. Shattuck DW and Leahy RM (2001) Graph Based Analysis and Correction of Cortical Volume Topology, IEEE Transactions on Medical Imaging, 20(11)1167-1177.
  51. Baillet S, Leahy RM, Singh M, Shattuck DW, J.C. Mosher, “Supplementary Motor Area Activation Preceding Voluntary Finger Movements as Evidenced by Magnetoencephalography and fMRI”, International Journal of Bioelectromagnetism, 2001.
  52. Arnold JB, Liow J-S, Schaper KA, Stern JJ, Sled JG, Shattuck DW, Worth AJ, Cohen MS, Leahy RM, Mazziotta JC, and Rottenberg DA (2001) Qualitative and Quantitative Evaluation of Six Bias-Correction Algorithms NeuroImage 13(5):931-943.
  53. Shattuck DW, Sandor-Leahy SR, Schaper KA, Rottenberg DA, and Leahy RM (2001) Magnetic Resonance Image Tissue Classification Using a Partial Volume Model NeuroImage 13(5):856-876.
    54.  
     

    Conference Articles

    peer-reviewed

  54. Kim Y, Malamut EJ, Meyer CE, MacKenzie-Graham A, Shattuck DW (2022) Mouse Brain Extraction using 2-Stage CNNs, SPIE Proceedings Volume 12032, Medical Imaging 2022: Image Processing 120321F (2022), , San Diego, CA, Feb 2022.
  55. Quachtran B, de la Torre Ubieta L, Yusupova M, Geschwind DH, Shattuck DW (2018) “Voting-based segmentation of overlapping nuclei in CLARITY images.” IEEE International Symposium on Biomedical Imaging, Washington, DC, April 2018.
  56. Chambers MC, Bhushan C, Haldar JP, Leahy RM, Shattuck DW (accepted) “Correcting inhomogeneity-induced distortion in FMRI using non-rigid registration”, IEEE International Symposium on Biomedicine (ISBI’15), Brooklyn, New York, April 2015.
  57. Joshi AA, Ashrafulla S, Shattuck DW, Damasio H, Leahy RM (2013) Cortical Shape Analysis using the Anisotropic Global Point Signature, MFCA 2013: 4th MICCAI workshop on Mathematical Foundations of Computational Anatomy, Nagoya, Japan, September 2013.
  58. Joshi AA, Ashrafulla S, Shattuck DW, Damasio H, Leahy RM (2012) “An Invariant Shape Representation using Anisotropic Helmholtz Equation” Medical Image Computing and Computer Assisted Intervention (MICCAI) 2012, Nice, France, October 2012.
  59. Joshi AA, Shattuck DW, Leahy RM (2012) A Fast and Accurate Method for Automated Cortical Surface Registration and Labeling Fifth Workshop on Biomedical Image Registration, Nashville, Tennessee, July 2012.
  60. Joshi AA, Shattuck DW, Damasio H, Leahy RM (2012) “Geodesic Curvature Flow on Surfaces for Automatic Sulcal Delineation”, IEEE International Symposium on Biomedicine (ISBI’12), Barcelona, May 2012.
  61. Wheland D, Joshi AA, McMahon K, Hansell N, Martin N, Wright M, Thompson PM, Shattuck DW, Leahy RM (2012) Robust Identification of Partial-Correlation Based Networks With Applications to Cortical Thickness Data, IEEE International Symposium on Biomedicine (ISBI’12), Barcelona, May 2012.
  62. Prasad G, Joshi A, Thompson P, Toga A, Shattuck D, Terzopoulos D (2011) Skull-stripping with deformable organisms, 8th IEEE International Symposium on Biomedical Imaging (ISBI 2011), Chicago, 30 March -2 April 2011
  63. Joshi AA, Joshi S, Dinov ID, Shattuck DW, Leahy RM, Toga AW (2010) Anatomical structural network analysis of human brain using partial correlations of gray matter volumes, IEEE International Symposium on Biomedicine (ISBI’10), Rotterdam, June 2010.
  64. Joshi AA, Chaudhari AA, Shattuck DW, Dutta J, Leahy RM, and Toga AW (2009) Posture Matching and Elastic Registration of a Mouse Atlas to Surface Tomography Range Data, IEEE International Symposium on Biomedical Imaging (ISBI’09), Boston, June 2009.
  65. Hageman NS, Leow AD, Shattuck DW, Zhan L, Thompson PM, Zhu S, and Toga AW (2009) Segmenting crossing fiber geometries using fluid mechanics tensor distribution function tractography, IEEE International Symposium on Biomedical Imaging (ISBI’09), Boston, June 2009.
  66. Joshi AA, Leahy RM, Toga AW, and Shattuck DW (2009) A Unified Framework for Simultaneous Surface and Volumetric Brain Registration Information Processing in Medical Imaging, 21st International Conference, IPMI 2009, Williamsburg, Virginia
  67. Joshi AA, Pantazis D, Damasio H, Li Q, Shattuck DW, Bernstein LE and Leahy RM (2009) Optimization of Landmark Selection for Cortical Surface Registration, CVPR: Computer Vision and Pattern Recognition 2009, Miami Beach, FL, June 2009.
  68. Shattuck DW, Chiang MC, Barysheva M, McMahon KL, de Zubicaray GI, Meredith M, Wright MJ, Toga AW, Thompson PM (2008). Visualization Tools for High Angular Resolution Diffusion Imaging, Medical Image Computing and Computer Assisted Intervention (MICCAI) 2008, New York, NY 8 September 2008.
  69. Yanovsky I, Thompson P, Osher S, Hua X, Shattuck D, Toga A, Leow A (2008) Validating Unbiased Registration on Longitudinal MRI Scans from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). ISBI 2008.
  70. Joshi AA, Shattuck DW, Thompson PM, and Leahy RM (2007) Brain Image Registration using Cortically Constrained Harmonic Mappings, Information Processing in Medical Imaging, 20th International Conference, IPMI 2007, Kerkrade, The Netherlands, July 2-6, 2007, p. 359-371
  71. Joshi AA, Shattuck DW, Thompson PM, and Leahy RM (2007) A finite element method for elastic parameterization and alignment of cortical surfaces using sulcal constraints, 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2007. (ISBI 2007). 12-15 April 2007 p. 640-643
  72. Joshi AA, Shattuck DW, Thompson PM, and Leahy RM (2007) Registration of cortical surfaces using sulcal landmarks for group analysis of MEG data, in D. Cheyne, B. Ross, G. Stroink and H. Weinberg (Eds.) International Congress Series Volume 1300, New Frontiers in Biomagnetism. Proceedings of the 15th International Conference on Biomagnetism, Vancouver, BC, Canada, August 21-25, 2006, p. 229-232.
  73. Hageman NS, Shattuck DW, Narr K, and Toga AW (2006) A diffusion tensor imaging tractography algorithm based on Navier-Stokes fluid mechanics, Proc. 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro in: J. Kovacevic’ and E. Meijering (Eds.) Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2006), Arlington, VA, USA, 6-9 April 2006. p. 798-801
  74. Joshi A, Shattuck DW, Thompson PM, and Leahy RM (2005) A Framework for Registration, Statistical Characterization and Classification of Cortically Constrained Functional Data, in: G.E. Christensen and M. Sonka (Eds.): 19th International Conference on Information Processing in Medical Imaging (IPMI 2005), Glenwood Springs, CO, USA, July 10-15, 2005, p. 186-196
  75. Joshi A, Shattuck DW, Thompson PM, and Leahy RM (2004) Cortical Surface Parameterization by P-Harmonic Energy Minimization. in: R. Leahy and C. Roux (Eds.), Proceedings of the 2004 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2004), Arlington, VA, USA, 15-18 April 2004, p. 428-431
  76. Shattuck DW, MacKenzie-Graham A, and Toga AW (2004) DUFF: Software Tools for Visualization and Processing of Neuroimaging Data. in: R. Leahy and C. Roux (Eds.), Proceedings of the 2004 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2004), Arlington, VA, USA, 15-18 April 2004, p. 644-647
  77. Dogdas B, Shattuck DW & Leahy RM (2002) Segmentation of Patient Specific MEG/EEG Skull, Scalp, and Brain Models, MRI. 13th Intl. Conf. on Biomagnetism, Aug. 2002.
  78. Shattuck DW and Leahy RM “BrainSuite: An Automated Cortical Surface Identification Tool,” in: S.L. Delp, A.M. DiGoia, and B. Jaramaz, (Eds.), Medical Image Computing and Computer-Assisted Intervention – MICCAI 2000, Lecture Notes in Computer Science, Vol. 1935, p. 51-61, Springer-Verlag, Berlin Heidelberg, 2000.
  79. Mosher JC, Leahy RM, Shattuck DW, and Baillet S, “MEG source imaging using multipolar expansions,” pdf in: A. Kuba, M. Samal, and A. Todd-Pokropek (Eds.), 16th International Conference on Information Processing in Medical Imaging (IPMI’99), Lecture Notes in Computer Science, Vol. 1643, p. 15-28, Springer-Verlag, Berlin Heidelberg, 1999.

    80. non peer-reviewed

  80. Joshi AA, Joshi SH, Leahy RM, Shattuck DW, Dinov I, and Toga AW (2010) Bayesian approach for network modeling of brain structural features, In Proceedings of the SPIE Vol. 7626, Medical Imaging 2010: Biomedical Applications in Molecular, Structural, and Functional Imaging, Robert C. Molthen; John B. Weaver (Eds.),.
  81. Tohka J, Krestyannikov E, Dinov I, Shattuck D, Ruotsalainen U, Toga AW (2005) Genetic algorithms for finite mixture model based tissue classification in brain MRI. In Proc. of European Medical and Biological Engineering Conference, IFMBE Proceedings 11:4077-4082, Prague, Czech Republic, 2005.
  82. Dogdas B, Shattuck DW & Leahy RM (2002) Segmentation of Skull in 3D Human MRI using Mathematical Morphology, Medical Imaging 2002: Image Processing, Milan Sonka; J. Michael Fitzpatrick; (Eds.), Proc. SPIE, 4684:1553-1562.
  83. Shattuck DW and Leahy RM (2000) Topologically constrained cortical surfaces from MRI in: Medical Imaging 2000: Image Processing, K.M. Hanson (Ed.), Proceedings of the SPIE, 3979:747-758.
  84. Shattuck DW and Leahy RM (1999) Topological refinement of volumetric data in: Medical Imaging 1999: Image Processing, K.M. Hanson (Ed.), Proceedings of the SPIE, 3661:204-213.
  85. Joshi AA, Shattuck DW, Thompson PM, and Leahy RM (2007) Simultaneous Surface and Volumetric Brain Registration Using Harmonic Maps, in CA Bouman, EL Miller, and I Pollak (Eds.) Proceedings of SPIE, Vol. 6498, Electronic Imaging 2007: Computational Imaging V, San Diego, CA, Feb. 2007, 649816-1:12
  86. Asma E, Shattuck DW & Leahy RM 2001 Lossless Compression of List-Mode 3D PET Data, in Proc. IEEE Nuclear Science Symposium and Medical Imaging Conference, San Diego, CA.
    87.  
     

    Conference Abstracts

  87. Kim Y, Joshi AA, Choi S, Joshi SH, Bhushan C, Varadarajan D, Haldar JP, Leahy RM, Shattuck DW (forthcoming) The BrainSuite BIDS App. accepted to 2023 Annual Meeting of the Organization for Human Brain Mapping, Montreal, Canada, July 2023.
  88. Joshi SH, Kim Y, Schroeder KA, Joshi AA, Leahy RM, Shattuck DW (forthcoming) MRI Volumetric and Surface Data Analysis with the BrainSuite Statistics in R (bssr) Toolbox. accepted to 2023 Annual Meeting of the Organization for Human Brain Mapping, Montreal, Canada, July 2023.
  89. Joshi AA, Chaudhari A, Shattuck DW Leahy RM, (forthcoming) Should Manual Dexterity be Investigated as a Marker of Early Alzheimers Disease? rs-fMRI Evidence. accepted to 2023 Annual Meeting of the Organization for Human Brain Mapping, Montreal, Canada, July 2023.
  90. Shattuck DW (2020) Visualization of Very Large Volumetric Images in Virtual Reality, 26th Annual Meeting of the Organization for Human Brain Mapping, Montreal, Canada, June 2020.
  91. Kim Y, Dennis EL, Humphreys KL, King LS, Gotlib IH, Shattuck DW (2020) Patch-based Tissue Classification in Infant Brain MRI using Two-Stage CNN, 26th Annual Meeting of the Organization for Human Brain Mapping, Montreal, Canada, June 2020.
  92. Joshi S, Kim Y, Schroeder K, Joshi A, Leahy R, Shattuck DW (2020) The BrainSuite Statistics Toolbox in R (bssr), 26th Annual Meeting of the Organization for Human Brain Mapping, Montreal, Canada.
  93. Połczyńska M, Monti M, Kuhn T, Wang H, Ly T, Japardi K, Shattuck D, Anderson A, Curtiss S, Dronkers N, Bookheimer S (2020) Optimizing grammar tasks for pre-operative fMRI based on task-based and resting-state activations, 26th Annual Meeting of the Organization for Human Brain Mapping, Montreal, Canada, June 2020.
  94. Kim Y, Dennis EL, Humphreys KL, King LS, Gotlib IH, Shattuck DW (2019), Tissue Classification of Infant Brain MRI Using Local Image Patch CNNs and VQ-VAEs, Women in Machine Learning Workshop (WiML), Vancouver, Canada, 9 December 2019.
  95. Visagan S, Martin MM, and Shattuck DW (2019) Modeling Transcranial Nonlinear Wave Propagation on Head Models for Low-Intensity Focused Ultrasound, 25th Annual Meeting of the Organization for Human Brain Mapping, Rome, Italy, June 2019.
  96. Joshi AA, Shattuck DW, Choi SY, Leahy RM (2019) A Method for Automatic Demarcation of Sulcal and Gyral Regions on the Cortical Surface, 25th Annual Meeting of the Organization for Human Brain Mapping, Rome, Italy, June 2019.
  97. Shattuck D (2018) Multi-user Visualization of Brain Imaging Data in Virtual Reality. 23rd Annual Meeting of the Organization for Human Brain Mapping Singapore, June 2018.
  98. Wong J, Shattuck D (2018) BrainSuite Workflow and Quality Control System. 23rd Annual Meeting of the Organization for Human Brain Mapping Singapore, June 2018.
  99. Kim Y, Wong J, Shattuck D (2018) BrainSuite BIDS-App: a Containerized Version of the BrainSuite Processing Pipelines. 23rd Annual Meeting of the Organization for Human Brain Mapping Singapore, June 2018.
  100. Quachtran B, Joshi A, Bhushan C, Leahy R, Shattuck D (2018). Combined T1-Diffusion MRI Registration. 23rd Annual Meeting of the Organization for Human Brain Mapping Singapore, June 2018.
  101. Joshi A, McCoy D, Chong M, Li J, Choi S, Shattuck D, Leahy R (2018) BFP: BrainSuite fMRI Pipeline. 23rd Annual Meeting of the Organization for Human Brain Mapping Singapore, June 2018.
  102. Joshi S, Kim Y, Joshi A, Leahy R, Shattuck D (2017) Reproducible TBM and ROI Analyses Using the BrainSuite Statistics Toolbox (BSS). 23rd Annual Meeting of the Organization for Human Brain Mapping Vancouver, Canada, June 2017.
  103. Kuhn T, Jin Y, Huang C, Kim Y, Nir T, Gullett J, Jones J, Singer E, Shattuck D, Jahanshad N, Bookheimer S, Hinkin C, Zhu H, Thompson P, Thames A (2017) The Joint Effect of Aging and HIV Infection on Integrity of the Corpus Callosum. 23rd Annual Meeting of the Organization for Human Brain Mapping Vancouver, Canada, June 2017.
  104. Joshi A, Choi S, Chong M, Sonkar G, Gonzalez-Martinez Y, Nair D, Shattuck D, Damasio H, Leahy R (2017) “BCI-DNIf Brain Atlas: A Volumetric and Surface Atlas Delineated by Anatomical and Functional MRI.” 23rd Annual Meeting of the Organization for Human Brain Mapping Vancouver, Canada, June 2017.
  105. Wang Y, Shattuck D, Saver J, Liebeskind D, Scalzo F (2017) Spatio-temporal Flow Tractography (SFT) for Evaluation of Collateral Patterns in Acute Stroke. International Stroke Conference, Houston, Texas, February 2017.
  106. Di Paola K, Phillips O, Joshi S, Piras F, Orfei M, Iorio M, Narr K, Shattuck D, Caltagirone C, Spalletta G (2016) The Superficial White Matter in Alzheimer’s Disease” 46th International Meeting of the Society for Neuroscience, San Diego, CA, November 2016.
  107. Joshi AA, Choi S, Shattuck DW, Leahy RM (2016) SVReg: Surface-Constrained Volumetric Registration in BrainSuite 22nd Annual Meeting of the Organization for Human Brain Mapping Geneva, Switzerland, June 2016.
  108. Philips OR, Joshi SH, Narr KL, Shattuck DW, Singh M, Ploner C, Pruess H, Paul F, Di Paola M, Finke C (2016) Returning to Normalcy: The Superficial White matter in Anti-NMDA Receptor Encephalitis, 22nd Annual Meeting of the Organization for Human Brain Mapping Geneva, Switzerland, June 2016.
  109. Varadarajan D, Wang ZI, Joshi AA, Shattuck DW, Jones SE, Leahy RM (2015) Detecting Focal Cortical Dysplasia using Population-Based Models of Cortical Thickness, 21st Annual Meeting of the Organization for Human Brain Mapping Honolulu, Hawaii, June 2015.
  110. Chong M, Joshi AA, Haldar JP, DuPre E, Luh W-M, Shattuck DW, Spreng RN, Leahy RM (2015) A Group Approach to Functional Cortical Parcellation from Resting-State fMRI, 21st Annual Meeting of the Organization for Human Brain Mapping Honolulu, Hawaii, June 2015.
  111. Jones S, Wang I, Alexopoulos A, Al-Sharif N, Burgess R, Joshi A, Krishnan B, Leahy R, Mosher J, Udayasankar U, Shattuck D (2015) Automated Quantitative Assessment of Rasmussen’s Encephalitis, American Society of Neuroradiology 53rd Annual Meeting, Chicago, IL, April 2015.
  112. Chambers M, Bhushan C, Pirnia T, Narr K, Haldar J, Leahy R, and Shattuck D (2014) Registration-Based Distortion and Intensity Correction in fMRI 20th Annual Meeting of the Organization for Human Brain Mapping Hamburg, Germany, June 2014.
  113. Joshi S, Woods, R, Joshi A, Fears S, Al-Sharif N, Leahy R, and Shattuck D (2014) A Statistical Toolbox for BrainSuite 20th Annual Meeting of the Organization for Human Brain Mapping Hamburg, Germany, June 2014.
  114. Joshi A, Bhushan C, Shattuck D, and Leahy R (2014) Estimation of cortical thickness from T1-weighted MRI images using tissue fractions 20th Annual Meeting of the Organization for Human Brain Mapping Hamburg, Germany, June 2014.
  115. Balasubramaniam E, Joshi A, Shattuck D, and Leahy R (2014) A PDE approach for automatic thickness estimation using partial volume classification ISMRM 22nd Annual Meeting & Exhibition Milan, Italy, April 2014.
  116. Bhushan C, Haldar JP, Joshi AA, Shattuck DW, and Leahy RM (2014) INVERSION: A Robust Method for Co-registration of T1 AND Diffusion Weighted MRI Images ISMRM 22nd Annual Meeting & Exhibition Milan, Italy, April 2014.
  117. Beroukhim D, Konersman M, Chong M, Joshi AA, Bhushan C, Shattuck DW, Haldar JP, Leahy RM, Winstein CJ (2013) Effects of rehabilitation post-stroke: DTI analysis of corticospinal tract characteristics using BrainSuite13, 43rd International Meeting of the Society for Neuroscience San Diego, CA, November 2013.
  118. Shattuck D Joshi A, Haldar J, Bhushan C, Choi S, Krause A, Wisnowski J, Damasio H, Toga A, and Leahy R (2013) New BrainSuite13 Tools for Image Segmentation, Registration Connectivity Analysis and Visualization, 19th Annual Meeting of the Organization for Human Brain Mapping, Seattle, WA, June 2013.
  119. Joshi A, Ashrafulla S, Shattuck D, Damasio H, and Leahy R (2013) Automated Analysis of the Shape of Sulcal Curves using the Anisotropic Helmholtz Equation, 19th Annual Meeting of the Organization for Human Brain Mapping, Seattle, WA, June 2013.
  120. Choi S, Bhushan C, Joshi AA, Raphel K, Tranel D, Shattuck D, Haldar J, Leahy RM, Damasio H, Wisnowski J (2013) Altered orbitofrontal tissue microstructure in patients with chronic anterior temporal lobe lesions, 19th Annual Meeting of the Organization for Human Brain Mapping, Seattle, WA, June 2013.
  121. Shattuck DW Joshi AA, Haldar JP, Bhushon C, Krause AC, Wisnowski JL, Toga AW, Leahy RM (2013) Software Tools for Anatomical ROI-based Connectivity Analysis, ISMRM 21st Annual Meeting & Exhibition, Salt Lake City, Utah, April 2013.
  122. Haldar JP, Shattuck DW Leahy RM (2013, press) Estimation of White Matter Fiber Orientations with the Funk-Radon and Cosine Transform, ISMRM 21st Annual Meeting & Exhibition, Salt Lake City, Utah, April 2013.
  123. Choi S, Joshi AA, Bhushan C, Shattuck DW Leahy RM, Damasio H, Panigrahy A, Wisnowski JL (2013) A Multimodal Investigation of Neuronal/Axonal Integrity Using Structural T1-weighted Imaging, Diffusion Tensor Imaging, and H1 MR Spectroscopy, ISMRM 21st Annual Meeting & Exhibition, Salt Lake City, Utah, April 2013.
  124. Haldar JP, Shattuck DW, Damasio H, Leahy RM (2012) Improved Diffusion Tractography with the Funk-Radon and Cosine Transform, 18th Annual Meeting of the Organization for Human Brain Mapping, Beijing, China, June 2012.
  125. Joshi AA, Shattuck DW, Leahy RM (2012) Refinement of Automated Cortical Surface Registration and Labelling using Gradient Curvature Flow, 18th Annual Meeting of the Organization for Human Brain Mapping, Beijing, China, June 2012.
  126. Klein A, Landman BA, Dal Canton T, Shattuck DW, Tourville JA, Worth AJ (2010) An interactive tool for constructing optimal brain colormaps 40th International Meeting of the Society for Neuroscience, San Diego, CA, Nov. 2010.
  127. Rosen B, Wedeen VJ, Van Horn JD, Fischl B, Buckner RL, Wald L, Hamalainen M, Stufflebeam S, Roffman J, Shattuck DW, Thompson PM, Woods RP, Freimer N, Bilder R & Toga AW (2010) The Human Connectome Project. 16th Annual Meeting of the Organization for Human Brain Mapping, Barcelona, Spain, June 2010
  128. Chiang MC, Barysheva M, Shattuck DW, Lee AD, Madsen SK, Avedissian S, Klunder A, Toga AW, McMahon KL, de Zubicaray GI, Wright MJ, Srivastava A, Balov N, Thompson PM (2009) Mapping Genetic Influences on Brain Fiber Architecture and Intellectual Performance — A High Angulare Resolution diffusion Imaging (HARDI) Study, 15th Annual Meeting of the Organization for Human Brain Mapping, San Francisco, CA, June 2009.
  129. Pantazis D, Joshi AA, Jintao J, Shattuck DW, Bernstein LE, Damasio H, and Leahy RM (2009) Evaluating the accuracy of cortical registration using landmark-based and automatic methods, 15th Annual Meeting of the Organization for Human Brain Mapping, San Francisco, CA, June 2009.
  130. Hageman NS, Thompson PM, Shattuck DW, Avedissian C, Barysheva M, McMahon KL, de Zubicaray GI, Wright MJ, Toga AW (2009) Genetic Influence on White Matter Architecture in Twins: A Diffusion Tensor Imaging Study, the 15th Annual Meeting of the Organization for Human Brain Mapping, San Francisco, CA, June 2009.
  131. Tohka J, Dinov ID, Shattuck DW, and Toga A (2008) Brain MRI Segmentation Based on Local Markov Random Fields and Sub Volume Probabilistic Atlases, 13th Annual Meeting of the Organization for Human Brain Mapping, Melbourne, Australia, June 2008.
  132. Bilder R, Parker D, Brown N, Kalar D, Sabb F, Glahn D, Bearden CE, Poldrack R, Shattuck D, Cannon T, London E, Freimer N, Toga A (2007) Cognitive Phenomics: Web-based tools for hypothesis development in neuropsychiatry. 38th International Meeting of the Society for Neuroscience, San Diego, CA, Nov. 2007.
  133. Tohka J, Dinov ID, Shattuck DW, and Toga AW (2007) GAMIXTURE+MRFSEG: A flexible tool for voxel classification. In: Proc. of Nordic Neuroinformatics Workshop, Espoo, Finland, Oct. 2007, p. 10.
  134. Narr KL, Hageman N, Hamilton L, Gurbani M, Woods RP, Asarnow RF, Shattuck D, Toga AW, Nuechterlein KH (2007) Mean diffusivity: A biomarker for CSF-related disease and genetic liability effects in schizophrenia, 13th Annual Meeting of the Organization for Human Brain Mapping, Chicago, IL, June 2007.
  135. Bilder RM, Parker DS, Brown N, Kalar D, Sabb F, Glahn D, Bearden C, Poldrack R, Shattuck D, Cannon TD, London E, Freimer N, Toga A (2007) Cognitive Phenomics: Informatics Strategies for Schizophrenia Research 2007 International Congress on Schizophrenia Research, Colorado Springs, Colorado, March. 2007
  136. Bilder RM, Parker DS, Brown N, Kalar D, Sabb FW, Glahn D, Bearden C, Poldrack R, Shattuck D, Cannon TD, London E, Freimer N, Toga A (2007) Informatics Solutions for Neuropsychiatric Phenomics, Society of Biological Psychiatry, 62nd Annual Scientific Convention & Program, San Diego, CA, May 2007.
  137. Boline J, MacKenzie-Graham A, Shattuck D, Yuan H, Anderson S, Sforza D, Williams R, Wong W, Martone M, Zaslavsky I, Toga A (2006) A digital atlas and neuroinformatics framework for query and display of disparate data. 36th International Meeting of the Society for Neuroscience, Atlanta, GA.
  138. Shattuck DW, Hojatkashani C, Mirza M, Adisetiyo V, Salamon G, Narr KL, Poldrack RA, Bilder RM, and Toga AW (2006) Construction of a 3D Probabilistic Atlas of Human Brain Structures 12th Annual Meeting of the Organization for Human Brain Mapping, Florence, Italy, June 2006.
  139. Joshi AA, Shattuck DW, Thompson PM and Leahy RM (2006) Simultaneous Surface and Volume Registration using Harmonic Maps SIAM conference on Imaging Sciences, Minneapolis, May 2006.
  140. MacKenzie-Graham AJ, Tinsley M, Shah KP, Aguilar C, Strickland LV, Boline J, Martin M, Morales L, Shattuck DW, Jacobs RE, Voskuhl R, Toga AW (2006) Cerebellar Cortical Atrophy in C57BL/6J Mice with Experimental Autoimmune Encephalomyelitis American Academy of Neurology AAN 58th Annual Meeting, San Diego, CA, April 2006
  141. Sicotte NL, Giesser BS, Tandon V, Steiner B, Klutch R, Drain A, Shattuck DW, Hull L, Swerdloff R, Voskuhl RR (2006) A Pilot Study of Testosterone Treatment for Men with Relapsing Remitting Multiple Sclerosis American Academy of Neurology AAN 58th Annual Meeting, San Diego, CA, April 2006
  142. Looi JCL, Shattuck DW, Toga AW, Wen W, Brodaty H, Sachdev PS. (2006) Fully automated quantitative methods for mapping the 3-D distribution of white matter hyperintensities in the Sydney stroke study. Neurology 66(5), March 2006 Suppl 2: A109-A110.
  143. Looi JCL, Shattuck DW, Toga, AW, Wen W, Brodaty H, Sachdev PS (2005) Piloting a method for longitudinal quantitation of white matter hyperintensities in the Sydney Stroke Study, International Psychogeriatric Association 12th Congress, Stockholm, Sweden [platform presentation] International Psychogeriatrics 2005; 17 suppl 2: 158-159.
  144. Shattuck DW, Joshi A, Leahy RM, & Toga AW (2005) Automated Parameterized Cortical Surface Models from MRI, Brain Mapping June 2005, Toronto, CA.
  145. Joshi A, Shattuck DW Thompson PM & Leahy RM (2005) Thin Plate Spline Registration in the Intrinsic Geometry of the Cortical Surface, Human Brain Mapping June 2005, Toronto, CA
  146. Rex DE, Shattuck DW, Woods RP, Stoltzner SE & Toga AW (2003) Meta-algorithm for automated brain extraction from a structural MRI, 33rd International Meeting of the Society for Neuroscience, New Orleans, LA, November 8-12, 2003.
  147. Mackenzie-Graham A, Martin M, Jones E, Shattuck D, Jacobs R, Voskuhl R & Toga AW (2003) An atlas of experimental autoimmune encephalomyelitis in the C57BL/6 brain, 33rd International Meeting of the Society for Neuroscience, New Orleans, LA, November 8-12, 2003.
  148. Shattuck DW, Rex DE, Darvas F, Leahy RM & Toga AW (2003) JohnDoe: Anonymizing MRI data for the protection of research subject confidentiality. 9th International Conference on Functional Mapping of the Human Brain, June 19-22, 2003,New York, NY.
  149. Leahy RM, B. Bai, E. Asma, Q. Li, and Shattuck DW (2002) MAP Image Reconstruction Software for Concorde MicroPET Scanners, 2002 Annual Academy of Molecular Imaging Conference.
  150. Shattuck DW, Rapela J, Asma E, Chatzioannou A, Qi J & Leahy R (2001) Internet-Based 3D PET Image Reconstruction using A Beowulf PC Cluster in Proc. The Sixth International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine, Asilomar, CA.
  151. Shattuck DW, Sutherling W & Leahy RM (2001) Improved Cortical MRI Segmentation of Brains with Intracranial Grid Electrodes, NeuroImage, 13(6):S244.
  152. Schaper KA, Arnold JB, Liow J-S, Stern JJ, Sled JG, Shattuck DW, Worth AJ, Cohen MS, Leahy RM, Mazziotta JC & Rottenberg DA (2001) Evaluation of Six Algorithms for Correcting Intensity Non-uniformity Effects in MRI Volumes, NeuroImage, 13(6):S237.
  153. Shattuck DW & Leahy RM (1999) Automated topologically correct cortical surfaces from MRI in Proceedings of the 21st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Atlanta.
  154. Zaini MR, Schaper KA, Anderson JR, Shattuck DW, Liow JS, Sled JG & Rottenberg DA (1999) Methods for evaluating the performance of MRI nonuniformity correction algorithms, NeuroImage, 9(6):S99.
  155. Rehm K, Shattuck DW, Leahy R, Schaper K & Rottenberg DA (1999) Semi-automated stripping of T1 MRI volumes: consensus of intensity-and edge-based methods, NeuroImage, 9(6):S86.
  156. Baillet S, Mosher JC, Leahy RM & Shattuck DW (1999) BrainStorm: A Matlab Toolbox for the Processing of MEG and EEG Signals, NeuroImage, 9(6):S246.