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Publications citing R01-NS074980 and listed on PubMed

  1. Medani T, Garcia-Prieto J, Tadel F, Antonakakis M, Erdbrügger T, Höltershinken M, Mead W, Schrader S, Joshi A, Engwer C, Wolters CH, Mosher JC, Leahy RM. Brainstorm-DUNEuro: An integrated and user-friendly Finite Element Method for modeling electromagnetic brain activity. Neuroimage. 2023;267:119851. Epub 20230101. doi: 10.1016/j.neuroimage.2022.119851 PubMed PMID: 36599389 PMCID: PMC9904282
  2. Setton R, Mwilambwe-Tshilobo L, Girn M, Lockrow AW, Baracchini G, Hughes C, Lowe AJ, Cassidy BN, Li J, Luh WM, Bzdok D, Leahy RM, Ge T, Margulies DS, Misic B, Bernhardt BC, Stevens WD, De Brigard F, Kundu P, Turner GR, Spreng RN. Age differences in the functional architecture of the human brain. Cereb Cortex. 2022;33(1):114-34. doi: 10.1093/cercor/bhac056 PubMed PMID: 35231927 PMCID: PMC9758585
  3. Kim TH, Haldar JP. Efficient iterative solutions to complex-valued nonlinear least-squares problems with mixed linear and antilinear operators. Optim Eng. 2022;23(2):749-68. Epub 20210313. doi: 10.1007/s11081-021-09604-4 PubMed PMID: 35656362 PMCID: PMC9159680
  4. Joshi AA, Choi S, Liu Y, Chong M, Sonkar G, Gonzalez-Martinez J, Nair D, Wisnowski JL, Haldar JP, Shattuck DW, Damasio H, Leahy RM. A hybrid high-resolution anatomical MRI atlas with sub-parcellation of cortical gyri using resting fMRI. J Neurosci Methods. 2022;374:109566. Epub 20220317. doi: 10.1016/j.jneumeth.2022.109566 PubMed PMID: 35306036 PMCID: PMC9302382
  5. Cain JA, Visagan S, Monti MM. S.M.A.R.T. F.U.S: Surrogate Model of Attenuation and Refraction in Transcranial Focused Ultrasound. PLoS One. 2022;17(10):e0264101. Epub 20221027. doi: 10.1371/journal.pone.0264101 PubMed PMID: 36302034 PMCID: PMC9612531
  6. Akrami H, Leahy RM, Irimia A, Kim PE, Heck CN, Joshi AA. Neuroanatomic Markers of Posttraumatic Epilepsy Based on MR Imaging and Machine Learning. AJNR Am J Neuroradiol. 2022;43(3):347-53. Epub 20220224. doi: 10.3174/ajnr.A7436 PubMed PMID: 35210268 PMCID: PMC8910810
  7. Akrami H, Joshi AA, Li J, Aydöre S, Leahy RM. A robust variational autoencoder using beta divergence. Knowl Based Syst. 2022;238. Epub 20211210. doi: 10.1016/j.knosys.2021.107886 PubMed PMID: 36714396 PMCID: PMC9881733
  8. Akrami H, Joshi AA, Aydöre S, Leahy RM. Deep Quantile Regression for Uncertainty Estimation in Unsupervised and Supervised Lesion Detection. J Mach Learn Biomed Imaging. 2022;1. Epub 20220427. PubMed PMID: 36712144 PMCID: PMC9881592
  9. Vu C, Chai Y, Coloigner J, Nederveen AJ, Borzage M, Bush A, Wood JC. Quantitative perfusion mapping with induced transient hypoxia using BOLD MRI. Magn Reson Med. 2021;85(1):168-81. Epub 20200727. doi: 10.1002/mrm.28422 PubMed PMID: 32767413 PMCID: PMC7728454
  10. Vu C, Bush A, Choi S, Borzage M, Miao X, Nederveen AJ, Coates TD, Wood JC. Reduced global cerebral oxygen metabolic rate in sickle cell disease and chronic anemias. Am J Hematol. 2021;96(8):901-13. Epub 20210512. doi: 10.1002/ajh.26203 PubMed PMID: 33891719 PMCID: PMC8273150
  11. Slator PJ, Palombo M, Miller KL, Westin CF, Laun F, Kim D, Haldar JP, Benjamini D, Lemberskiy G, de Almeida Martins JP, Hutter J. Combined diffusion-relaxometry microstructure imaging: Current status and future prospects. Magn Reson Med. 2021;86(6):2987-3011. Epub 20210819. doi: 10.1002/mrm.28963 PubMed PMID: 34411331 PMCID: PMC8568657
  12. Lobos RA, Hoge WS, Javed A, Liao C, Setsompop K, Nayak KS, Haldar JP. Robust autocalibrated structured low-rank EPI ghost correction. Magn Reson Med. 2021;85(6):3403-19. Epub 20201217. doi: 10.1002/mrm.28638 PubMed PMID: 33332652 PMCID: PMC8820934
  13. Liu Y, Haldar JP. PALMNUT: An Enhanced Proximal Alternating Linearized Minimization Algorithm with Application to Separate Regularization of Magnitude and Phase. IEEE Trans Comput Imaging. 2021;7:530-18. Epub 20210506. doi: 10.1109/tci.2021.3077806 PubMed PMID: 34458504 PMCID: PMC8386764
  14. Kim D, Cauley SF, Nayak KS, Leahy RM, Haldar JP. Region-optimized virtual (ROVir) coils: Localization and/or suppression of spatial regions using sensor-domain beamforming. Magn Reson Med. 2021;86(1):197-212. Epub 20210216. doi: 10.1002/mrm.28706 PubMed PMID: 33594732 PMCID: PMC8248187
  15. Chan CC, Haldar JP. Local perturbation responses and checkerboard tests: Characterization tools for nonlinear MRI methods. Magn Reson Med. 2021;86(4):1873-87. Epub 20210603. doi: 10.1002/mrm.28828 PubMed PMID: 34080720 PMCID: PMC8880254
  16. Cain JA, Visagan S, Johnson MA, Crone J, Blades R, Spivak NM, Shattuck DW, Monti MM. Real time and delayed effects of subcortical low intensity focused ultrasound. Sci Rep. 2021;11(1):6100. Epub 20210317. doi: 10.1038/s41598-021-85504-y PubMed PMID: 33731821 PMCID: PMC7969624
  17. Bush A, Vu C, Choi S, Borzage M, Miao X, Li W, Qin Q, Nederveen AJ, Coates TD, Wood JC. Calibration of T(2) oximetry MRI for subjects with sickle cell disease. Magn Reson Med. 2021;86(2):1019-28. Epub 20210314. doi: 10.1002/mrm.28757 PubMed PMID: 33719133 PMCID: PMC8076101
  18. Akrami H, Joshi A, Aydore S, Leahy R. Quantile Regression for Uncertainty Estimation in VAEs with Applications to Brain Lesion Detection. Inf Process Med Imaging. 2021;12729:689-700. Epub 20210614. doi: 10.1007/978-3-030-78191-0_53 PubMed PMID: 34334982 PMCID: PMC8321392
  19. Li J, Joshi AA, Leahy RM. A NETWORK-BASED APPROACH TO STUDY OF ADHD USING TENSOR DECOMPOSITION OF RESTING STATE FMRI DATA. Proc IEEE Int Symp Biomed Imaging. 2020;2020:544-8. Epub 20200522. doi: 10.1109/isbi45749.2020.9098584 PubMed PMID: 33500749 PMCID: PMC7831393
  20. Li J, Choi S, Joshi AA, Wisnowski JL, Leahy RM. Temporal non-local means filtering for studies of intrinsic brain connectivity from individual resting fMRI. Med Image Anal. 2020;61:101635. Epub 20200107. doi: 10.1016/ PubMed PMID: 32007699 PMCID: PMC7062584
  21. Kim D, Wisnowski JL, Nguyen CT, Haldar JP. Multidimensional correlation spectroscopic imaging of exponential decays: From theoretical principles to in vivo human applications. NMR Biomed. 2020;33(12):e4244. Epub 20200107. doi: 10.1002/nbm.4244 PubMed PMID: 31909534 PMCID: PMC7338241
  22. Haldar JP, Setsompop K. Linear Predictability in MRI Reconstruction: Leveraging Shift-Invariant Fourier Structure for Faster and Better Imaging. IEEE Signal Process Mag. 2020;37(1):69-82. Epub 20200117. doi: 10.1109/msp.2019.2949570 PubMed PMID: 33746468 PMCID: PMC7971148
  23. Haldar JP, Liu Y, Liao C, Fan Q, Setsompop K. Fast submillimeter diffusion MRI using gSlider-SMS and SNR-enhancing joint reconstruction. Magn Reson Med. 2020;84(2):762-76. Epub 20200110. doi: 10.1002/mrm.28172 PubMed PMID: 31919908 PMCID: PMC7968733
  24. Coloigner J, Vu C, Borzage M, Bush A, Choi S, Miao X, Chai Y, Galarza C, Lepore N, Tamrazi B, Coates TD, Wood JC. Transient Hypoxia Model Revealed Cerebrovascular Impairment in Anemia Using BOLD MRI and Near-Infrared Spectroscopy. J Magn Reson Imaging. 2020;52(5):1400-12. Epub 20200709. doi: 10.1002/jmri.27210 PubMed PMID: 32648323 PMCID: PMC7655661
  25. Choi S, Leahy RM, Wood JC. Lower white matter volume in beta-thalassemia associated with anemia and cognitive performance. Am J Hematol. 2020;95(6):E144-e6. Epub 20200407. doi: 10.1002/ajh.25787 PubMed PMID: 32180241 PMCID: PMC7416506
  26. Akrami H, Joshi AA, Li J, Aydore S, Leahy RM. BRAIN LESION DETECTION USING A ROBUST VARIATIONAL AUTOENCODER AND TRANSFER LEARNING. Proc IEEE Int Symp Biomed Imaging. 2020;2020:786-90. Epub 20200522. doi: 10.1109/isbi45749.2020.9098405 PubMed PMID: 33500750 PMCID: PMC7831448
  27. Tadel F, Bock E, Niso G, Mosher JC, Cousineau M, Pantazis D, Leahy RM, Baillet S. MEG/EEG Group Analysis With Brainstorm. Front Neurosci. 2019;13:76. Epub 20190208. doi: 10.3389/fnins.2019.00076 PubMed PMID: 30804744 PMCID: PMC6378958
  28. Kuhn T, Jin Y, Huang C, Kim Y, Nir TM, Gullett JM, Jones JD, Sayegh P, Chung C, Dang BH, Singer EJ, Shattuck DW, Jahanshad N, Bookheimer SY, Hinkin CH, Zhu H, Thompson PM, Thames AD. The joint effect of aging and HIV infection on microstructure of white matter bundles. Hum Brain Mapp. 2019;40(15):4370-80. Epub 20190704. doi: 10.1002/hbm.24708 PubMed PMID: 31271489 PMCID: PMC6865715
  29. Kim TH, Bilgic B, Polak D, Setsompop K, Haldar JP. Wave-LORAKS: Combining wave encoding with structured low-rank matrix modeling for more highly accelerated 3D imaging. Magn Reson Med. 2019;81(3):1620-33. Epub 20180925. doi: 10.1002/mrm.27511 PubMed PMID: 30252157 PMCID: PMC6347537
  30. Joshi AA, Li J, Akrami H, Leahy RM. Predicting Cognitive Scores from Resting fMRI Data and Geometric Features of the Brain. Proc SPIE Int Soc Opt Eng. 2019;10949. Epub 20190315. doi: 10.1117/12.2512063 PubMed PMID: 34305256 PMCID: PMC8301598
  31. Joshi AA, Akrami H, Li J, Leahy RM. A Matched Filter Decomposition of fMRI into Resting and Task Components. Med Image Comput Comput Assist Interv. 2019;11766:673-81. Epub 20191010. doi: 10.1007/978-3-030-32248-9_75 PubMed PMID: 32161932 PMCID: PMC7065573
  32. Jian L, Haldar JP, Mosher JC, Nair DR, Gonzalez-Martinez JA, Leahy RM. Scalable and Robust Tensor Decomposition of Spontaneous Stereotactic EEG Data. IEEE Trans Biomed Eng. 2019;66(6):1549-58. Epub 20181011. doi: 10.1109/tbme.2018.2875467 PubMed PMID: 30307856 PMCID: PMC6677658
  33. Haldar JP, Kim D. OEDIPUS: An Experiment Design Framework for Sparsity-Constrained MRI. IEEE Trans Med Imaging. 2019;38(7):1545-58. Epub 20190201. doi: 10.1109/tmi.2019.2896180 PubMed PMID: 30716031 PMCID: PMC6669033
  34. Choi S, O’Neil SH, Joshi AA, Li J, Bush AM, Coates TD, Leahy RM, Wood JC. Anemia predicts lower white matter volume and cognitive performance in sickle and non-sickle cell anemia syndrome. Am J Hematol. 2019;94(10):1055-65. Epub 20190723. doi: 10.1002/ajh.25570 PubMed PMID: 31259431 PMCID: PMC6857783
  35. Varadarajan D, Haldar JP. TOWARDS OPTIMAL LINEAR ESTIMATION OF ORIENTATION DISTRIBUTION FUNCTIONS WITH ARBITRARILY SAMPLED DIFFUSION MRI DATA. Proc IEEE Int Symp Biomed Imaging. 2018;2018:743-6. Epub 20180524. doi: 10.1109/isbi.2018.8363680 PubMed PMID: 30956753 PMCID: PMC6448790
  36. Shattuck DW. Multiuser virtual reality environment for visualising neuroimaging data. Healthc Technol Lett. 2018;5(5):183-8. Epub 20181019. doi: 10.1049/htl.2018.5077 PubMed PMID: 30464851 PMCID: PMC6222246
  37. Quachtran B, de la Torre Ubieta L, Yusupova M, Geschwind DH, Shattuck DW. VOTING-BASED SEGMENTATION OF OVERLAPPING NUCLEI IN CLARITY IMAGES. Proc IEEE Int Symp Biomed Imaging. 2018;2018:658-62. Epub 20180524. doi: 10.1109/isbi.2018.8363660 PubMed PMID: 32038768 PMCID: PMC7007201
  38. Phillips OR, Joshi SH, Narr KL, Shattuck DW, Singh M, Di Paola M, Ploner CJ, Prüss H, Paul F, Finke C. Superficial white matter damage in anti-NMDA receptor encephalitis. J Neurol Neurosurg Psychiatry. 2018;89(5):518-25. Epub 20171103. doi: 10.1136/jnnp-2017-316822 PubMed PMID: 29101253 PMCID: PMC5899027
  39. Lobos RA, Kim TH, Hoge WS, Haldar JP. Navigator-Free EPI Ghost Correction With Structured Low-Rank Matrix Models: New Theory and Methods. IEEE Trans Med Imaging. 2018;37(11):2390-402. Epub 20180402. doi: 10.1109/tmi.2018.2822053 PubMed PMID: 29993978 PMCID: PMC6309699
  40. Lobos RA, Javed A, Nayak KS, Hoge WS, Haldar JP. ROBUST AUTOCALIBRATED LORAKS FOR EPI GHOST CORRECTION. Proc IEEE Int Symp Biomed Imaging. 2018;2018:663-6. Epub 20180524. doi: 10.1109/isbi.2018.8363661 PubMed PMID: 30984344 PMCID: PMC6461404
  41. Li J, Choi S, Joshi AA, Wisnowski JL, Leahy RM. GLOBAL PDF-BASED TEMPORAL NON-LOCAL MEANS FILTERING REVEALS INDIVIDUAL DIFFERENCES IN BRAIN CONNECTIVITY. Proc IEEE Int Symp Biomed Imaging. 2018;2018:15-9. Epub 20180524. doi: 10.1109/isbi.2018.8363513 PubMed PMID: 30713593 PMCID: PMC6354009
  42. Kim TH, Haldar JP. THE FOURIER RADIAL ERROR SPECTRUM PLOT: A MORE NUANCED QUANTITATIVE EVALUATION OF IMAGE RECONSTRUCTION QUALITY. Proc IEEE Int Symp Biomed Imaging. 2018;2018:61-4. Epub 20180524. doi: 10.1109/isbi.2018.8363523 PubMed PMID: 31007839 PMCID: PMC6472927
  43. Kim D, Wisnowski JL, Nguyen CT, Haldar JP. PROBING IN VIVO MICROSTRUCTURE WITH T (1)-T (2) RELAXATION CORRELATION SPECTROSCOPIC IMAGING. Proc IEEE Int Symp Biomed Imaging. 2018;2018:675-8. Epub 20180524. doi: 10.1109/isbi.2018.8363664 PubMed PMID: 30854157 PMCID: PMC6405227
  44. Joshi AA, Li J, Chong M, Akrami H, Leahy RM. rfDemons: Resting fMRI-based Cortical Surface Registration using the BrainSync Transform. Med Image Comput Comput Assist Interv. 2018;11072:198-205. Epub 20180913. doi: 10.1007/978-3-030-00931-1_23 PubMed PMID: 30714047 PMCID: PMC6355247
  45. Joshi AA, Chong M, Li J, Choi S, Leahy RM. Are you thinking what I’m thinking? Synchronization of resting fMRI time-series across subjects. Neuroimage. 2018;172:740-52. Epub 20180208. doi: 10.1016/j.neuroimage.2018.01.058 PubMed PMID: 29428580 PMCID: PMC6338442
  46. Joshi AA, Bhushan C, Salloum R, Wisnowski J, Shattuck DW, Leahy RM. Using the Anisotropic Laplace Equation to Compute Cortical Thickness. Med Image Comput Comput Assist Interv. 2018;11072:549-56. Epub 20180913. doi: 10.1007/978-3-030-00931-1_63 PubMed PMID: 30734031 PMCID: PMC6363343
  47. Joshi AA. Registration. Neuromethods. 2018;136:3-12. Epub 20180228. doi: 10.1007/978-1-4939-7647-8_1 PubMed PMID: 30842692 PMCID: PMC6398434
  48. Coletti AM, Singh D, Kumar S, Shafin TN, Briody PJ, Babbitt BF, Pan D, Norton ES, Brown EC, Kahle KT, Del Bigio MR, Conover JC. Characterization of the ventricular-subventricular stem cell niche during human brain development. Development. 2018;145(20). Epub 20181026. doi: 10.1242/dev.170100 PubMed PMID: 30237244 PMCID: PMC6215394
  49. Varadarajan D, Haldar JP. A theoretical signal processing framework for linear diffusion MRI: Implications for parameter estimation and experiment design. Neuroimage. 2017;161:206-18. Epub 20170819. doi: 10.1016/j.neuroimage.2017.08.048 PubMed PMID: 28830765 PMCID: PMC5696014
  50. Thomason ME, Marusak HA. Toward understanding the impact of trauma on the early developing human brain. Neuroscience. 2017;342:55-67. Epub 20160215. doi: 10.1016/j.neuroscience.2016.02.022 PubMed PMID: 26892294 PMCID: PMC4985495
  51. Kim TH, Setsompop K, Haldar JP. LORAKS makes better SENSE: Phase-constrained partial fourier SENSE reconstruction without phase calibration. Magn Reson Med. 2017;77(3):1021-35. Epub 20160401. doi: 10.1002/mrm.26182 PubMed PMID: 27037836 PMCID: PMC5045741
  52. Joshi AA, Chong M, Leahy RM. BrainSync: An Orthogonal Transformation for Synchronization of fMRI Data Across Subjects. Med Image Comput Comput Assist Interv. 2017;10433:486-94. Epub 20170904. doi: 10.1007/978-3-319-66182-7_56 PubMed PMID: 29075682 PMCID: PMC5654560
  53. Chong M, Bhushan C, Joshi AA, Choi S, Haldar JP, Shattuck DW, Spreng RN, Leahy RM. Individual parcellation of resting fMRI with a group functional connectivity prior. Neuroimage. 2017;156:87-100. Epub 20170503. doi: 10.1016/j.neuroimage.2017.04.054 PubMed PMID: 28478226 PMCID: PMC5774339
  54. Choi S, Bush AM, Borzage MT, Joshi AA, Mack WJ, Coates TD, Leahy RM, Wood JC. Hemoglobin and mean platelet volume predicts diffuse T1-MRI white matter volume decrease in sickle cell disease patients. Neuroimage Clin. 2017;15:239-46. Epub 20170429. doi: 10.1016/j.nicl.2017.04.023 PubMed PMID: 28540180 PMCID: PMC5430155
  55. Awate SP, Leahy RM, Joshi AA. Kernel Methods for Riemannian Analysis of Robust Descriptors of the Cerebral Cortex. Inf Process Med Imaging. 2017;10265:28-40. Epub 20170523. doi: 10.1007/978-3-319-59050-9_3 PubMed PMID: 29398876 PMCID: PMC5794037
  56. Wang ZI, Suwanpakdee P, Jones SE, Jaisani Z, Moosa AN, Najm IM, von Podewils F, Burgess RC, Krishnan B, Prayson RA, Gonzalez-Martinez JA, Bingaman W, Alexopoulos AV. Re-review of MRI with post-processing in nonlesional patients in whom epilepsy surgery has failed. J Neurol. 2016;263(9):1736-45. Epub 20160613. doi: 10.1007/s00415-016-8171-7 PubMed PMID: 27294258 PMCID: PMC5011447
  57. Wang ZI, Krishnan B, Shattuck DW, Leahy RM, Moosa AN, Wyllie E, Burgess RC, Al-Sharif NB, Joshi AA, Alexopoulos AV, Mosher JC, Udayasankar U, Jones SE. Automated MRI Volumetric Analysis in Patients with Rasmussen Syndrome. AJNR Am J Neuroradiol. 2016;37(12):2348-55. Epub 20160908. doi: 10.3174/ajnr.A4914 PubMed PMID: 27609620 PMCID: PMC5161540
  58. Wang I, Alexopoulos A. MRI postprocessing in presurgical evaluation. Curr Opin Neurol. 2016;29(2):168-74. doi: 10.1097/wco.0000000000000305 PubMed PMID: 26900745 PMCID: PMC4932912
  59. Phillips OR, Joshi SH, Squitieri F, Sanchez-Castaneda C, Narr K, Shattuck DW, Caltagirone C, Sabatini U, Di Paola M. Major Superficial White Matter Abnormalities in Huntington’s Disease. Front Neurosci. 2016;10:197. Epub 20160523. doi: 10.3389/fnins.2016.00197 PubMed PMID: 27242403 PMCID: PMC4876130
  60. Phillips OR, Joshi SH, Piras F, Orfei MD, Iorio M, Narr KL, Shattuck DW, Caltagirone C, Spalletta G, Di Paola M. The superficial white matter in Alzheimer’s disease. Hum Brain Mapp. 2016;37(4):1321-34. Epub 20160123. doi: 10.1002/hbm.23105 PubMed PMID: 26801955 PMCID: PMC5125444
  61. Murakami H, Wang ZI, Marashly A, Krishnan B, Prayson RA, Kakisaka Y, Mosher JC, Bulacio J, Gonzalez-Martinez JA, Bingaman WE, Najm IM, Burgess RC, Alexopoulos AV. Correlating magnetoencephalography to stereo-electroencephalography in patients undergoing epilepsy surgery. Brain. 2016;139(11):2935-47. doi: 10.1093/brain/aww215 PubMed PMID: 27567464 PMCID: PMC5091043
  62. Marusak HA, Kuruvadi N, Vila AM, Shattuck DW, Joshi SH, Joshi AA, Jella PK, Thomason ME. Interactive effects of BDNF Val66Met genotype and trauma on limbic brain anatomy in childhood. Eur Child Adolesc Psychiatry. 2016;25(5):509-18. Epub 20150819. doi: 10.1007/s00787-015-0759-4 PubMed PMID: 26286685 PMCID: PMC4760899
  63. Kim JH, Song SK, Haldar JP. Signal-to-noise ratio-enhancing joint reconstruction for improved diffusion imaging of mouse spinal cord white matter injury. Magn Reson Med. 2016;75(2):852-8. Epub 20150330. doi: 10.1002/mrm.25691 PubMed PMID: 25824472 PMCID: PMC4589425
  64. Kim D, Haldar JP. Greedy Algorithms for Nonnegativity-Constrained Simultaneous Sparse Recovery. Signal Processing. 2016;125:274-89. Epub 20160206. doi: 10.1016/j.sigpro.2016.01.021 PubMed PMID: 26973368 PMCID: PMC4784713
  65. Joshi AA, Leahy RM, Badawi RD, Chaudhari AJ. Registration-Based Morphometry for Shape Analysis of the Bones of the Human Wrist. IEEE Trans Med Imaging. 2016;35(2):416-26. doi: 10.1109/tmi.2015.2476817 PubMed PMID: 26353369 PMCID: PMC4779077
  66. Haldar JP, Zhuo J. P-LORAKS: Low-rank modeling of local k-space neighborhoods with parallel imaging data. Magn Reson Med. 2016;75(4):1499-514. Epub 20150507. doi: 10.1002/mrm.25717 PubMed PMID: 25952136 PMCID: PMC4637005
  67. Bhushan C, Chong M, Choi S, Joshi AA, Haldar JP, Damasio H, Leahy RM. Temporal Non-Local Means Filtering Reveals Real-Time Whole-Brain Cortical Interactions in Resting fMRI. PLoS One. 2016;11(7):e0158504. Epub 20160708. doi: 10.1371/journal.pone.0158504 PubMed PMID: 27391481 PMCID: PMC4938391
  68. Awate SP, Leahy RM, Joshi AA. Riemannian Statistical Analysis of Cortical Geometry with Robustness to Partial Homology and Misalignment. Med Image Comput Comput Assist Interv. 2016;9900:237-46. Epub 20161002. doi: 10.1007/978-3-319-46720-7_28 PubMed PMID: 28105471 PMCID: PMC5240952
  69. Wang ZI, Jones SE, Jaisani Z, Najm IM, Prayson RA, Burgess RC, Krishnan B, Ristic A, Wong CH, Bingaman W, Gonzalez-Martinez JA, Alexopoulos AV. Voxel-based morphometric magnetic resonance imaging (MRI) postprocessing in MRI-negative epilepsies. Ann Neurol. 2015;77(6):1060-75. Epub 20150423. doi: 10.1002/ana.24407 PubMed PMID: 25807928 PMCID: PMC4447617
  70. Varadarajan D, Haldar JP. A majorize-minimize framework for Rician and non-central chi MR images. IEEE Trans Med Imaging. 2015;34(10):2191-202. Epub 20150428. doi: 10.1109/tmi.2015.2427157 PubMed PMID: 25935028 PMCID: PMC4596756
  71. Marusak HA, Furman DJ, Kuruvadi N, Shattuck DW, Joshi SH, Joshi AA, Etkin A, Thomason ME. Amygdala responses to salient social cues vary with oxytocin receptor genotype in youth. Neuropsychologia. 2015;79(Pt A):1-9. Epub 20151023. doi: 10.1016/j.neuropsychologia.2015.10.015 PubMed PMID: 26477647 PMCID: PMC4679629
  72. Joshi AA, Salloum R, Bhushan C, Leahy RM. Measuring Asymmetric Interactions in Resting State Brain Networks. Inf Process Med Imaging. 2015;24:399-410. doi: 10.1007/978-3-319-19992-4_31 PubMed PMID: 26221690 PMCID: PMC4519983
  73. Chambers MC, Bhushan C, Haldar JP, Leahy RM, Shattuck DW. CORRECTING INHOMOGENEITY-INDUCED DISTORTION IN FMRI USING NON-RIGID REGISTRATION. Proc IEEE Int Symp Biomed Imaging. 2015;2015:1364-7. doi: 10.1109/isbi.2015.7164129 PubMed PMID: 26617955 PMCID: PMC4662423
  74. Bhushan C, Haldar JP, Choi S, Joshi AA, Shattuck DW, Leahy RM. Co-registration and distortion correction of diffusion and anatomical images based on inverse contrast normalization. Neuroimage. 2015;115:269-80. Epub 20150327. doi: 10.1016/j.neuroimage.2015.03.050 PubMed PMID: 25827811 PMCID: PMC4461504
  75. Wang ZI, Alexopoulos AV, Jones SE, Najm IM, Ristic A, Wong C, Prayson R, Schneider F, Kakisaka Y, Wang S, Bingaman W, Gonzalez-Martinez JA, Burgess RC. Linking MRI postprocessing with magnetic source imaging in MRI-negative epilepsy. Ann Neurol. 2014;75(5):759-70. Epub 20140516. doi: 10.1002/ana.24169 PubMed PMID: 24777960 PMCID: PMC4346132
  76. Kakisaka Y, Jehi L, Alkawadri R, Wang ZI, Enatsu R, Mosher JC, Dubarry AS, Alexopoulos AV, Burgess RC. Cephalic aura after frontal lobe resection. J Clin Neurosci. 2014;21(8):1450-2. Epub 20140306. doi: 10.1016/j.jocn.2013.11.024 PubMed PMID: 24613491 PMCID: PMC4340243
  77. Haldar JP. Low-rank modeling of local k-space neighborhoods (LORAKS) for constrained MRI. IEEE Trans Med Imaging. 2014;33(3):668-81. doi: 10.1109/tmi.2013.2293974 PubMed PMID: 24595341 PMCID: PMC4122573
  78. Habibi A, Ilari B, Crimi K, Metke M, Kaplan JT, Joshi AA, Leahy RM, Shattuck DW, Choi SY, Haldar JP, Ficek B, Damasio A, Damasio H. An equal start: absence of group differences in cognitive, social, and neural measures prior to music or sports training in children. Front Hum Neurosci. 2014;8:690. Epub 20140909. doi: 10.3389/fnhum.2014.00690 PubMed PMID: 25249961 PMCID: PMC4158792
  79. Chaudhari AJ, Leahy RM, Wise BL, Lane NE, Badawi RD, Joshi AA. Global point signature for shape analysis of carpal bones. Phys Med Biol. 2014;59(4):961-73. Epub 20140207. doi: 10.1088/0031-9155/59/4/961 PubMed PMID: 24503490 PMCID: PMC3966902
  80. Bhushan C, Joshi AA, Leahy RM, Haldar JP. Improved B0 -distortion correction in diffusion MRI using interlaced q-space sampling and constrained reconstruction. Magn Reson Med. 2014;72(5):1218-32. Epub 20131111. doi: 10.1002/mrm.25026 PubMed PMID: 24464424 PMCID: PMC4017008
  81. Wang ZI, Ristic AJ, Wong CH, Jones SE, Najm IM, Schneider F, Wang S, Gonzalez-Martinez JA, Bingaman W, Alexopoulos AV. Neuroimaging characteristics of MRI-negative orbitofrontal epilepsy with focus on voxel-based morphometric MRI postprocessing. Epilepsia. 2013;54(12):2195-203. Epub 20131001. doi: 10.1111/epi.12390 PubMed PMID: 24116733 PMCID: PMC3982614
  82. Wang ZI, Alexopoulos AV, Nair D, Krishnan B, Mosher JC, Burgess RC, Kakisaka Y. Feasibility of magnetoencephalography recording in an epilepsy patient with implanted responsive cortical stimulation device. Clin Neurophysiol. 2013;124(8):1705-6. Epub 20130307. doi: 10.1016/j.clinph.2013.01.019 PubMed PMID: 23474057 PMCID: PMC4349520
  83. Kakisaka Y, Wang ZI, Enatsu R, Dubarry AS, Mosher JC, Alexopoulos AV, Burgess RC. Magnetoencephalography correlate of EEG POSTS (positive occipital sharp transients of sleep). J Clin Neurophysiol. 2013;30(3):235-7. doi: 10.1097/WNP.0b013e31827681a3 PubMed PMID: 23733086 PMCID: PMC3992251
  84. Kakisaka Y, Mosher JC, Wang ZI, Jin K, Dubarry AS, Alexopoulos AV, Burgess RC. Utility of temporally-extended signal space separation algorithm for magnetic noise from vagal nerve stimulators. Clin Neurophysiol. 2013;124(7):1277-82. Epub 20120623. doi: 10.1016/j.clinph.2012.03.082 PubMed PMID: 22727713 PMCID: PMC3980452
  85. Kakisaka Y, Gupta A, Enatsu R, Wang ZI, Alexopoulos AV, Mosher JC, Dubarry AS, Hino-Fukuyo N, Burgess RC. Magnetoencephalography reveals a unique neurophysiological profile of focal-onset epileptic spasms. Tohoku J Exp Med. 2013;229(2):147-51. doi: 10.1620/tjem.229.147 PubMed PMID: 23343709 PMCID: PMC3904381
  86. Kakisaka Y, Alkawadri R, Wang ZI, Enatsu R, Mosher JC, Dubarry AS, Alexopoulos AV, Burgess RC. Sensitivity of scalp 10-20 EEG and magnetoencephalography. Epileptic Disord. 2013;15(1):27-31. doi: 10.1684/epd.2013.0554 PubMed PMID: 23531601 PMCID: PMC3988277
  87. Haldar JP, Wedeen VJ, Nezamzadeh M, Dai G, Weiner MW, Schuff N, Liang ZP. Improved diffusion imaging through SNR-enhancing joint reconstruction. Magn Reson Med. 2013;69(1):277-89. Epub 20120305. doi: 10.1002/mrm.24229 PubMed PMID: 22392528 PMCID: PMC3407310
  88. Haldar JP, Leahy RM. Linear transforms for Fourier data on the sphere: application to high angular resolution diffusion MRI of the brain. Neuroimage. 2013;71:233-47. Epub 20130124. doi: 10.1016/j.neuroimage.2013.01.022 PubMed PMID: 23353603 PMCID: PMC3594568
  89. Wheland D, Joshi AA, McMahon KL, Hansell NK, Martin NG, Wright MJ, Thompson PM, Shattuck DW, Leahy RM. Robust Identification of Partial-Correlation Based Networks with Applications to Cortical Thickness Data. Proc IEEE Int Symp Biomed Imaging. 2012;2012:1551-4. doi: 10.1109/isbi.2012.6235869 PubMed PMID: 26753056 PMCID: PMC4705556
  90. Wang ZI, Jones SE, Ristic AJ, Wong C, Kakisaka Y, Jin K, Schneider F, Gonzalez-Martinez JA, Mosher JC, Nair D, Burgess RC, Najm IM, Alexopoulos AV. Voxel-based morphometric MRI post-processing in MRI-negative focal cortical dysplasia followed by simultaneously recorded MEG and stereo-EEG. Epilepsy Res. 2012;100(1-2):188-93. Epub 20120304. doi: 10.1016/j.eplepsyres.2012.02.011 PubMed PMID: 22391138 PMCID: PMC3361571
  91. Wang ZI, Jin K, Kakisaka Y, Burgess RC, Gonzalez-Martinez JA, Wang S, Ito S, Mosher JC, Hantus S, Alexopoulos AV. Interconnections in superior temporal cortex revealed by musicogenic seizure propagation. J Neurol. 2012;259(10):2251-4. Epub 20120720. doi: 10.1007/s00415-012-6556-9 PubMed PMID: 23010942 PMCID: PMC3632445
  92. Somayajula S, Joshi AA, Leahy RM. Non-Rigid Image Registration Using Gaussian Mixture Models. Biomed Image Registration. 2012;7359:286-95. doi: 10.1007/978-3-642-31340-0_30 PubMed PMID: 26753181 PMCID: PMC4702048
  93. Kakisaka Y, Wang ZI, Mosher JC, Dubarry AS, Alexopoulos AV, Enatsu R, Kotagal P, Burgess RC. Clinical evidence for the utility of movement compensation algorithm in magnetoencephalography: successful localization during focal seizure. Epilepsy Res. 2012;101(1-2):191-6. Epub 20120414. doi: 10.1016/j.eplepsyres.2012.03.014 PubMed PMID: 22503605 PMCID: PMC3621737
  94. Kakisaka Y, Kubota Y, Wang ZI, Piao Z, Mosher JC, Gonzalez-Martinez J, Jin K, Alexopoulos AV, Burgess RC. Use of simultaneous depth and MEG recording may provide complementary information regarding the epileptogenic region. Epileptic Disord. 2012;14(3):298-303. doi: 10.1684/epd.2012.0517 PubMed PMID: 22940092
  95. Kakisaka Y, Iwasaki M, Alexopoulos AV, Enatsu R, Jin K, Wang ZI, Mosher JC, Dubarry AS, Nair DR, Burgess RC. Magnetoencephalography in fronto-parietal opercular epilepsy. Epilepsy Res. 2012;102(1-2):71-7. Epub 20120531. doi: 10.1016/j.eplepsyres.2012.05.003 PubMed PMID: 22658720 PMCID: PMC3645283
  96. Joshi AA, Shattuck DW, Leahy RM. A Method for Automated Cortical Surface Registration and Labeling. Biomed Image Regist Proc. 2012;7359:180-9. doi: 10.1007/978-3-642-31340-0_19 PubMed PMID: 26213720 PMCID: PMC4511281
  97. Joshi AA, Shattuck DW, Damasio H, Leahy RM. GEODESIC CURVATURE FLOW ON SURFACES FOR AUTOMATIC SULCAL DELINEATION. Proc IEEE Int Symp Biomed Imaging. 2012;2012:430-3. doi: 10.1109/isbi.2012.6235576 PubMed PMID: 26770662 PMCID: PMC4710142
  98. Joshi AA, Ashrafulla S, Shattuck DW, Damasio H, Leahy RM. An invariant shape representation using the anisotropic Helmholtz equation. Med Image Comput Comput Assist Interv. 2012;15(Pt 3):607-14. doi: 10.1007/978-3-642-33454-2_75 PubMed PMID: 23286181 PMCID: PMC3632444
  99. Bhushan C, Haldar JP, Joshi AA, Leahy RM. Correcting Susceptibility-Induced Distortion in Diffusion-Weighted MRI using Constrained Nonrigid Registration. Signal Inf Process Assoc Annu Summit Conf APSIPA Asia Pac. 2012;2012. PubMed PMID: 26767197 PMCID: PMC4708288


  1. Deblieck C, Christov-Moore L, Wu AD, Shattuck D, Iacoboni M. Diffusion MRI Parameters Mediating the Behavioral Effects Of TMS, Non Invasive Brain stimulation technics (NIBS) for psychiatric disorders: First European Meeting. Ghent, Belgium, Dec 2015.
  2. Wang ZI, Krishnan B, Al-Sharif N, Shattuck D, Joshi A, Leahy R, Alexopoulos A, Burgess R, Mosher J, Udayasankar U, Moosa AN, Wyllie E, Jones S. Automated MRI Volumetric Analysis Of Rasmussen’s Encephalitis. 69th Annual Meeting of the American Epilepsy Society, Philadelphia, PA, Dec 2015.
  3. Kim B, Kay DB, Yi Y, Lee D, Chaudhry Y, Haldar JP, Leahy RM, Winstein CJ. DTI analysis of corticospinal tract using BrainSuite: A potential biomarker of upper extremity therapeutic response to neurorehabilitation in chronic stroke. Society for Neuroscience (SfN) 2014 Annual Meeting. Washington D.C. Nov 2014.
  4. Kim B, Oh Y, Leahy RM, Haldar JP, Schweighofer N, Winstein CJ. Brain sensorimotor structural network difference between two hemispheres in chronic stroke. Society for Neuroscience (SfN) 2015 Annual Conference. Chicago, IL. Oct 2015.
  5. Kim B, Oh Y, Leahy RM, Haldar JP, Schweighofer N, Winstein CJ. Is structural connectivity of basal ganglia associated with learned non-use in chronic stroke? American Society for Neurorehabilitation (ASNR) 2015 annual meeting. Chicago, IL. Oct 2015.
  6. Varadarajan D, Wang ZI, Joshi AA, Shattuck DW, Jones SE, Leahy RM. 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.
  7. Chong M, Joshi AA, Haldar JP, DuPre E, Luh W-M, Shattuck DW, Spreng RN, Leahy RM. 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.
  8. Phillips O, Joshi S, Piras F, Orfei M, Iorio M, Narr K, Shattuck D, Caltagirone C, Gianfranco Spalletta3, Margherita Di Paola. Is the Superficial White Matter important in Alzheimer’s Disease? 21st Annual Meeting of the Organization for Human Brain Mapping Honolulu, Hawaii, June 2015.
  9. Jones S, Wang I, Alexopoulos A, Al-Sharif N, Burgess R, Joshi A, Krishnan B, Leahy R, Mosher J, Udayasankar U, Shattuck D. Automated Quantitative Assessment of Rasmussen’s Encephalitis. American Society of Neuroradiology 53rd Annual Meeting, Chicago, IL, April 2015.
  10. Chambers M, Bhushan C, Pirnia T, Narr K, Haldar J, Leahy R, Shattuck D. Registration-Based Distortion and Intensity Correction in fMRI. 20th Annual Meeting of the Organization for Human Brain Mapping Hamburg, Germany, June 2014.
  11. Joshi S, Woods, R, Joshi A, Fears S, Al-Sharif N, Leahy R, Shattuck D. A Statistical Toolbox for BrainSuite 20th Annual Meeting of the Organization for Human Brain Mapping Hamburg, Germany, June 2014.
  12. Joshi A, Bhushan C, Shattuck D, Leahy R. 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.
  13. Balasubramaniam E, Joshi A, Shattuck D, Leahy R. A PDE approach for automatic thickness estimation using partial volume classification. Joint Annual Meeting ISMRM-ESMRMB Milan, Italy, April 2014.
  14. Bhushan C, Haldar JP, Joshi AA, Shattuck DW, Leahy RM. INVERSION: A Robust Method for Co-registration of T1 and Diffusion Weighted MRI Images. Joint Annual Meeting ISMRM-ESMRMB, Milan, Italy, April 2014.
  15. J. P. Haldar. LORAKS: Low-Rank Modeling of Local k-Space Neighborhoods. Joint Annual Meeting ISMRM-ESMRMB, Milan, April 2014.
  16. D. Varadarajan, J. P. Haldar. A Novel Approach for Statistical Estimation of HARDI Diffusion Parameters from Rician and Non-Central Chi Magnitude Images. Joint Annual Meeting ISMRM-ESMRMB, Milan, April 2014.
  17. J. Zhuo, J. P. Haldar. P-LORAKS: Low-rank modeling of local k-space neighborhoods with parallel imaging data. Joint Annual Meeting ISMRM-ESMRMB, Milan, April 2014.
  18. Beroukhim D, Konersman M, Chong M, Joshi AA, Bhushan C, Shattuck DW, Haldar JP, Leahy RM, Winstein CJ. 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.
  19. Shattuck D Joshi A, Haldar J, Bhushan C, Choi S, Krause A, Wisnowski J, Damasio H, Toga A, Leahy R. 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.
  20. Joshi A, Ashrafulla S, Shattuck D, Damasio H, Leahy R. 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.
  21. Choi S, Bhushan C, Joshi AA, Raphel K, Tranel D, Shattuck D, Haldar J, Leahy RM, Damasio H, Wisnowski J. 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.
  22. Shattuck DW Joshi AA, Haldar JP, Bhushon C, Krause AC, Wisnowski JL, Toga AW, Leahy RM. Software Tools for Anatomical ROI-based Connectivity Analysis, International Society for Magnetic Resonance in Medicine 21st Scientific Meeting, Salt Lake City, Utah, April 2013.
  23. Haldar JP, Shattuck DW Leahy RM. Estimation of White Matter Fiber Orientations with the Funk-Radon and Cosine Transform, International Society for Magnetic Resonance in Medicine 21st Scientific Meeting, Salt Lake City, Utah, April 2013.
  24. Bhushan C, Joshi AA, Leahy RM, Haldar JP. Accelerating Data Acquisition for Reversed-Gradient Distortion Correction in Diffusion MRI: A Constrained Reconstruction Approach. International Society for Magnetic Resonance in Medicine 21st Scientific Meeting, Salt Lake City, April 2013.
  25. Choi S, Joshi AA, Bhushan C, Shattuck DW Leahy RM, Damasio H, Panigrahy A, Wisnowski JL. A Multimodal Investigation of Neuronal/Axonal Integrity Using Structural T1-weighted Imaging, Diffusion Tensor Imaging, and H1 MR Spectroscopy, International Society for Magnetic Resonance in Medicine 21st Scientific Meeting, Salt Lake City, Utah, April 2013.
  26. Haldar JP, Shattuck DW, Damasio H, Leahy RM. Improved Diffusion Tractography with the Funk-Radon and Cosine Transform, 18th Annual Meeting of the Organization for Human Brain Mapping, Beijing, China, June 2012.
  27. Joshi AA, Shattuck DW, Leahy RM. 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.

Related work

We have published several earlier papers describing and validating many of the methods included within the BrainSuite tools. These include:

Methods papers

  1. Joshi AA, Pantazis D, Li Q, Damasio H, Shattuck D, Toga A, Leahy RM (2010) Sulcal set optimization for cortical surface registration, NeuroImage 50(3):950-9
  2. 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, NeuroImage49(3):2479-93
  3. Joshi AA, Shattuck DW, Thompson PM, and Leahy RM (2010) A Parameterization-based Numerical Method for Isotropic and Anisotropic Diffusion Smoothing on Non-Flat Surfaces, IEEE Trans. on Image Processing 18(6):1358-1365.
  4. 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
  5. 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
  6. Shattuck DW and Leahy RM (2002) BrainSuite: An Automated Cortical Surface Identification Tool Medical Image Analysis, 8(2):129-142.
  7. Shattuck DW and Leahy RM (2001) Graph Based Analysis and Correction of Cortical Volume Topology, IEEE Transactions on Medical Imaging, 20(11)1167-1177.
  8. Shattuck DW, Sandor-Leahy SR, Schaper KA, Rottenberg DA, and Leahy RM, “Magnetic Resonance Image Tissue Classification Using a Partial Volume Model,” NeuroImage, 13(5):856-876.

Validation Studies

  1. 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):99-113PMCID: PMC2757616
  2. 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, 5(13):931-943.