PREPRINTS
Attarpour A, Raffiee M, Xu T, Osmann J, Patel S, Yu F, Au B, Clappison A, Biparva M, Zhu R, Crow A, Gharagoz BE, Rozak M, Aubert I, McLaurin J, Deisseroth K, Stefanovic B, Goubran M. Quantitative profiling of whole-brain connectomes at single-axon resolution using deep learning and high-resolution light sheet microscopy. bioRxiv. 2025.
Ntiri EE, Xu T, Rozak MW, Attarpour A, Dorr A, Stefanovic B, Goubran M. A self-supervised deep learning pipeline for segmentation in two-photon fluorescence microscopy. bioRxiv. 2025.
Zhang AH, He-Mo A, Yin RF, Li C, Tang Y, Gurve D, Ghahjaverestan NM, Goubran M, Wang B, Lim AS. Mamba-based Deep Learning Approaches for Sleep Staging on a Wireless Multimodal Wearable System without Electroencephalography. arXiv. 2025.
SELECTED ARTICLES
Xu T, Hosseini S, Anderson C, Rinaldi A, Krishnan RG, Martel AL, Goubran M. A generalizable 3D framework and model for self-supervised learning in medical imaging. npj Digital Medicine. 2025.
Tan J X, Kang MS, Yeh Y, Bezgin G, Lussier, F. Z., Hong, S., Isen, J., Rahmouni, N., Vitali, P., Montembeault, M., Klostranec, J. M., Macedo, A. C., Chan, T., McLaurin, J., Swardfager, W., Bernhardt, B. C., Stefanovic, B., Soucy, J, Gauthier S, Black SE, Rosa-Neto P, Ottoy J,* Goubran M*. Stepwise connectivity of the entorhinal cortex along connectomic gradients in Alzheimer’s disease. Brain Communications. 2025
De Schlichting E, Huang Y, Jones RM, Meng Y, Cao X, Baskaran A, Hynynen K, Hamani C, Lipsman N, Goubran M, Davidson B. Focused ultrasound capsulotomy: predicting the probability of successful lesioning based on skull morphology. Journal of Neurosurgy. 2025.
Ottoy J, Owsicki N, Bilgel M, Binette AP, Salvadó G, Kang MS, Cash DM, Ewers M, La Joie R, Wisse LEM, Goubran M, Betthauser T. Recent advances in neuroimaging of Alzheimer’s disease and related dementias. Alzheimer’s & Dementia. 2025.
Attarpour A, Osmann J, Rinaldi A, Qi T, Lal N, Patel S, Rozak M, Yu F, Cho N, Squair J, McLaurin J, Raffiee M, Deisseroth K, Courtine G, Ye L, Goubran M. A deep learning pipeline for three-dimensional brain-wide mapping of local neuronal ensembles in teravoxel light-sheet microscopy. Nature Methods. 2025.
Rozak M, Mester J, Attarpour A, Dorr A, Patel S, Koletar M, Hill M, McLaurin J, Goubran M, Stefanovic B. A Deep Learning Pipeline for Mapping in situ Network-level Neurovascular Coupling in Multi-photon Fluorescence Microscopy. eLife. 2025.
Mollica A, Cash RFH, Leochico CFD, Giacobbe P, Sewell IJ, Zalesky A, Rabin JS, Goubran M, Graham SJ, Davidson B, Lin FH, Lipsman N, Hamani C, Burke MJ, Nestor SM. The network-based underpinnings of persisting symptoms after concussion: a multimodal neuroimaging meta-analysis. Nature Mental Health. 2025
Gibson E, Ramirez J, Woods LA, Ottoy J, Berberian S, Scott CJM, Yhap V, Gao F, Coello RD, Valdes Hernandez M, Lang AE, Tartaglia CM, Kumar S, Binns MA, Bartha R, Symons S, Swartz RH, Masellis M, Singh N, Moody A, MacIntosh BJ, Wardlaw JM, Black SE, Lim ASP, Goubran M. segcsvdWMH: A Convolutional Neural Network-Based Tool for Quantifying White Matter Hyperintensities in Heterogeneous Patient Cohorts. Human Brain Mapping. 2024.
Cho N, Squair JW, Aureli V, James ND, Bole-Feysot L, Dewany I, Hankov N, Baud L, Leonhartsberger A, Sveistyte K, Skinnider MA, Gautier M, Laskaratos A, Galan K, Goubran M….Courtine G. Hypothalamic deep brain stimulation augments walking after spinal cord injury. Nature Medicine. 2024.
Ottoy J, Kang MS, Tan JXM, Boone L, Vos de Wael R, Park BY, … Goubran M. Tau follows principal axes of functional and structural brain organization in Alzheimer’s disease. Nature Communications. 2024.
Xhima K, Ottoy J, Gibson E, Zukotynski K, Scott C, Feliciano GJ, Adamo S, Kuo PH, Borrie MJ, Chertkow H, Frayne R, Laforce R Jr, Noseworthy MD, Prato FS, Sahlas DJ, Smith EE, Sossi V, Thiel A, Soucy JP, Tardif JC, Goubran M, Black SE, Ramirez J. Distinct spatial contributions of amyloid pathology and cerebral small vessel disease to hippocampal morphology. Alzheimer’s & Dementia. 2024
Hamani C, Davidson B, Rabin JS, Goubran M, Boone L, Hynynen K, De Schlichting E, Meng Y, Huang Y, Jones RM, Baskaran A, Marawi T, Richter MA, Levitt A, Nestor SM, Giacobbe P, Lipsman N. Long-term safety and efficacy of focused ultrasound capsulotomy for obsessive-compulsive disorder and major depressive disorder. Biological Psychiatry. 2024
Chen JS, Goubran M, Kim G, Kim MJ, Willmann JK, Zeineh M, Hristov D, Kaffas AE. **Motion correction of 3D dynamic contrast-enhanced ultrasound imaging without anatomical B-Mode images: Pilot evaluation in eight patients. Medical Physics. 2024
Goubran M, Mills BD, Georgdiadis M, Karimpoor M, Mouchawar N, Sami S, Dennis EL, Akers C, Mitchell LA, Boldt B, Douglas D, DiGiacomo P, Rosenberg J, Camarillo D, Grant G, Wintermark M, Zeineh M. Microstructural Alterations in Tract Development in College Football and Volleyball Players: A Longitudinal Diffusion MRI Study Neurology. 2023.
Boone L, Biparva M, Mojiri Forooshani P, Ramirez J, Masellis M, Bartha R, Symons S, Strother S, Black SE, Heyn C, Martel AL, Swartz R, Goubran M. ROOD-MRI: Benchmarking the robustness of deep learning segmentation models to out-of-distribution and corrupted data in MRI. NeuroImage. 2023.
Hsueh B, Chen R, Jo Y, Tang D, Raffiee M, Kim YS, Inoue M, Randles S, Ramakrishnan C, Patel S, Kim DK…Goubran M, Deisseroth K, Cardiogenic control of affective behavioural state. Nature. 2023.
Meng Y, Goubran M, Rabin JS, McSweeney M, Ottoy J, Pople CB, Huang Y, Storace A, Ozzoude M, Bethune A, Lam B, Swardfager W, Heyn C, Abrahao A, Davidson B, Hamani C, Aubert I, Zetterberg H, Ashton NJ, Karikari TK, Blennow K, Black SE, Hynynen K, Lipsman N. Blood–brain barrier opening of the default mode network in Alzheimer’s disease with magnetic resonance-guided focused ultrasound. Brain. 2023.
Ottoy J, Ozzoude M, Zukotynski K, Kang MS, Adamo S, Scott C, Ramirez J, Swardfager W, Lam B, Bhan A, Mojiri P … Black SE, Goubran M. Amyloid-PET of the white matter: Relationship to free water, fiber integrity, and cognition in patients with dementia and small vessel disease. Journal of Cerebral Flow & Metabolism. 2023.
Ottoy J, Ozzoude M, Zukotynski K, Adamo S, Scott C, Gaudet V, Ramirez J, Swardfager W, Cogo-Moreira H, Lam B, Bhan A … Goubran M. Vascular burden and cognition: Mediating roles of neurodegeneration and amyloid-PET. Alzheimer’s and Dementia. 2022.
Mojiri PF, Biparva M, Ntiri EE, Ramirez J, Boone L, Holmes M, Adamo S, Gao F, Ozzoude M, Scott CJM, Dowlatshahi D, Lawrence-Dewar JM, Kwan D, Lang AE, Marcotte K, Leonard C, Rochon E, Heyn C, Bartha R, Strother S, Tardif J-C, Symons S, Masellis M, Swartz RH, Moody A, Black SE, Goubran M. Deep Bayesian Unet for uncertainty estimation and adversarial resistance of white matter hyperintensity segmentation. Human Brain Mapping. 2022.
Luciw NJ, Shirzadi Z, Black SE, Goubran M, MacIntosh BJ. A deep learning approach for simultaneous estimation of quantitative cerebral blood flow and arterial transit time from multiple-delay arterial spin-labelled magnetic resonance images. Magnetic Resonance in Medicine. 2022.
Khan AR, Ottoy J, Goubran M. Towards a comprehensive 3D mapping of tau progression in early Alzheimer’s disease. Brain. 2021
Xhima K, McMahon D, Ntiri E, Goubran M, Hynynen K, Aubert I. Intravenous and noninvasive drug delivery to the mouse basal forebrain using MRI-guided focused ultrasound. Bio-protocol. 2021. Accepted.
Ntiri E, Holmes M, Forooshani P, Ramirez J, Gao F, Ozzoude M, Adamo S, Scott C, Dowlatshahi D, Lawrence-Dewar J, Kwan D, Lang T, Symons S, Bartha R, Strother S, Tardif J-C, Masellis M, Swartz R, Moody A, Black SE, Goubran M. Improved segmentation of the intracranial and ventricular volumes in populations with cerebrovascular lesions and atrophy using 3D CNNs. Neuroinformatics. 2020.
Leuze C,* Goubran M,* Barakovic M,* Aswendt M, Tian Q, Hsueh B, Crow A, Weber E, Steinberg G, Zeineh M, Plowey E, Daducci A, Innocenti G, Thiran JP, Deisseroth K, McNab JA. Comparison of diffusion MRI and CLARITY fiber orientation estimates in both gray and white matter regions of human and primate brain. Neuroimage. 2021;228:117692.
Mills BD,* Goubran M,* Parivash SN, Dennis EL, Rezaii P, Akers C, Bian W, Mitchell LA, Boldt B, Douglas D, Sami S, Mouchawar N, Wilson EW, DiGiacomo P, Parekh M, Do H, Lopez J, Rosenberg J, Camarillo D, Grant G, Wintermark M, Zeineh M. Longitudinal alteration of cortical thickness and volume in high-impact sports. NeuroImage. 2020;217:116864
Davidson B, Hamani C, Rabin JS, Goubran M, Meng Y, Huang Y, Baskaran A, Sharma S, Ozzoude M, Richter MA, Levitt A, Giacobbe P, Hynynen K, Lipsman N. Magnetic resonance-guided focused ultrasound capsulotomy for refractory obsessive compulsive disorder and major depressive disorder: clinical and imaging results from two phase I trials. Molecular Psychiatry.2020.
Guo F, Ng M, Goubran M, Petersen SE, Piechnik SK, Neubauer S, Wright G. Improving cardiac MRI convolutional neural network segmentation on small training datasets and dataset shift: A continuous kernel cut approach. Medical Image Analysis. 2020;61:101636
Boillat M, Hammoudi P-M, Dogga SK, Pagès S, Goubran M, Rodriguez I, Soldati-Favre D. Neuroinflammation-Associated Aspecific Manipulation of Mouse Predator Fear by Toxoplasma gondii. Cell Reports. 2020;30(2):320-334.e6.
Goubran M, Ntiri EE, Akhavein H, Holmes M, Nestor S, Ramirez J, Adamo S, Ozzoude M, Scott C, Gao F, Martel A, Swardfager W, Masellis M, Swartz R, MacIntosh B, Black SE. Hippocampal segmentation for brains with extensive atrophy using three‐dimensional convolutional neural networks. Human Brain Mapping. 2020;41(2):291-308
Goubran M, Leuze C, Hsueh B, Aswendt M, Ye L, Tian Q, Cheng MY, Crow A, Steinberg GK, McNab JA, Deisseroth K, Zeineh M. Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Nature Communications. 2019;10(1):5504
Parivash SN,* Goubran M,* Mills BD, Rezaii P, Thaler C, Wolman D, Bian W, Mitchell LA, Boldt B, Douglas D, Wilson EW, Choi J, Xie L, Yushkevich PA, DiGiacomo P, Wongsripuemtet J, Parekh M, Fiehler J, Do H, Lopez J, Rosenberg J, Camarillo D, Grant G, Wintermark M, Zeineh M. Longitudinal Changes in Hippocampal Subfield Volume Associated with Collegiate Football. Journal of Neurotrauma. 2019;36(19):2762-2773.
Hernandez F,* Giordano C,* Goubran M,* Parivash S, Grant G, Zeineh M, Camarillo D. Lateral impacts correlate with falx cerebri displacement and corpus callosum trauma in sports-related concussions. Biomechanics and Modeling in Mechanobiology. 2019;18(3):631-649.
Guo J, Gong E, Fan AP, Goubran M, Khalighi MM, Zaharchuk G. Predicting 15 O-Water PET cerebral blood flow maps from multi-contrast MRI using a deep convolutional neural network with evaluation of training cohort bias. Journal of Cerebral Blood Flow & Metabolism.2019:0271678X1988812.
Terem I, Ni WW, Goubran M, Rahimi MS, Zaharchuk G, Yeom KW, Moseley ME, Kurt M, Holdsworth SJ. Revealing sub-voxel motions of brain tissue using phase-based amplified MRI (aMRI) Magnetic Resonance in Medicine. 2018;80(6):2549-2559.
Ito M, Aswendt M, Lee AG, Ishizaka S, Cao Z, Wang EH, Levy SL, Smerin DL, McNab JA, Zeineh M, Leuze C, Goubran M, Cheng MY, Steinberg GK. RNA-Sequencing Analysis Revealed a Distinct Motor Cortex Transcriptome in Spontaneously Recovered Mice After Stroke. Stroke. 2018;49(9):2191-2199.
Federau C,* Goubran M,* Rosenberg J, Henderson J, Halpern CH, Santini V, Wintermark M, Butts Pauly K, Ghanouni P. Transcranial MRI-guided high-intensity focused ultrasound for treatment of essential tremor: A pilot study on the correlation between lesion size, lesion location, thermal dose, and clinical outcome: Transcranial MRgFUS. Journal of Magnetic Resonance Imaging. 2018;48(1):58-65.
Santyr BG, Goubran M, Lau JC, Kwan BYM, Salehi F, Lee DH, Mirsattari SM, Burneo JG, Steven DA, Parrent AG, de Ribaupierre S, Hammond RR, Peters TM, Khan AR. Investigation of hippocampal substructures in focal temporal lobe epilepsy with and without hippocampal sclerosis at 7T: Hippocampal Substructures at 7T. Journal of Magnetic Resonance Imaging. 2017;45(5):1359-1370
Zeineh MM, Palomero-Gallagher N, Axer M, Gräβel D, Goubran M, Wree A, Woods R, Amunts K, Zilles K. Direct Visualization and Mapping of the Spatial Course of Fiber Tracts at Microscopic Resolution in the Human Hippocampus. Cerebral Cortex.2016:bhw010.
Goubran M, Bernhardt BC, Cantor-Rivera D, Lau JC, Blinston C, Hammond RR, de Ribaupierre S, Burneo JG, Mirsattari SM, Steven DA, Parrent AG, Bernasconi A, Bernasconi N, Peters TM, Khan AR. In vivo MRI signatures of hippocampal subfield pathology in intractable epilepsy: Subfield-Specific MRI Signatures of HS. Human Brain Mapping. 2016;37(3):1103-1119.
Bernhardt BC, Bernasconi A, Liu M, Hong S-J, Caldairou B, Goubran M, Guiot MC, Hall J, Bernasconi N. The spectrum of structural and functional imaging abnormalities in temporal lobe epilepsy: Imaging Spectrum of TLE. Annals of Neurology. 2016;80(1):142-153.
Pujol S, Wells W, Pierpaoli C, Brun C, Gee J, Cheng G, Vemuri B, Commowick O, Prima S, Stamm A, Goubran M, Khan A, Peters T, Neher P, Maier-Hein KH, Shi Y, Tristan-Vega A, Veni G, Whitaker R, Styner M, Westin C-F, Gouttard S, Norton I, Chauvin L, Mamata H, Gerig G, Nabavi A, Golby A, Kikinis R. The DTI Challenge: Toward Standardized Evaluation of Diffusion Tensor Imaging Tractography for Neurosurgery: The DTI Challenge on Tractography for Neurosurgery. Journal of Neuroimaging. 2015;25(6):875-882.
Goubran M, Hammond RR, de Ribaupierre S, Burneo JG, Mirsattari S, Steven DA, Parrent AG, Peters TM, Khan AR. Magnetic resonance imaging and histology correlation in the neocortex in temporal lobe epilepsy: MRI-Histology in Epilepsy.Annals of Neurology. 2015;77(2):237-250.
Goubran M, de Ribaupierre S, Hammond RR, Currie C, Burneo JG, Parrent AG, Peters TM, Khan AR. Registration of in-vivo to ex-vivo MRI of surgically resected specimens: A pipeline for histology to in-vivo registration. Journal of Neuroscience Methods. 2015;241:53-65
Ali R,* Goubran M,* Choudhri O, Zeineh MM. Seven-Tesla MRI and neuroimaging biomarkers for Alzheimer’s disease. Neurosurgical Focus. 2015;39(5):E4
Goubran M, Rudko DA, Santyr B, Gati J, Szekeres T, Peters TM, Khan AR. In vivo normative atlas of the hippocampal subfields using multi‐echo susceptibility imaging at 7 Tesla. Human Brain Mapping. 2014;35(8):3588-3601.
Goubran M, Crukley C, de Ribaupierre S, Peters TM, Khan AR. Image registration of ex-vivo MRI to sparsely sectioned histology of hippocampal and neocortical temporal lobe specimens. NeuroImage. 2013;83:770-781
LIST OF PUBLISHED JOURNAL ARTICLES