Kunio Nakamura Laboratory

Research

Research

Our objective is to develop new methods of analyzing medical images to gain a better understanding of diseases such as multiple sclerosis (MS). Traditional image processing and machine learning algorithms are used to quantify lesion burden and classify and predict prognosis.

Standard MRIs are difficult to interpret because several different types of tissue damage all appear the same, and some types cannot be seen at all. One example is brain atrophy, which happens too slowly to be seen by the eye, and requires specialized image analysis software to measure. In addition, although MS affects both white matter and gray matter, only white matter lesions can be seen on standard MRIs.

Therefore, we are developing techniques to quantify the different MS pathologic processes, to accurately measure small changes over time, and to assess damage in gray matter and white matter. These new tools can help us understand MS better, help doctors make treatment decisions, and help pharmaceutical companies determine if new drugs are effective.

Selected Publications

View publications for Kunio Nakamura, PhD
(Disclaimer: This search is powered by PubMed, a service of the U.S. National Library of Medicine. PubMed is a third-party website with no affiliation with Cleveland Clinic.)

Toljan K, Amin M, Daboul l, Nakamura K, Solomon AJ, Sicotte NL, Shinohara RT, Reich DS, Sati P, Ontaneda D, Comparison of central FLAIR hypointensity and central vein sign on FLAIR* in a diagnostic cohort. Eur J Radiol. 2026 Mar:196:112707. doi: 10.1016/j.ejrad.2026.112707.

Wang X, Yang M, Tosun S, Nakamura K, Li S, Li X, CalDiff: Capture uncertainty in lesion segmentation via step-wise and sequence-aware calibrated diffusion model. IEEE J Biomed Health Inform. Author manuscript; available in PMC: 2025 Dec 8.

Amin M, Nakamura K, Ontaneda D. Artificial Intelligence and Multiple Sclerosis: Past, Present, and Future. 2025 Nov 10. doi: 10.1055/a-2730-8997. Online ahead of print.

Hu F, Ren Z, Chen L, Valcarcel AM, Dworkin J, Renner B, Daboul L, O’Donnell CM, Verter ED, Manning AR, Clark KA, Bae CE, Chen C, Lou C, Satterthwaite TD, Shou H, Li M, Bilello M, Nakamura K, Bar-Or A, Calabresi PA, Freeman L, Henry RG, Longbrake EE, Oh J, Pelletier D, Schindler MK, Absinta M, Solomon AJ, Sicotte NL, Ontaneda D, Reich DS, Sati P, Shinohara RT, and North American Imaging in MS Cooperative. Automated Segmentation of Multiple Sclerosis Lesions, Paramagnetic Rims, and Central Vein Sign on MRI. Imaging Neuroscience. 2025 Sep 25.

Lambe J, Thompson NR, Li Y, Nakamura K, Ontaneda D, Association of Spinal Cord Radiomic Features and Disability in Multiple Sclerosis. Journal of Neuroimaging 35, no. 5 (2025): e70089.

Amin M, Scullin K, Nakamura K, Ontaneda D, Galioto R, Cognitive Profiles Associated with Faster Thalamic Atrophy in Multiple Sclerosis. Multiple Sclerosis and Related Disorders 2025 Jul 31:103:106662. doi: 10.1016/j.msard.2025.106662.

Kunchok A, Ontaneda D, Milinovich A, Abbatemarco J, Bermel R, Jones SE, Cohen JA, Nakamura K, MOGAD is associated with lower white matter lesion volume and preservation of the thalamic and caudate volumes than MS on quantitative MRI. Annals of Neurology. 2025. https://doi.org/10.1002/ana.27309

Mahajan KR, Herman D, Zheng Y, Androjna C, Thoomukuntla B, Ontaneda D, Nakamura K, Trapp BD, Neurodegeneration and Demyelination in the Multiple Sclerosis Spinal Cord: Clinical, Pathological, and 7T MRI Perspectives. Neurology. 2025 Apr 8;104(7):e210259. PMID: 40080735 PMCID: PMC11907641

Galvani E, Cohen JA, Martin JT, Nakamura K, Kunchok A, Galioto R, Cognitive outcomes in myelin oligodendrocyte glycoprotein-IgG associated disease compared to multiple sclerosis. Brain Behav. 2025 Feb 28;15(3):e70310. doi: 10.1002/brb3.70310. PMC11870788.

Gaj S, Thoomukuntla, B, Ontaneda D, Nakamura K, Subject-based Transfer Learning in Longitudinal Multiple Sclerosis Lesion Segmentation. J Neuroimaging. 2025 Jan-Feb;35(1):e7002. PMID: 39923192 PMCID: PMC11807364 DOI: 10.1111/jon.70024

Amin M, Nakamura K, Daboul L, O’Donnel C, Cao G, Rodrigues P, Derbyshire J, Azevedo C, Bar-Or A, Cavezasi E, Calabresi PA, Cree B, Freeman L, Henry R, Longbrake E, Oh J, Papinutto N, Pelletier D, Prckovska V, Raza P, Ramos M, Smudralwar R, Schindler M, Sotichos E, Sicotte N, Solomon A, Shinohara R, Reich D, Sati P, Ontaneda D, Incorporation of the Central Vein Sign into the McDonald Criteria. Multiple Sclerosis and Related Disorders. 2024 Nov 25:106182. PMID: 39622133 PMCID: PMC11779579

Chien C, Cruz e Silva V, Geiter E, Meier D, Zimmermann H, Bichuetti DB, Idagawa MI, Altintas A, Tanriverdi U, Siritho S, Pandit L, Dcunha A, Sá MJ, Figueiredo R, Tongco C, Qian P,  Lotan I, Khasminsky V, Hellmann M, Stiebel-Kalish H, Rotstein D, Waxman L, Ontaneda D, Nakamura K,  Abboud H, Subei M, Mao-Draayer Y, Havla J, Asgari N, Skejø P, Kister I, Ringelstein M, Broadley S, Arnett S, Marron B, Jolley A, Wunderlich M, Green S, Cook L, Yeaman MR, Smith TJ, Brandt A, Wuerfel J, Paul F, with the GJCF International Clinical Consortium for NMOSD, Aquaporin-4 Immunoglobulin G-seropositive Neuromyelitis Optica Spectrum Disorder MRI Characteristics: Data Analysis from the International Real-World PAMRINO Study Cohort. Radiology 313 (2), e233099 PMCID: PMC7425339

Singh V, Zheng Y, Ontaneda D, Mahajan KR, Fox RJ, Nakamura K, Trapp BD, Disability independent of cerebral white matter demyelination in progressive multiple sclerosis. Acta Neuropathol 148, 34 (2024). https://doi.org/10.1007/s00401-024-02796-w

Huerta MM, Conway DS, Planchon SM, Thoomukuntla B, Oh S, Sakaie KE, Ontaneda D*, Nakamura K*, Myelin Content Measures of Slowly Expanding Lesions using 7T MRI. Journal of Neuroimaging.  * Contributed equally.

Hancock L, Galioto R, Rhoads T, Ontaneda D, Nakamura K, Ly B, Krishnan K, Miller JB, Hua LH, Comparing Cognitive Profiles in Older Adults with Multiple Sclerosis and Alzheimer Disease: More Similarities than Differences. Neurology: Clinical Practice. 2024 Aug;14(4):e200327.

Koenig K, Sakaie KE, Ontaneda D, Mahajan KR, Oh S-H, Nakamura K, Rao S, Lowe MJ, High resolution diffusion tensor imaging of the fornix predicts memory function in MS. Multiple Sclerosis Journal – Experimental, Translational and Clinical 10, no. 2 (2024): 20552173241240937. https://doi.org/10.1177/20552173241240937

Nakamura K, Sun Z, Hara-Cleaver C, Bodhinathan K, Avila RL, Natalizumab reduces loss of gray matter and thalamic volume in patients with relapsing-remitting multiple sclerosis: analysis from AFFIRM. Multiple Sclerosis Journal. 2024 Mar 12:13524585241235055. PMCID: PMC11190892

Nakamura K, Thoomukuntla B, Bena J, Cohen JA, Fox RJ, Ontaneda D, Ibudilast reduces slowly-enlarging lesions in progressive multiple sclerosis. Multiple Sclerosis Journal. 2024;30(3):369-380. doi:10.1177/13524585231224702. PMCID: PMC11190892

Amin M, Nakamura K, Ontaneda D, Differentiating intracranial white matter disease in multiple sclerosis from non-specific changes using a convolutional neural network image classification model. Multiple Sclerosis and Related Disorders, 2024. Volume 82, 105420.  PMCID: PMC10356911

Nakamura K, Elliott C, Lee HY, Narayanan S, Arnold DL, Brain volume increase after treatment interruption of natalizumab: evidence for reversible pseudoatrophy effect. Multiple Sclerosis and Related Disorders. 2024, Volume 81, January 2024, 105123.

Ontaneda D, Deshmane A, Sha A, Guruprakash DK, Jian Y, Ma D, Fisher E, Rudick RA, Cohen JA, Sakaie K, Lowe MJ, Gulani V, Griswold MA, Nakamura K, Magnetic Resonance Fingerprinting in Multiple Sclerosis. Multiple Sclerosis and Related Disorders. 2023 Nov:79:105024. doi: 10.1016/j.msard.2023.105024. Epub 2023 Sep 27. PMID: 37783196

Nakamura K, Zheng Y, Mahajan KR, Cohen JA, Fox RJ, Ontaneda D, Effect of ibudilast on thalamic magnetization transfer ratio and volume. Multiple Sclerosis Journal. 2023 Sep;29(10):1257-65.

Aboseif A, Amin M, Bena J, Nakamura K, Macaron G, Ontaneda D, Effect of Disease Modifying Therapy on Information Processing Speed in Multiple Sclerosis. International Journal of MS Care.

Wilcox O, Ontaneda D, Nakamura K, Lace J, Galioto R, Associations between Cognitive Impairment and Neuroimaging in Patients with Multiple Sclerosis. Archives of Clinical Neuropsychology. 2023 Sep 12:acad070.

Alshehri A, Cohen JA, Ontaneda D, Nakamura K, Husak S, Love T, Fox RJ, Briggs F, Conway D, The Impact of Cigarette Smoking on Cognitive Processing Speed and Brain Atrophy in Multiple Sclerosis. Multiple Sclerosis Journal. 2023;29(7):846-855. doi:10.1177/13524585231172490 

Chen PH, Nakamura K, Obuchowski N, Juan MCY, Zhang S, Flamm SD, Desai MY, Hovest T, Meese T, Schoenhagen P, Identification of acute aortic syndromes based on cross-sectional variability of Hounsfield units. International Journal of Cardiology. 2023 Jul 1;382:91-5.

Shimoyama T, Gaj S, Nakamura K, Kovi S, Man S, Uchino K, Vascular calcification, atherosclerosis burden, and stroke mechanism in patients with ischemic stroke. Journal of Neurological Sciences, 120667.

Grezmak T, Lace JW, Nakamura K, Ontaneda D, Galioto R, “It’s on the Tip of My Tongue!” Exploring Confrontation Naming Difficulties in Patients with Multiple Sclerosis. Multiple Sclerosis and Related Disorders. 2023 Mar 1;71:104579. 

Dan EB, Desai AD, Deniz C, Rajamohan HR, Regatte R, Iriondo C, Pedoia V, Majumdar S, Perslev M, Igel C, Pai A, Gaj S, Yan M, Nakamura K, Li X, Maqbool H, Irmakci I, Son SE, Hargreaves B, Gold G, Chaudhari A, Towards Automatic Cartilage Quantification in Clinical Trials – Continuing from the 2019 IWOAI Knee Segmentation Challenge, 2023, Osteoarthritis Imaging. 3(1): 100087. 

Gaj S, Eck BL, Xie D, Lartey R, Lo C, Zaylor W, Yang M, Nakamura K, Winalski CS, Spindler KP, Li X, Deep Learning Based Automatic Pipeline for Quantitative Assessment of Thigh Muscle Morphology and Fatty Infiltration. Magnetic Resonance in Medicine. 2023; 89: 2441- 2455. doi: 10.1002/mrm.29599 

Lartey R, Nanavati A, Kim J, Li M, Xu K, Nakamura K, Shin W, Winalski CS, Obuchowski N, Bahroos E, Link TM, Hardy PA, Peng Q, Kim J, Liu K, Fung M, Wu C, Li X. Reproducibility of T1ρ and T2 Quantification in a Multi-vendor Multi-site Study. Osteoarthritis Cartilage. 2023 Feb;31(2):249-257. doi: 10.1016/j.joca.2022.10.017. Epub 2022 Nov 10.

Nakamura K, McGinley MP, Jones SE, Lowe MJ, Cohen JA, Ruggieri PM, Ontaneda D, Gadolinium-based contrast agent exposures and physical and cognitive disability in multiple sclerosis. Journal of Neuroimaging. 2023 Jan;33(1):85-93. http://doi.org/10.1111/jon.13057

Babier A, Mahmood R, Zhang B, Alves V, Barragán-Montero AM, Beaudry J, Cardenas C, Chang Y, Chen Z, Chun J, Diaz K, Eraso HD, Faustmann E, Gaj S, Gay S, Gronberg M, Guo B, He J; Heilemann G, Hira S, Huang Y, Ji F, Jiang D; Giraldo JCJ, Lee H, Lian J; Liu S; Liu KC; Marrugo J; Miki K; Nakamura K; Netherton; Nguyen TN; Nourzadeh H; Osman A; Peng Z; Muñoz JDQ; Ramsl C; Rhee DJ; Rodriguez JD; Shan H; Siebers J; Soomro M; Sun K; Hoyos AU; Valderrama C; Verbeek R; Wang E; Willems S; Wu Q; Xu X; Yang S; Yuan L; Zhu S; Zimmermann L; Moore K; Purdie T; McNiven A; Chan T, OpenKBP-Opt: An international and reproducible development of 76 knowledge-based planning pipelines for radiotherapy. Phys Med Biol. 2022 Sep 12;67(18). doi: 10.1088/1361-6560/ac8044.

Daboul L, O’Donnell CM, Cao Q, Amin M, Rodrigues P, Derbyshire J, Azevedo C, Bar-Or A, Caverzasi E, Calabresi P, Cree BAC, Freeman L, Henry RG, Longbrake EE, Nakamura K, Oh J, Papinutto N, Pelletier D, Samudralwar RD, Suthiphosuwan S, Schindler MK, Sotirchos ES, Sicotte NL, Solomon AJ, Shinohara RT, Reich DS, Ontaneda D, Sati P, Effect of GBCA Use on Detection and Diagnostic Performance of the Central Vein Sign: Evaluation Using a 3-T FLAIR* Sequence in Patients With Suspected Multiple Sclerosis. American Journal of Roentgenology. 2022. DOI: 10.2214/AJR.22.27731.

Mey GM, Evonuk KS, Chappell MK, Wolfe LM, Singh R, Batoki J, Yu M, Peachey N, Anand-Apte B, Bermel R, Ontaneda D, Nakamura K, Mahajan KR, Desilva TM, Visual imaging as a predictor of neurodegeneration in experimental autoimmune demyelination and multiple sclerosis. Acta neuropathologica communications. 2022 Jun 15;10(1):87. doi: 10.1186/s40478-022-01391-y.

Nakamura K, Mokliatchouk O, Arnold DL, Yousry TA, Kappos L, Richert N, Ayling-Rouse K, Miller C, Fisher E, Effects of Dimethyl Fumarate on Brain Atrophy in Relapsing-Remitting Multiple Sclerosis: Pooled Analysis Phase 3 DEFINE and CONFIRM Studies. Frontiers in Neurology. 13, 809273.

Anand A, Hu B, Cha J, Fullerton J, Hesam-Shariati S, Nakamura K, Nurnberger J, Genetic and Environment Effects on Structural Neuroimaging Endophenotype for Bipolar Disorder: A Novel Molecular Approach. Translational Psychiatry. (2022) 12:137 ; https://doi.org/10.1038/s41398-022-01892-3.

Gaj S, Ontaneda D, Nakamura K, Automated Segmentation and Detection of Gadolinium-Enhancing Lesions in Multiple Sclerosis Using Deep Learning From Clinical MRI. PLOS ONE. 2021. 2021 Sep 1;16(9):e0255939.

Lee H, Nakamura K, Narayanan S, Brown RA, Nash RA, Griffith LM, Steinmiller KC, Devine SM, Hutton GJ, Popat U, Racke M, Georges GE, Bowen JD, Arnold DL, Brain volume change after autologous hematopoietic cell transplantation for multiple sclerosis. Multiple Sclerosis and Related Disorders. 2021

Koenig KA, Beall EB, Sakaie KE, Ontaneda D, Stone LA, Rao S, Nakamura K, Jones SE, Lowe MJ, Evaluation of a connectivity-based imaging metric that reflects functional decline in Multiple Sclerosis. PLOS ONE. 2021 Jun 8;16(6):e0251338. doi: 10.1371/journal.pone.0251338. eCollection 2021.

Zheng Y, Dudman J, Chen JT, Fox RJ, Ontaneda D, Trapp BD, Nakamura K, Cortical demyelination detection using MRI in post-mortem brains. Multiple Sclerosis Journal. 2021 May 20:13524585211014760

Coles AJ, Arnold DL, Bass AD, Boster AL, Compston DAS, Fernandez O, Havrdova EK, Nakamura K, Traboulsee A, Ziemssen Tajlf, Jacobs A, Margolin DH, Huang X, Daizadeh N, Chirleac MC, Selmaj KW; on behalf of the CARE-MS I, CARE-MS II, and CAMMS03409 Investigators. Efficacy and Safety of Alemtuzumab Over 6 Years: Results of the CARE-MS Extension Trial. Therapeutic Advances in Neurological Disorders. 2021 Apr;14:1756286420982134.

Sakaie K, Fedler JK, Yankey J, Nakamura K, Debbins J, Lowe MJ, Raska P, Fox RJ, Influence of equipment changes on MRI measures of brain atrophy and brain microstructure in a placebo-controlled trial of ibudilast in progressive multiple sclerosis. Multiple Sclerosis Journal: Experimental, Translation, and Clinical. 2021 May;7(2):20552173211010843.

Mahajan KR, Amin M, Poturalski M, Lee J, Herman D, Zheng Y, Androjna C, Howell M, Fox RJ, Trapp BD, Jones SE, Nakamura K, Ontaneda D. Juxtacortical susceptibility changes in progressive multifocal leukoencephalopathy at the gray-white matter junction correlates with iron-enriched macrophages. Mult Scler. 2021 Mar 22;:1352458521999651. doi: 10.1177/1352458521999651. [Epub ahead of print] PubMed PMID: 33749379.

Desai AD, Caliva F, Iriondo C, Mortazi A, Jambawalikar S, Bagci U, Perslev M, Igel C, Dam EB, Gaj S, Yang M, Li X, Deniz CM, Juras V, Regatte R, Gold GE, Hargreaves BA, Pedoia V, Chaudhari AS, on behalf of the IWOAI Segmentation Challenge Writing Group. The international workshop on osteoarthritis imaging knee MRI segmentation challenge: a multi-institute evaluation and analysis framework on a standardized dataset. Radiology: Artificial Intelligence. 2021 Feb 10;3(3):e200078. (Group Member)

Obuchowski NA, Remer EM, Sakaie K, Schneider E, Fox RJ, Nakamura K, Avila R, Guimaraes A. Importance of incorporating quantitative imaging biomarker technical performance characteristics when estimating treatment effects. Clin Trials. 2021 Apr;18(2):197-206. doi: 10.1177/1740774520981934. Epub 2021 Jan 10. PubMed PMID: 33426918.

Abbatemarco JR, Ontaneda D, Nakamura K, Husak S, Wang Z, Alshehri S, Bermel RA, Conway DS, Comorbidity Effect on Processing Speed Test and MRI Measures in Multiple Sclerosis Patients. Multiple Sclerosis and Related Disorder. 2020 Nov 1;46:102593.

Conway DS, Planchon-Pope S, Oh S-H, Nakamura K, Thompson N, Sakaie KE, Ontaneda D, The Relationship Between Thalamic Volume and Cognitive Function in Fingolimod-Treated Multiple Sclerosis Patients. Multiple Sclerosis and Related Disorders. 2021 Jan 1;47:102635.

Naismith RT, Bermel RA, Coffey CS, Goodman AD, Fedler J, Kearney M, Klawiter EC, Nakamura K, Narayanan S, Goebel C, Yankey J, Klingner E, Fox RJ, on behalf of SPRINT-MS investigators. Effects of Ibudilast on MRI measures in the Phase 2 SPRINT-MS study. Neurology. 2021 Jan 26;96(4):e491-e500. doi: 10.1212/WNL.0000000000011314. Epub 2020 Dec 2.

Pulido-Valdeolivas I, Andorrà M, Gómez-Andrés D, Nakamura K, Alba-Arbalat S, Lampert EJ, Zubizarreta I, Llufriu S, Martinez-Heras E, Solana E, Sola-Valls N, Sepulveda M, Tercero-Uribe A, Blanco Y, Camos-Carreras A, Sanchez-Dalmau B, Villoslada P, Saiz A, Martinez-Lapiscina EH, Retinal and brain damage during the course of multiple sclerosis: inflammatory activity is a key factor in the first five years. Scientific Reports. 2020 Aug 7;10(1):13333. doi: 10.1038/s41598-020-70255-z.

Nakamura K, Rudick RA, Ontaneda D, Fox RJ, Trapp BD, Fisher E, Fourteen-year serial MRI with mild and severe brain atrophy in patients with multiple sclerosis. Neurology: Clinical Practice. 01 Feb 2020, 10(1):e5-e6 DOI: 10.1212/cpj.0000000000000695

Kim JH, Mamoto K, Lartey R, Xu K, Nakamura K, Shin W, Winalski CS, Obuchowski N, Tanaka M, Bahroos E, Link TM, Hardy PA, Peng Q, Botto-van Bemden A, Liu K, Peters RD, Wu C, Li X, Multi-vendor multi-site T1ρ and T2 quantification of knee cartilage. Osteoarthritis and Cartilage. 2020 Dec;28(12):1539-1550. doi: 10.1016/j.joca.2020.07.005. Epub 2020 Jul 30.

Ontaneda D, Tallantyre  EC, Raza PC, Planchon SM, Nakamura K, Miller D, Hersh C, Craner M, Bale C, Chaudhry B, Gunzler DD, Love TE, Gerry S, Coles A, Cohen JA, Evangelou N, Determining the Effectiveness of early Intensive Versus Escalation approaches for the treatment of Relapsing-Remitting Multiple Sclerosis: The DELIVER-MS Study Protocol. Contemporary Clinical Trials. 2020 Apr 19:106009.

Macaron G, Baldassari LE, Nakamura K, Rao SM, McGinley MP, Moss BP, Li H, Miller DM, Jones SE, Bermel RA, Cohen JA, Ontaneda D, Conway DS. Cognitive processing speed in multiple sclerosis clinical practice. European Journal of Neurology. 2020 Mar 28. doi: 10.1111/ene.14239.

Mahajan K, Nakamura K, Cohen JA, Trapp BD, Ontaneda D, Intrinsic and extrinsic mechanisms of thalamic pathology in multiple sclerosis. Annals of Neurology. https://doi.org/10.1002/ana.25743 2020 Jul;88(1):81-92.

Anand A, Nakamura K, Spielberg J, Cha JU, Karne H, Hu B, Integrative Analysis of Lithium Treatment Associated Effects on Brain Structure and Peripheral Gene Expression Reveals Novel Molecular Insights into Mechanism of Action. Translational Psychiatry. 2020 Apr 6;10(1):103. doi: 10.1038/s41398-020-0784-z.

Narayanan S, Nakamura K*, Fonov VS, Maranzano J, Caramanos Z, Giacomini PS, Collins DL, Arnold DL, Brain volume loss in individuals over time: source of variance and limits of detectability. NeuroImage. Volume 214, 1 July 2020, 116737. *Co-first author.

Gaj S, Yang M, Nakamura K, Li X, Automated cartilage and meniscus segmentation of knee MRI with conditional generative adversarial networks. Magnetic Resonance in Medicine. 2020 Jul;84(1):437-449. doi: 10.1002/mrm.28111. Epub 2019 Dec 2.

Baldassari L, Planchon S, Bermel R, Nakamura K, Fisher E, Feng J, Sakaie K, Ontaneda D, Cohen JA, Serum neurofilament light chain concentration in a phase 1/2 trial of autologous mesenchymal stem cell transplantation. Multiple Sclerosis Journal: Experimental, Translation, and Clinical, 2019 Nov 5;5(4):2055217319887198. 

Baldassari LE, Nakamura K, Moss BP, Macaron G, Li H, Weber M, Jones, SE, Rao SM, Miller, D, Bermel R, Cohen JA, Ontaneda D, McGinley M, Technology-Enabled Comprehensive Characterization of Multiple Sclerosis in Clinical Practice. Multiple Sclerosis and Related Disorders, 2019 Nov 14;38:101525.

Dutta R, Mahajan KR, Nakamura K, Ontaneda D, Chen J, Volsko C, Dudman J, Christie E, Dunham J, Fox RJ, Trapp BD. Comprehensive Autopsy Program for Individuals with Multiple Sclerosis. J. Vis. Exp. (149), e59511, doi:10.3791/59511 (2019).

Feng J, Offerman E, Lin J, Fisher E, Planchon SM, Sakaie KE, Lowe MJ, Nakamura K, Cohen JA, Ontaneda D. Exploratory MRI Measures after Intravenous Autologous Culture-Expanded Mesenchymal Stem Cell Transplantation in Multiple Sclerosis. Multiple Sclerosis Journal: Experimental, Translation, and Clinical, (April 2019). doi:10.1177/2055217319856035.

Lee HW, Nakamura K, Narayanan S, Brown RA, Arnold DL. Estimating and accounting for the effect of MRI scanner changes on longitudinal whole-brain volume change measurements. NeuroImage. 2018 Sep 22;184:555-565. doi: 10.1016/j.neuroimage.2018.09.062.

Nakamura K, Eskildsen SF, Narayanan S, Arnold DL, Collins DL, The Alzheimer’s Disease Neuroimaging Initiative, Improving SIENA Performance using BEaST Brain Extraction. PLOS ONE 13(9): e0196945. https://doi.org/10.1371/journal.pone.0196945.

Fox RJ, Coffey CS,  Conwit R, Cudkowicz ME, Gleason T, Goodman A, Klawiter EC, Matsuda K, McGovern M, Naismith RT, Ashokkumar A, Barnes J, Ecklund D, Klingner E, Koepp M, Long JD, Natarajan S, Thornell B, Yankey J, Bermel RA, Debbins JP, Huang X, Jagodnik P, Lowe MJ, Nakamura K, Narayanan S, Sakaie KE, Thoomukuntla B, Zhou X, Krieger S, Alvarez E, Apperson M, Bashir K, Cohen BA, Coyle OK, Delgado S, Dewitt LD, Flores A, Geisser BS, Goldman MD, Jubelt B, Lava N, Lynch SG, Moses H, Ontaneda D, Perumal JS, Racke M, Repovic P, Riley CS, Severson C, Shinnar S, Suski V, Weinstock-Gutman B, Yadav V, Zabeti A, on behalf of the NN102/SPRINT-MS Trial Investigators. Phase 2 Trial of Ibudilast in Progressive Multiple Sclerosis. New England Journal of Medicine. 2018; 379:846-855. DOI: 10.1056/NEJMoa1803583.

Trapp BD, Vignos M, Dudman J, Chang A, Fisher E, Staugaitis S, Battapady H, Mork S, Fox RJ, Chen JT, Nakamura K, Rudick RA. Cortical neuronal densities and cerebral white matter demyelination in multiple sclerosis: a retrospective study. Lancet Neurology 2018. August 21, 2018 DOI:https://doi.org/10.1016/S1474-4422(18)30245-X.

Andorrà M, Nakamura K, Lampert EJ, Pulido-Valdeolivas, Llufriu S, Martinez-Heras E, Sola-Valls N, Sepulveda M, Blanco Y, Saiz A, Villoslada P, Martinez-Lapiscina EH, Assessing Biological and Methodological Aspects of Brain Volume Loss in Multiple Sclerosis. JAMA Neurology. 2018. doi:10.1001/jamaneurol.2018.1596.

Nakamura K, Chen JT, Ontaneda D, Fox RJ, Trapp BD, T1-/T2-weighted ratio differs in demyelinated cortex in multiple sclerosis. Annals of Neurology 2017 82: 635–639. doi:10.1002/ana.25019.

Maranzano J, Rudko DA, Nakamura K, Cook S, Cadavid D, Wolansky L, Arnold DL, Narayanan S. MRI evidence of acute inflammation in leukocortical lesions of patients with early multiple sclerosis. Neurology. 2017 Jul 19:10-212.

Lee H, Nakamura K, Narayanan S, Brown R, Chen J, Atkins HL, Freedman MS, Arnold DL. Impact of immunoablation and autologous hematopoietic stem cell transplantation on gray and white matter atrophy in multiple sclerosis. Multiple Sclerosis Journal. 2017 Jun 1:1352458517715811.

Rudko DA, Derakhshan M, Maranzano J, Nakamura K, Arnold DL, Narayanan S. Delineation of cortical pathology in multiple sclerosis using multi-surface magnetization transfer ratio imaging, 2016 NeuroImage: Clinical. 12: 858-868.

Voskuhl RR, Wang H, Wu TCJ, Sicotte N, Nakamura K, Kurth F, Calabresi P, Corboy J, Cross A, Dhib-Jalbut S, Ford C, Frohman E, Giesser B, Jacobs D, Kasper L, Lynch S, Parry G, Racke M, Reder A, Rose J, Wingerchuk D, MacKenzie-Graham AJ, Arnold DL, Tseng CH, and Elashoff R. Estriol combined with glatiramer acetate for women with relapsing-remitting multiple sclerosis: a randomised, placebo-controlled, phase 2 trial. 2016 Lancet Neurology 15(1): 35-46.

Guizard N, Nakamura K, Coupe P, Fonov, VS, DL Arnold, Collins DL, Non-local means inpainting of MS lesion inpainting in longitudinal image processing. 2015, Frontiers in Neuroscience, 9:456doi: 10.3389/fnins.2015.00456.

Guizard N, Fonov VS, García-Lorenzo D, Nakamura K, Aubert-Broche B, Collins DL, The Alzheimer's Disease Neuroimaging Initiative. Spatio-temporal regularization for longitudinal registration to an unbiased 3D individual template. 2015 PLoS One. 10(8): e0133352. doi:10.1371/journal.pone.0133352.

Fisher E, Nakamura K, Lee JC, You X, Sperling B, Rudick RA. Effect of Intramuscular Interferon Beta-1a on Gray Matter Atrophy in Relapsing Remitting Multiple Sclerosis: A Retrospective Analysis. 2015 Multiple Sclerosis Journal (DOI: 10.1177/1352458515599072)

Nakamura K, Brown RA, Narayanan S, Collins DL, Arnold DL, The Alzheimer's Disease Neuroimaging Initiative, Diurnal fluctuations in brain volume: statistical analyses of MRI from large populations. 2015 NeuroImage. doi:10.1016/j.neuroimage.2015.05.077 

Nakamura K, Brown RA, Araujo D, Narayanan S, Arnold DL, Correlation between brain volume change and T2 relaxation time induced by dehydration and rehydration: implications for monitoring atrophy in clinical studies. NeuroImage: Clinical, 2014, 166-170. (doi:10.1016/j.nicl.2014.08.014)

Ghassemi R, Brown R, Banwell B, Narayanan S, Nakamura K, Arnold DL, Normalization of Intensity on T1-weighted Images of Patients with Acquired Central Nervous System Demyelination. Journal of Neuroimaging 2015; 25 (2), 184-190. (doi: 10.1111/jon.12129)

Nakamura K, Guizard N, Fonov SV, Narayanan S, Collins DL, Arnold DL, Jacobian integration method increases the statistical power to measure gray matter atrophy in multiple sclerosis. NeuroImage: Clinical 2014; 4: 10-17. (doi:10.1016/j.nicl.2013.10.015)

Chen JT, Easley K, Schneider C, Nakamura K, Kidd GJ, Chang A, Staugaitis SM, Fox RJ, Fisher E, Arnold DL, Trapp BD, Clinically feasible MTR is sensitive to cortical demyelination in MS. Neurology 2013; Jan 15;80(3):246-52.

Nakamura K, Fox R, Fisher E, CLADA: cortical longitudinal atrophy detection algorithm. NeuroImage. 2011; 54(1): 278-289.

Rudick R, Lee J, Nakamura K, Fisher E, Gray matter atrophy correlates with MS disability progression measured with MSFC but not EDSS, Journal of Neurological Sciences. 2009; 106-111. 

Nakamura K and Fisher E, Segmentation of Brain Magnetic Resonance Images for Measurement of Gray Matter Atrophy in Multiple Sclerosis Patients, NeuroImage. 2009; 44(3): 769-776.

Fisher E, Lee J, Nakamura K, Rudick RA, Gray Matter Atrophy in Multiple Sclerosis: A Longitudinal Study, Annals of Neurology 2008; 64(3): 255-265.

Fisher E, Chang A, Fox RJ, Tkach JA, Svarovsky T, Nakamura K, Rudick RA, Trapp BD, Imaging correlates of axonal swelling in chronic multiple sclerosis brains. Annals of Neurology 2007; 62(3): 219-228.