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Md Nasir Uddin, Ph.D.

Md Nasir Uddin, Ph.D.


About Me

Faculty Appointments

Assistant Professor - Department of Neurology, General Neurology (SMD)

Assistant Professor - Department of Biomedical Engineering (SMD) - Joint



PhD | University of Alberta. Biomedical Engineering. 2015


Office of AIDS Research (OAR) Innovation Award. 2023 - 2025

Magna Cum Laude. 2014

Student Scholarship. 2010

SGS Merit Award. 2008


Dr. Uddin is an Assistant Professor in the Department of Neurology and Department of Biomedical Engineering at the University of Rochester, New York. He received his B.Sc. Honours and M.Sc. in Physics and Ph.D. in Biomedical Engineering.

His research revolves around the development and appli...
Dr. Uddin is an Assistant Professor in the Department of Neurology and Department of Biomedical Engineering at the University of Rochester, New York. He received his B.Sc. Honours and M.Sc. in Physics and Ph.D. in Biomedical Engineering.

His research revolves around the development and application of advanced MRI techniques to gain profound insights into the structure and function of the human brain, encompassing both healthy and diseased states. Notably, his expertise extends to the investigation of various neurological conditions, including Multiple Sclerosis, HIV, Cerebral Small Vessel Disease, Stroke, Parkinson's Disease, and Hypertension.

His research interests span across several key areas, including:

1. Development of novel MRI methods and image processing pipelines to study neuroinflammation and neuronal injury.

2. Investigation of neuroinflammation and neurodegeneration through diffusion MRI methods, such as free water imaging (FWI), neurite orientation dispersion and density imaging (NODDI), b-tensor encoding; T2-based myelin water imaging (MWI), and multifrequency MR Elastography.

3.. Exploration of iron-sensitive measures using quantitative susceptibility mapping (QSM) and relaxometry mappings (T2, T2*, T2’) to identify potential biomarkers.

4. Examination of vascular dysfunction using perfusion MRI and resting-state fMRI-based cerebrovascular reactivity. In addition, he is delving into vascular remodeling using time-of-flight MR Angiography, with the exciting aim of developing an automated AI-based approach for the segmentation and classification of brain arteries, as well as extracting essential vascular features with minimum training datasets.

5. Analysis of the intricate relationship between structural and functional MRI measures, blood markers, and cognitive performance, encompassing both healthy, aging, and clinical populations.

Key Words: MRI, Brain, Neuroimaging, Iron, Myelin, Neuroinflammation, diffusion MRI, Free Water, Multiple Sclerosis, HIV, CSVD, Machine Learning, Deep Learning, Artificial Intelligence.


Journal Articles

Altered voxel-based and surface-based morphometry in inflammatory bowel disease.

Kornelsen J, McIver T, Uddin MN, Figley CR, Marrie RA, Patel R, Fisk JD, Carter S, Graff L, Mazerolle EL, Bernstein CN,

Brain research bulletin.. 2023 October 4203 :110771. Epub 10/04/2023.

Vascular Disease Is Associated With Differences in Brain Structure and Lower Cognitive Functioning in Inflammatory Bowel Disease: A Cross-Sectional Study.

Patel R, Marrie RA, Bernstein CN, Bolton JM, Graff LA, Marriott JJ, Figley CR, Kornelsen J, Mazerolle EL, Helmick C, Uddin MN, Fisk JD

Inflammatory bowel diseases.. 2023 September 22 Epub 09/22/2023.

Validation of deep learning techniques for quality augmentation in diffusion MRI for clinical studies.

Aja-Fernández S, Martín-Martín C, Planchuelo-Gómez Á, Faiyaz A, Uddin MN, Schifitto G, Tiwari A, Shigwan SJ, Kumar Singh R, Zheng T, Cao Z, Wu D, Blumberg SB, Sen S, Goodwin-Allcock T, Slator PJ, Yigit Avci M, Li Z, Bilgic B, Tian Q, Wang X, Tang Z, Cabezas M, Rauland A, Merhof D, Manzano Maria R, Campos VP, Santini T, da Costa Vieira MA, HashemizadehKolowri S, DiBella E, Peng C, Shen Z, Chen Z, Ullah I, Mani M, Abdolmotalleby H, Eckstrom S, Baete SH, Filipiak P, Dong T, Fan Q, de Luis-García R, Tristán-Vega A, Pieciak T

NeuroImage. Clinical.. 2023 July 2839 :103483. Epub 07/28/2023.

Vascular comorbidity is associated with decreased cognitive functioning in inflammatory bowel disease.

Patel R, Marrie RA, Bernstein CN, Bolton JM, Graff LA, Marriott JJ, Figley CR, Kornelsen J, Mazerolle EL, Uddin MN, Fisk JD,

Scientific reports.. 2023 March 1513 (1):4317. Epub 03/15/2023.

Brain iron imaging markers in the presence of white matter hyperintensities.

Murray KD, Tivarus ME, Schifitto G, Uddin MN, Zhong J

Magnetic resonance imaging.. 2023 January 19 Epub 01/19/2023.

Role of non-classical monocytes in HIV-associated vascular cognitive impairment

Singh, MV; Uddin, MN; Covacevich, VM; Sutton, KR; Boodoo, ZD; Peterson, A; Tyrell, A; Brenner, R; Tivarus, ME; Wang, HZ; Sahin, B; Zhong, J; Weber, M; Wang, L; Qiu, X; Maggiwar, SB; Schifitto G.

medRxiv. 2023; : 2023-03.

Artificial intelligence for diffusion MRI-based tissue microstructure estimation in the human brain: an overview

Faiyaz, A; Doyley, M; Schifitto, G; Uddin, MN.

Frontiers in Neurology. 2023; 14(700): 1-9.

Periventricular and juxtacortical characterization of UManitoba-JHU functionally defined human white matter atlas networks

Figley, CR; Figley, TD; Wong, K; Uddin, MN; da Silva, RDC; and Kornelsen, J.

Front. Hum. Neurosci. 2023; 17: 1-8.

Initiation of combined antiretroviral therapy confers suboptimal beneficial effects on neurovascular function in people with HIV

Singh M, Uddin MN, Singh VB, Peterson AN, Murray KD, Zhuang Y, Tyrell A, Wang L, Tivarus ME, Zhong J, Qiu X, Schifitto G.

Frontiers in Neurology. 2023; 14: 1240300.

Differences in resting state functional connectivity relative to multiple sclerosis and impaired information processing speed

Carter SL, Patel R, Fisk JD, Figley CR, Marrie RA, Mazerolle EL, Uddin MN, Wong K, Graff LA, Bolton JM and Marriott JJ.

Frontiers in Neurology. 2023; 14: 1250894.

Neuroimaging of Neuroinflammation in Neurological Disorders

Uddin, MN; Tivarus, ME; Schifitto, G; & Rudko, DA.

Frontiers in Neurology. 2023; 14(1328511).

Longitudinal Effects of Combination Antiretroviral Therapy on Cognition and Neuroimaging Biomarkers in Treatment-Naïve People with HIV.

Weber MT, Finkelstein A, Uddin MN, Reddy EA, Arduino RC, Wang L, Tivarus ME, Zhong J, Qui X, Schifitto G

Neurology.. 2022 June 22 Epub 06/22/2022.

The Comorbidity and Cognition in Multiple Sclerosis (CCOMS) neuroimaging protocol: study rationale, MRI acquisition, and minimal image processing pipelines

Uddin, MN; Figley, TD; Kornelsen, J; Mazerolle, EL; Helmick, CA; O'Grady, CB; Pirzada, S; Patel, R; Carter, S; Wong, K; Essig, MR; Graff, LA; Bolton, JM; Marriott, JJ; Bernstein, CN; Fisk, JD; Marrie, RA; Figley CR.

Frontiers in Neuroimaging. 2022; 1(970385): 30.

Vascular comorbidity is associated with decreased cognitive functioning in inflammatory bowel disease

Patel, R; Marrie, RA; Bernstein, CN; Bolton, JM; Graff, LA; Marriott, JJ; Figley, CR; Kornelsen, J; Mazerolle, EL; Uddin, MN; Fisk, JD.

2022; .

Effects of Vascular Comorbidity on Cognition in Multiple Sclerosis Are Partially Mediated by Changes in Brain Structure.

Marrie RA, Patel R, Figley CR, Kornelsen J, Bolton JM, Graff LA, Mazerolle EL, Helmick C, Uddin MN, Figley TD, Marriott JJ, Bernstein CN, Fisk JD

Frontiers in neurology. 2022 13 :910014. Epub 05/24/2022.

Single-shell NODDI using dictionary-learner-estimated isotropic volume fraction.

Faiyaz A, Doyley M, Schifitto G, Zhong J, Uddin MN

NMR in biomedicine.. 2021 October 12 :e4628. Epub 10/12/2021.

Increased risk for cerebral small vessel disease is associated with quantitative susceptibility mapping in HIV infected and uninfected individuals.

Murray KD, Uddin MN, Tivarus ME, Sahin B, Wang HZ, Singh MV, Qiu X, Wang L, Spincemaille P, Wang Y, Maggirwar SB, Zhong J, Schifitto G

NeuroImage. Clinical.. 2021 August 2832 :102786. Epub 08/28/2021.

Higher Framingham Risk Scores are associated with greater loss of brain volume over time in multiple sclerosis.

Marrie RA, Patel R, Figley CR, Kornelsen J, Bolton JM, Graff LA, Mazerolle EL, Helmick C, O'Grady C, Uddin MN, Marriott JJ, Bernstein CN, Fisk JD,

Multiple sclerosis and related disorders.. 2021 June 1754 :103088. Epub 06/17/2021.

A longitudinal analysis of brain extracellular free water in HIV infected individuals.

Uddin MN, Faiyaz A, Wang L, Zhuang Y, Murray KD, Descoteaux M, Tivarus ME, Weber MT, Zhong J, Qiu X, Schifitto G

Scientific reports.. 2021 April 1511 (1):8273. Epub 04/15/2021.

Magnetic Resonance Imaging in Childhood Primary Hypertension: Potential in the Study of Cognitive Outcomes.

Uddin MN, Tivarus M, Adams H, Little E, Schifitto G, Lande MB

Hypertension.. 2021 March 377 (3):751-758. Epub 02/10/2021.

Mixed Bangla-English Spoken Digit Classification Using Convolutional Neural Network

Das, S; Yasmin, MR; Arefin, M; Taher, KA; Uddin, MN; Rahman, MA.

Applied Intelligence and Informatics pp 371–383. 2021; 1435: 371–383.

Brain Iron Imaging Markers in the Presence of White Matter Hyperintensities

Murray, KD; Tivarus, MT; Schifitto, G; Uddin, MN; Zhong J.

bioRxiv. 2021; .

Fixel-Based Analysis and Free Water Corrected DTI Evaluation of HIV-Associated Neurocognitive Disorders.

Finkelstein A, Faiyaz A, Weber MT, Qiu X, Uddin MN, Zhong J, Schifitto G

Frontiers in neurology. 2021 12 :725059. Epub 11/04/2021.

Potential Pitfalls of Using Fractional Anisotropy, Axial Diffusivity, and Radial Diffusivity as Biomarkers of Cerebral White Matter Microstructure.

Figley CR, Uddin MN, Wong K, Kornelsen J, Puig J, Figley TD

Frontiers in neuroscience.. 2021 15 :799576. Epub 01/14/2022.

The Aging Imageomics Study: rationale, design and baseline characteristics of the study population.

Puig J, Biarnes C, Pedraza S, Vilanova JC, Pamplona R, Fernández-Real JM, Brugada R, Ramos R, Coll-de-Tuero G, Calvo-Perxas L, Serena J, Ramió-Torrentà L, Gich J, Gallart L, Portero-Otin M, Alberich-Bayarri A, Jimenez-Pastor A, Camacho-Ramos E, Mayneris-Perxachs J, Pineda V, Font R, Prats-Puig A, Gacto ML, Deco G, Escrichs A, Clotet B, Paredes R, Negredo E, Triaire B, Rodríguez M, Heredia-Escámez A, Coronado R, de Graaf W, Prevost V, Mitulescu A, Daunis-I-Estadella P, Thió-Henestrosa S, Miralles F, Ribas-Ripoll V, Puig-Domingo M, Essig M, Figley CR, Figley TD, Albensi B, Ashraf A, Reiber JHC, Schifitto G, Md Nasir U, Leiva-Salinas C, Wintermark M, Nael K, Vilalta-Franch J, Barretina J, Garre-Olmo J

Mechanisms of ageing and development.. 2020 May 11189 :111257. Epub 05/11/2020.

Spatial normalization of multiple sclerosis brain MRI data depends on analysis method and software package.

Pirzada S, Uddin MN, Figley TD, Kornelsen J, Puig J, Marrie RA, Mazerolle EL, Fisk JD, Helmick CA, O'Grady CB, Patel R, Figley CR,

Magnetic resonance imaging.. 2020 January 3068 :83-94. Epub 01/30/2020.

Linking Neuroinflammation and Extracellular Free Water in HIV Infection: A Longitudinal Study (PDF)

Uddin, MN; Faiyaz, A; Wang, L; Zhuang, Y; Murray, KD; Descoteaux, M; Tivarus, ME; Weber, MT; Zhong, J; Qiu, X; Schifitto, G.

2020; .

Pathomechanisms of HIV-Associated Cerebral Small Vessel Disease: A Comprehensive Clinical and Neuroimaging Protocol and Analysis Pipeline.

Murray KD, Singh MV, Zhuang Y, Uddin MN, Qiu X, Weber MT, Tivarus ME, Wang HZ, Sahin B, Zhong J, Maggirwar SB, Schifitto G

Frontiers in neurology. 2020 11 :595463. Epub 12/15/2020.

Comparisons between multi-component myelin water fraction, T1w/T2w ratio, and diffusion tensor imaging measures in healthy human brain structures.

Uddin MN, Figley TD, Solar KG, Shatil AS, Figley CR

Scientific reports.. 2019 February 219 (1):2500. Epub 02/21/2019.

Effect of echo time and T-weighting on GRASE-based Tw/Tw ratio measurements at 3T.

Uddin MN, Figley TD, Figley CR

Magnetic resonance imaging.. 2018 September 51 :35-43. Epub 04/20/2018.

Recovery of accurate T from historical 1.5 tesla proton density and T-weighted images: Application to 7-year T changes in multiple sclerosis brain.

Uddin MN, McPhee KC, Blevins G, Wilman AH

Magnetic resonance imaging.. 2017 April 37 :21-26. Epub 11/14/2016.

Spin echo transverse relaxation and atrophy in multiple sclerosis deep gray matter: A two-year longitudinal study.

Uddin MN, Lebel RM, Seres P, Blevins G, Wilman AH

Multiple sclerosis : clinical and laboratory research.. 2016 August 22 (9):1133-43. Epub 10/26/2015.

Value of transverse relaxometry difference methods for iron in human brain.

Uddin MN, Lebel RM, Wilman AH

Magnetic resonance imaging.. 2016 January 34 (1):51-9. Epub 10/03/2015.

Transverse relaxometry with reduced echo train lengths via stimulated echo compensation.

Uddin MN, Marc Lebel R, Wilman AH

Magnetic resonance in medicine.. 2013 November 70 (5):1340-6. Epub 01/16/2013.