Jean Chen

Dr. Jean Chen

Canada Research Chair in Neuroimaging of Aging

Associate Professor Medical Biophysics, University of Toronto

Senior Scientist Rotman Research Institute, Baycrest

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Research Focus

Normal brain function is predicated upon a continuous neuronal and vascular interplay, a mechanism that is likely to deteriorate during the cognitive decline associated with aging as well as neurological disorders. Despite previous research efforts, the causes of aging-related illnesses such as dementia remain unclear, and the key to preventative treatment elusive. My research is driven by the need to better understand disease mechanisms by using neuroimaging to observe the living brain. My research is focused on functional magnetic resonance imaging (fMRI) methodological development, physiological modeling, and the application of our methods in characterizing diseases/treatments. Specifically, we are interested in:

  • Functional MRI methodological development

  • Measurement of cerebral perfusion and metabolism using MRI techniques

  • Measurement of tissue microstructure using diffusion-weighted MRI

  • Investigating the relationship between functional and structural brain changes in neurodegenerative diseases


Title Source (Journal/Book/Conference) Authors/Presenters Published On Type
Intrinsic Frequencies of the Resting-state fMRI Signal: The Frequency dependence of Functional Connectivity and the Effect of Mode Mixing Front Neurosci Yuen NH, Osachoff N, Chen JJ 1566532800 Journal Article
Characterizing signal and noise origins of spin-echo BOLD fMRI at 3 Tesla Magn Reson Imaging Ragot DM, Chen JJ 1545282000 Journal Article
Functional MRI of brain physiology in aging and neurodegenerative diseases NeuroImage Chen JJ 1531713600 Journal Article
The effect of music-support rehabilitation on motor, cognitive and psychosocial functions in chronic stroke. Ann New York Acad Sci Fujioka T, Ross B, Wright R, Chen JJ, Chen JL, Black SE, Stuss DT, Dawson D 1531627200 Journal Article
Re-examining age-effects on white matter microstructure with free-water corrected diffusion tensor imaging Neurobiol Aging Chad JA, Pasternak O, Salat DH, Chen JJ 1531108800 Journal Article
Variability in stroke motor outcome is explained by structural and functional integrity of the motor system. Nat Sci Rep Lam TK, Dawson DR, Honjo K, Ross B, Binns MA, Stuss DT, Black SE, Chen JJ, Levine, BT, Fujioka, T, Chen, JL 1529035200 Journal Article
Cerebrovascular-reactivity Mapping using MRI: Considerations for Alzheimer’s Disease Front Aging Neurosci Chen JJ 1527652800 Journal Article
MRI techniques to measure arterial and venous cerebral blood volume NeuroImage Hua J, Liu P, Kim T, Donahue M, Rane S, Chen JJ, Qin Q, Kim SG 1519275600 Journal Article
Characterizing the modulation of resting-state fMRI metrics by baseline physiology NeuroImage Chu PP, Golestani AM, Kwinta JB, Khatamian YB, Chen JJ 1516942800 Journal Article
The resting-state arterial-venous blood signal differential predicts blood transit time J Cereb Blood Flow Metab Tong Y, Yao J, Chen JJ, Frederick B 1515992400 Journal Article
Neural coupling between contralesional motor and frontoparietal networks correlates with motor ability in individuals with chronic stroke J Neurol Sci Lam TK, Dawson DR, Honjo K, Ross B, Binns MA, Stuss DT, Black SE, Chen JJ, Levine BT, Fujioka T, Chen JL 1515992400 Journal Article
Simultaneous multi-slice resting-state fMRI at 3 Tesla: Slice-acceleration related biases in physiological-noise effects Brain Connect Golestani AM, Faraji-Dana Z, Kayvanrad MA, Setsompop K, Khatamian Y, Graham SJ, Chen JJ 1501646400 Journal Article
Functional Magnetic Resonance Imaging Encyclopedia of Biomedical Engineering, Major Reference Works Chen JJ, Cohen-Adad J 1498968000 Book Chapter
The effect of low-frequency physiological correction on the reproducibility and specificity of resting-state fMRI metrics: Functional connectivity, ALFF and ReHo Front Neurosci Golestani AM, Kwinta JB, Chen JJ 1498536000 Journal Article
Interactions between head motion and coil sensitivity in accelerated fMRI J Neurosci Methods Faraji-Dana Z, Tam F, Chen JJ, Graham SJ 1473134400 Journal Article
A robust method for suppressing motion induced coil sensitivity variations during prospective correction of head motion in fMRI Magn Reson Imaging Faraji-Dana Z, Tam F, Chen JJ, Graham SJ 1473134400 Journal Article
Suppressing respiration effects when geometric distortion is corrected dynamically by phase labeling for additional coordinate encoding (PLACE) during functional MRI PLoS ONE Faraji-Dana Z, Tam F, Chen JJ, Graham SJ 1463716800 Journal Article
Cerebrovascular reactivity quantification using resting-state BOLD fMRI: Validation in healthy adults NeuroImage Golestani, AM, Wei LL, Kwinta JB, Chen JJ 1462161600 Journal Article
Identifying dysfunctional cortex: Dissociable effects of stroke and aging on resting state dynamics in MEG and fMRI. Front Aging Neurosci Kielar A, Deschamps T, Chu RK, Jokel R, Khatamian YB, Chen JJ, Meltzer JA 1456981200 Journal Article
The association between cerebrovascular reactivity and resting-state fMRI functional connectivity in healthy adults: The influence of basal carbon dioxide NeuroImage Golestani AM, Kwinta JB, Strother SC, Khatamian YB, Chen JJ 1455512400 Journal Article
Spin-echo resting-state functional connectivity in high-susceptibility regions: Accuracy, reliability and the impact of physiological noise Brain Connectivity Khatamian YB, Golestani AM, Ragot DM, Chen JJ 1454821200 Journal Article
White-matter physiological fluctuations are increased in Alzheimer’s disease on resting-state magnetic resonance imaging Neurobiol Aging Makedonov I, Chen JJ, Masellis M, MacIntosh BJ 1446526800 Journal Article
Characterizing resting-state brain function using arterial-spin labeling Brain Connectivity Chen JJ, Jann K, Wang DJ 1435118400 Journal Article
Metabolic and vascular origins of the BOLD effect: Implications for imaging pathology and resting-state brain function J Magn Reson Imaging Mark CI, Mazerolle EL, Chen JJ 1424149200 Journal Article
Comparing cerebrovascular reactivity measured using BOLD and cerebral blood flow MRI: The effect of basal vascular tension on vasodilatory and vasoconstrictive reactivity NeuroImage Halani S, Kwinta JB, Golestani AM, Khatamian YB, Chen JJ 1422507600 Journal Article
Associations of resting-state fMRI functional connectivity with flow-BOLD coupling and regional vasculature Brain Connectivity Tak S, Polimeni JR, Wang DJ, Yan L, Chen JJ 1415682000 Journal Article
Mapping the end-tidal CO2 response function in the resting-state BOLD fMRI signal: Spatial specificity, test-retest reliability and effect of fMRI sampling rate NeuroImage Golestani AM, Chang C, Kwinta JB, Khatamian YB, Chen JJ 1413604800 Journal Article
Non-Gaussian water diffusion in aging white matter Neurobiol Aging Coutu JP, Chen JJ, Rosas HD, Salat DH 1401595200 Journal Article
Dynamic and static contributions of the cerebrovasculature to the resting-state BOLD signal NeuroImage Tak S, Wang DJ, Polimeni JR, Yan L, Chen JJ 1390971600 Journal Article
Stroke induced reorganization of the neural networks for sentence comprehension, and relationship to perilesional dysfunction revealed by MEG and ASL Frontiers 52nd Annual Meeting of Academy of Aphasia Kielar A, Deschamps T, Chu R K O, Panamsky L, Khatamian Y B, Chen J J, and Meltzer J A 1390366800 Abstract
The relationship between cortical blood flow and sub-cortical white-matter health across the adult age span PLoS One Chen JJ, Rosas HD, Salat DH 1361422800 Journal Article
Complex relationships between cerebral blood flow and brain atrophy in early Huntington's disease NeuroImage Chen JJ, Salat DH, Rosas HD 1325394000 Journal Article
Age-associated reductions in cerebral blood flow are independent from regional atrophy NeuroImage Chen JJ, Rosas HD, Salat DH 1293858000 Journal Article
Hippocampal degeneration is associated with temporal and limbic gray matter/white matter tissue contrast in Alzheimer's disease NeuroImage Salat DH, Chen JJ, van der Kouwe AJ, Greve DN, Fischl B, Rosas HD 1293858000 Journal Article
MRI measurement of the BOLD-specific flow-volume relationship during hypercapnia and hypocapnia in humans NeuroImage Chen JJ, Pike GB 1262322000 Journal Article
Global cerebral oxidative metabolism during hypercapnia and hypocapnia in humans: implications for BOLD fMRI Journal of cerebral blood flow and metabolism Chen JJ, Pike GB 1262322000 Journal Article
BOLD-specific cerebral blood volume and blood flow changes during neuronal activation in humans NMR in biomedicine Chen JJ, Pike GB 1230786000 Journal Article
Origins of the BOLD post-stimulus undershoot NeuroImage Chen JJ, Pike GB 1230786000 Journal Article
Human whole blood T2 relaxometry at 3 Tesla Magn Reson Med Chen JJ, Pike GB 1230786000 Journal Article
Cerebral blood flow measurement using fMRI and PET: a cross-validation study Intl J Biomed Imaging Chen JJ, Wieckowska M, Meyer E, Pike GB 1199163600 Journal Article
The impact of partial-volume effects in dynamic susceptibility contrast magnetic resonance perfusion imaging J Magn Reson Imaging Chen JJ, Smith MR, Frayne R 1104555600 Journal Article
Reassessing the clinical efficacy of two MR quantitative DSC PWI CBF algorithms following cross-calibration with PET images Phys Med Biol Chen JJ, Frayne R, Smith MR 1104555600 Journal Article
Advantages of frequency-domain modeling in dynamic-susceptibility contrast magnetic resonance cerebral blood flow quantification Magnetic Resonance in Medicine Chen JJ, Smith MR, Frayne R 1104555600 Journal Article
Partial volume effect in quantitative magnetic resonance perfusion imaging Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference Chen JJ, Smith MR, Frayne R 1072933200 Abstract


  • 2011: Postdoctorate, Biomedical Imaging, Harvard Medical School, Massachusetts General Hospital
  • 2009: PhD, Biomedical Engineering, McGill University, Montreal Neurological Institute
  • 2004: MSc, Electrical Engineering, University of Calgary

Academic Appointments

  • 2011–2018: Scientist, Rotman Research Institute
  • 2011–2018: Assistant Professor, Medical Biophysics, University of Toronto
  • 2016–Present: Canada Research Chair in Neuroimaging of Aging
  • 2018–Present: Associate Professor, Medical Biophysics, University of Toronto
  • 2018–Present: Senior Scientist, Rotman Research Institute, Baycrest



  • NeuroImage
  • Magnetic Resonance in Medicine
  • Journal of Cerebral Blood Flow and Metabolism
  • Journal of Magnetic Resonance Imaging
  • PLoS ONE
  • Journal of Gerontology
  • Journal of Pharmacology and Experimental Therapeutics
  • 2010–Present: Neurobiology of Aging

Research Projects


  • 2012–2017: Discovery Grant: "Investigating the Neuronal and Vascular Contributions to the Spontaneous BOLD fMRI Signal Fluctuations Underlying Functional Connectivity"
    Collaborators: Jean Chen (Principal Investigator)

    Sponsors: NSERC, 145,000 (CAD)

    Research Grant
  • 2009–2011: Postdoctoral Fellowship
    Supervisor: David Salat
    Collaborators: Jean Chen (Principal Investigator)

    Sponsors: CIHR, 108,050 (CAD)

  • 2013–2017: Operating Grant: "Physiological Basis of Resting-State fMRI"
    Collaborators: Jean Chen (Principal Investigator), Tomas Paus (Co-investigator), Stephen Strother (Co-investigator), Randy McIntosh (Collaborator), Joseph Fisher (Collaborator)

    Sponsors: CIHR, 398,028 (CAD)

    Research Grant
  • 2012–2014: Hakim Award: "Characterizing functional lesions in stroke using MEG and fMRI"
    Collaborators: Jed Meltzer (Principal Investigator), Jean Chen (Co-Investigator)

    Sponsors: Heart and Stroke Foundation, 100,000 (CAD)

    Research Grant
  • 2014–2016: Catalyst Grant: "Identifying new physiological biomarkers of Alzheimer's disease from functional and perfusion MRI"
    Collaborators: Bradley MacIntosh (Principal Investigator), Jean Chen (Co-Investigator), Mario Masellis (Co-Investigator), Greg Zaharchuk (Collaborator)

    Sponsors: CIHR, 100,000 (CAD)

    Research Grant
  • 2013–2014: Trainee Fund: "Novel functional imaging methods for non-invasive monitoring of stroke recovery"
    Collaborators: Jean Chen (Principal Investigator)

    Sponsors: Heart and Stroke Foundation, 35,000 (CAD)

    Research Grant
  • 2016–2023: Foundation Grant
    Collaborators: Jean Chen (Principal Investigator)

    Sponsors: CIHR, 1,008,631 (CAD)

    Research Grant
  • 2016–2021: Canada Research Chair (Tier 2)
    Collaborators: Jean Chen (Principal Investigator)

    Sponsors: CIHR, 500,000 (CAD)

    Research Grant


  • 2017:

Curriculum Vitae


The Rotman Research Institute
3560 Bathurst Street, 1056
Toronto, Ontario
Canada M6A 2E1 Phone: (416) 785-2500 x2017 Fax: (416) 785-2862