Pratik Mukherjee, MD, PhD

Pratik Mukherjee, MD, PhD

Assistant Professor, Department of Radiology, UCSF

Phone: (415) 353-2573 (appts)
Box 0628, UCSF
San Francisco, CA 94143-0628

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Cancer Center Membership

Associate Member » Neurologic Oncology

Research Summary

Pratik Mukherjee, MD, PhD, is a Professor in Residence in the Department Radiology and Biomedical Imaging, Bioengineering, and he is an attending neuroradiologist at the University of California, San Francisco. He is the Director of the Center for Imaging of Neurodegenerative Disease (CIND) based at the San Francisco VA Medical Center. He also directs the Neural Connectivity Laboratory (NCL) at UCSF China Basin.

Dr. Mukherjee received his PhD in Neuroscience from Rockefeller University, New York in 1994 and his MD from Cornell University, New York, in 1995. He completed his internship in Internal Medicine at New York Hospital - Cornell Medical Center, followed by a residency in Radiology and fellowship in Neuroradiology at Washington University Medical Center in St. Louis, Missouri, completed in 2002.

Dr. Mukherjee’s primary clinical research is the study of neurodevelopmental disorders and traumatic brain injury (TBI) using advanced MRI. His research has been focused on technical development, neuroscience and clinical applications of advanced imaging methods for mapping structure and function of the human brain, especially diffusion MRI, which is a popular technique for assessing the development and integrity of white matter and for mapping axonal fiber pathways.

Dr. Mukherjee has served as Principal Investigator or Co-Principal Investigator for several NIH grants. His work has also been funded by grants from the Dept. of Defense, the Simons Foundation, McDonnell Foundation, Dana Foundation, Wallace Research Foundation, GE Healthcare and the GE-NFL Head Health Initiative. He has published over 80 peer-reviewed papers.


Radiology, Neuroradiology, Pediatric Neuroradiology, Cognitive Neuroscience, Computational Neuroscience


Neuroradiology, traumatic brain injury (TBI), neurodevelopmental disorders

Professional Interests:

Brain development, computational neuroscience, connectomics, diffusion tensor imaging (DTI), epilepsy, functional MRI (fMRI), machine learning, magnetoencephalography (MEG), pediatric neuroradiology, traumatic brain injury (TBI), ultra-high field MRI, white matter tractography

Education and Training:

• Medical School: Cornell University, New York - Medicine

• Internship: New York Cornell Medical Center - Internal Medicine

• Residency: Washington University of Medical Center, St. Louis, Missouri - Radiology

• Fellowship: Washington University Medical Center, St. Louis, Missouri - Neuroradiology

• Doctor of Philosophy: Rockefeller University, New York - Neuroscience

• National Board of Medical Examiners Certificate

• American Board of Radiology Certificate

• Missouri Medical License

• California Medical License

• American Board of Radiology Certificate of Added Qualification Neuroradiology


Yale University, New Haven, CT, B.A., 1988, Computer Science & Psychology
Rockefeller Univ., New York, NY, Ph.D., 1994, Neuroscience
Cornell University, New York, NY, M.D., 1995, Medicine

Professional Experience

  • 1995-1996
    Internal Medicine Internship, New York Hospital - Cornell Medical Center, New York, NY
  • 1996-2000
    Radiology Residency, Washington University Medical Center, St. Louis, MO
  • 2000-2002
    Neuroradiology Fellowship, Washington University Medical Center, St. Louis, MO
  • 2002-present
    Assistant Professor, University of California, San Francisco, CA

Honors & Awards

  • 1988-95
    Medical Scientist Training Program Grant, National Institutes of Health
  • 1994
    S. Koide Memorial Fellowship, Rockefeller University
  • 1999
    Roentgen Resident/Fellow Research Award, Radiological Society of North America
  • 2001
    Berlex/ASNR Award in Basic Science Research, American Society of Neuroradiology

Selected Publications

  1. Friedman EJ, Landsberg AS, Owen J, Hsieh W, Kam L, Mukherjee P. Edge Correlations in Spatial Networks. Journal of Complex Networks. 2015.
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  2. Jenkins J, Chow V, Blaskey L, Kuschner E, Qasmieh S, Gaetz L, Edgar JC, Mukherjee P, Buckner R, Nagarajan SS, Chung WK, Spiro JE, Sherr EH, Berman JI, Roberts TP. Auditory Evoked M100 Response Latency is Delayed in Children with 16p11.2 Deletion but not 16p11.2 Duplication. Cereb Cortex. 2015 Feb 11.
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  3. McMahon PJ, Panczykowski DM, Yue JK, Puccio AM, Inoue T, Sorani MD, Lingsma HF, Maas AI, Valadka AB, Yuh EL, Mukherjee P, Manley GT, Okonkwo DO, Casey SS, Cheong M, Cooper SR, Dams-O'Connor K, Gordon WA, Hricik AJ, Lawless K, Menon D, Schnyer DM, Vassar MJ. Measurement of the Glial Fibrillary Acidic Protein and Its Breakdown Products GFAP-BDP Biomarker for the Detection of Traumatic Brain Injury Compared to Computed Tomography and Magnetic Resonance Imaging. J Neurotrauma. 2015 Apr 15; 32(8):527-33.
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  4. Owen JP, Chang YS, Mukherjee P. Edge density imaging: Mapping the anatomic embedding of the structural connectome within the white matter of the human brain. Neuroimage. 2015 Apr 1; 109:402-17.
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  5. Sorani MD, Yue JK, Sharma S, Manley GT, Ferguson AR. Genetic data sharing and privacy. Neuroinformatics. 2015 Jan; 13(1):1-6.
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  6. Lingsma HF, Yue JK, Maas AI, Steyerberg EW, Manley GT, Cooper SR, Dams-O'Connor K, Gordon WA, Menon DK, Mukherjee P, Okonkwo DO, Puccio AM, Schnyer DM, Valadka AB, Vassar MJ, Yuh EL. Outcome Prediction after Mild and Complicated Mild Traumatic Brain Injury: External Validation of Existing Models and Identification of New Predictors Using the TRACK-TBI Pilot Study. J Neurotrauma. 2015 Jan 15; 32(2):83-94.
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  7. Qureshi AY, Mueller S, Snyder AZ, Mukherjee P, Berman JI, Roberts TP, Nagarajan SS, Spiro JE, Chung WK, Sherr EH, Buckner RL. Opposing brain differences in 16p11.2 deletion and duplication carriers. J Neurosci. 2014 Aug 20; 34(34):11199-211.
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  8. Chang YS, Owen JP, Desai SS, Hill SS, Arnett AB, Harris J, Marco EJ, Mukherjee P. Autism and sensory processing disorders: shared white matter disruption in sensory pathways but divergent connectivity in social-emotional pathways. PLoS One. 2014; 9(7):e103038.
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  9. Friedman EJ, Landsberg AS, Owen JP, Li YO, Mukherjee P. Stochastic geometric network models for groups of functional and structural connectomes. Neuroimage. 2014 Nov 1; 101:473-84.
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  10. Yuh EL, Cooper SR, Mukherjee P, Yue JK, Lingsma HF, Gordon WA, Valadka AB, Okonkwo DO, Schnyer DM, Vassar MJ, Maas AI, Manley GT, Casey SS, Cheong M, Dams-O'Connor K, Hricik AJ, Inoue T, Menon DK, Morabito DJ, Pacheco JL, Puccio AM, Sinha TK. Diffusion tensor imaging for outcome prediction in mild traumatic brain injury: a TRACK-TBI study. J Neurotrauma. 2014 Sep 1; 31(17):1457-77.
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  11. McMahon P, Hricik A, Yue JK, Puccio AM, Inoue T, Lingsma HF, Beers SR, Gordon WA, Valadka AB, Manley GT, Okonkwo DO. Symptomatology and functional outcome in mild traumatic brain injury: results from the prospective TRACK-TBI study. J Neurotrauma. 2014 Jan 1; 31(1):26-33.
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  12. Dams-O'Connor K, Spielman L, Singh A, Gordon WA, Lingsma HF, Maas AI, Manley GT, Mukherjee P, Okonkwo DO, Puccio AM, Schnyer DM, Valadka AB, Yue JK, Yuh EL. The impact of previous traumatic brain injury on health and functioning: a TRACK-TBI study. J Neurotrauma. 2013 Dec 15; 30(24):2014-20.
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  13. Diaz-Arrastia R, Wang KK, Papa L, Sorani MD, Yue JK, Puccio AM, McMahon PJ, Inoue T, Yuh EL, Lingsma HF, Maas AI, Valadka AB, Okonkwo DO, Manley GT. Acute biomarkers of traumatic brain injury: relationship between plasma levels of ubiquitin C-terminal hydrolase-L1 and glial fibrillary acidic protein. J Neurotrauma. 2014 Jan 1; 31(1):19-25.
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  14. Yue JK, Vassar MJ, Lingsma HF, Cooper SR, Okonkwo DO, Valadka AB, Gordon WA, Maas AI, Mukherjee P, Yuh EL, Puccio AM, Schnyer DM, Manley GT. Transforming research and clinical knowledge in traumatic brain injury pilot: multicenter implementation of the common data elements for traumatic brain injury. J Neurotrauma. 2013 Nov 15; 30(22):1831-44.
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  15. Li YO, Yang FG, Nguyen CT, Cooper SR, LaHue SC, Venugopal S, Mukherjee P. Independent component analysis of DTI reveals multivariate microstructural correlations of white matter in the human brain. Hum Brain Mapp. 2012 Jun; 33(6):1431-51.
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  16. Haacke EM, Duhaime AC, Gean AD, Riedy G, Wintermark M, Mukherjee P, Brody DL, DeGraba T, Duncan TD, Elovic E, Hurley R, Latour L, Smirniotopoulos JG, Smith DH. Common data elements in radiologic imaging of traumatic brain injury. J Magn Reson Imaging. 2010 Sep; 32(3):516-43.
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  17. Raj A, Hess C, Mukherjee P. Spatial HARDI: improved visualization of complex white matter architecture with Bayesian spatial regularization. Neuroimage. 2011 Jan 1; 54(1):396-409.
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  18. Mukherjee P, Berman JI, Chung SW, Hess CP, Henry RG. Diffusion tensor MR imaging and fiber tractography: theoretic underpinnings. AJNR Am J Neuroradiol. 2008 Apr; 29(4):632-41.
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  19. Mukherjee P, Chung SW, Berman JI, Hess CP, Henry RG. Diffusion tensor MR imaging and fiber tractography: technical considerations. AJNR Am J Neuroradiol. 2008 May; 29(5):843-52.
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  20. Rodriguez-Carranza CE, Mukherjee P, Vigneron D, Barkovich J, Studholme C. A framework for in vivo quantification of regional brain folding in premature neonates. Neuroimage. 2008 Jun; 41(2):462-78.
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