Ashish Raj, PhD

+1 415 353-3442

I have more than 15 years experience in computer vision, signal processing, graph theory, medical imaging and informatics. I have had continuous and successive experiences in forming and leading research teams comprising of basic and clinical scientists in executing NIH-funded research projects. I have published more than 70 peer reviewed papers ranging from microwave engineering, superconductivity, image/signal processing, vision, graph theory and neuroscience, and two US patents. I have attracted several NIH grants, on graph algorithms for accelerated MRI, theoretical neuroscience and network modeling of dementia and Parkinson’s.

The defining characteristic of my work has been inter-disciplinarity: finding innovative ways to apply computation and algorithms to biomedical applications. My group was an early adopter of mathematical models of brain connectivity networks, a subject that marries computer science with neuroradiology. I have deep interest in the graph properties of brain networks, and how they are altered in neurological disorders like epilepsy, dementia, movement disorders, traumatic brain injury and stroke. A recent project on dementia modeling was selected by the NIH for the prestigious EUREKA award that supports highly innovative but risky research, and another by the BRAIN Initiative. My team has developed novel image reconstruction algorithms for fast MRI, motion correction for MR angiography, and new methods in tractography, Q-ball imaging, brain connectivity networks and computational neurology.

My research program is now perfectly poised to help bring the fields of neurology and radiology into the era of personalized, precision medicine, using mathematical modeling and data science.


High activity and high functional connectivity are mutually exclusive in resting state zebrafish and human brains.

BMC biology

Zarei M, Xie D, Jiang F, Bagirov A, Huang B, Raj A, Nagarajan S, Guo S

Matrix Inversion and Subset Selection (MISS): A pipeline for mapping of diverse cell types across the murine brain.

Proceedings of the National Academy of Sciences of the United States of America

Mezias C, Torok J, Maia PD, Markley E, Raj A

Time-varying Dynamic Network Model For Dynamic Resting State Functional Connectivity in fMRI and MEG imaging.


Jiang F, Jin H, Gao Y, Xie X, Cummings J, Raj A, Nagarajan S

Modelling seeding and neuroanatomic spread of pathology in amyotrophic lateral sclerosis.


Pandya S, Maia PD, Freeze B, Menke RAL, Talbot K, Turner MR, Raj A

Emergence of directional bias in tau deposition from axonal transport dynamics.

PLoS computational biology

Torok J, Maia PD, Verma P, Mezias C, Raj A

Combined Model of Aggregation And Network Diffusion Recapitulates Alzheimer's Regional Tau-PET.

Brain connectivity

Raj A, Tora V, Gao X, Cho H, Choi JY, Ryu Y, Lyoo C, Franchi B

Network-constrained technique to characterize pathology progression rate in Alzheimer's disease.

Brain communications

Powell F, Tosun D, Raj A, Alzheimer’s Disease Neuroimaging Initiative

Emergence of canonical functional networks from the structural connectome.


Xie X, Cai C, Damasceno PF, Nagarajan SS, Raj A

Molecular Imaging of Striatal Dopaminergic Neuronal Loss and the Neurovascular Unit in Parkinson Disease.

Frontiers in neuroscience

Ivanidze J, Skafida M, Pandya S, Patel D, Osborne JR, Raj A, Gupta A, Henchcliffe C, Dyke JP

A dictionary-based graph-cut algorithm for MRI reconstruction.

NMR in biomedicine

Xu J, Pannetier N, Raj A

Origins of atrophy in Parkinson linked to early onset and local transcription patterns.

Brain communications

Maia PD, Pandya S, Freeze B, Torok J, Gupta A, Zeighami Y, Raj A

Network mediation of pathology pattern in sporadic Creutzfeldt-Jakob disease.

Brain communications

Freeze B, Maia P, Pandya S, Raj A

Spectral graph theory of brain oscillations.

Human brain mapping

Raj A, Cai C, Xie X, Palacios E, Owen J, Mukherjee P, Nagarajan S

Stereotaxic Diffusion Tensor Imaging White Matter Atlas for the in vivo Domestic Feline Brain.

Frontiers in neuroanatomy

Johnson PJ, Pascalau R, Luh WM, Raj A, Cerda-Gonzalez S, Barry EF

Regional transcriptional architecture of Parkinson's disease pathogenesis and network spread.

Brain : a journal of neurology

Freeze B, Pandya S, Zeighami Y, Raj A

Editorial: Network Spread Models of Neurodegenerative Diseases.

Frontiers in neurology

Raj A, Iturria-Medina Y

Normal diffusivity of the domestic feline brain.

The Journal of comparative neurology

Barry EF, Cerda-Gonzalez S, Luh WM, Daws RE, Raj A, Johnson PJ

Models of Network Spread and Network Degeneration in Brain Disorders.

Biological psychiatry. Cognitive neuroscience and neuroimaging

Raj A, Powell F

A method for inferring regional origins of neurodegeneration.

Brain : a journal of neurology

Torok J, Maia PD, Powell F, Pandya S, Raj A

Regional vulnerability in Alzheimer's disease: The role of cell-autonomous and transneuronal processes.

Alzheimer's & dementia : the journal of the Alzheimer's Association

Acosta D, Powell F, Zhao Y, Raj A

Age-Related Changes in Topological Degradation of White Matter Networks and Gene Expression in Chronic Schizophrenia.

Brain connectivity

Powell F, LoCastro E, Acosta D, Ahmed M, O'Donoghue S, Forde N, Cannon D, Scanlon C, Rao T, McDonald C, Raj A

Mature Hippocampal Neurons Require LIS1 for Synaptic Integrity: Implications for Cognition.

Biological psychiatry

Sudarov A, Zhang XJ, Braunstein L, LoCastro E, Singh S, Taniguchi Y, Raj A, Shi SH, Moore H, Ross ME

MRI Analysis of White Matter Myelin Water Content in Multiple Sclerosis: A Novel Approach Applied to Finding Correlates of Cortical Thinning.

Frontiers in neuroscience

Dayan M, Hurtado Rúa SM, Monohan E, Fujimoto K, Pandya S, LoCastro EM, Vartanian T, Nguyen TD, Raj A, Gauthier SA

Diffuse reduction of cerebral grey matter volumes in Erdheim-Chester disease.

Orphanet journal of rare diseases

Diamond EL, Hatzoglou V, Patel S, Abdel-Wahab O, Rampal R, Hyman DM, Holodny AI, Raj A

Structural connectome disruption at baseline predicts 6-months post-stroke outcome.

Human brain mapping

Kuceyeski A, Navi BB, Kamel H, Raj A, Relkin N, Toglia J, Iadecola C, O'Dell M

Profilometry: A new statistical framework for the characterization of white matter pathways, with application to multiple sclerosis.

Human brain mapping

Dayan M, Monohan E, Pandya S, Kuceyeski A, Nguyen TD, Raj A, Gauthier SA

Measuring longitudinal myelin water fraction in new multiple sclerosis lesions.

NeuroImage. Clinical

Vargas WS, Monohan E, Pandya S, Raj A, Vartanian T, Nguyen TD, Hurtado Rúa SM, Gauthier SA

Feasibility and reproducibility of whole brain myelin water mapping in 4 minutes using fast acquisition with spiral trajectory and adiabatic T2prep (FAST-T2) at 3T.

Magnetic resonance in medicine

Nguyen TD, Deh K, Monohan E, Pandya S, Spincemaille P, Raj A, Wang Y, Gauthier SA

Exploring the brain's structural connectome: A quantitative stroke lesion-dysfunction mapping study.

Human brain mapping

Kuceyeski A, Navi BB, Kamel H, Relkin N, Villanueva M, Raj A, Toglia J, O'Dell M, Iadecola C

Simultaneous phase unwrapping and removal of chemical shift (SPURS) using graph cuts: application in quantitative susceptibility mapping.

IEEE transactions on medical imaging

Dong J, Liu T, Chen F, Zhou D, Dimov A, Raj A, Cheng Q, Spincemaille P, Wang Y

Widespread white matter degeneration preceding the onset of dementia.

Alzheimer's & dementia : the journal of the Alzheimer's Association

Maier-Hein KH, Westin CF, Shenton ME, Weiner MW, Raj A, Thomann P, Kikinis R, Stieltjes B, Pasternak O

Multi-compartment T2 relaxometry using a spatially constrained multi-Gaussian model.

PloS one

Raj A, Pandya S, Shen X, LoCastro E, Nguyen TD, Gauthier SA

Discriminative random field segmentation of lung nodules in CT studies.

Computational and mathematical methods in medicine

Liu B, Raj A

Robust myelin quantitative imaging from multi-echo T2 MRI using edge preserving spatial priors.

Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention

Shen X, Nguyen TD, Gauthier SA, Raj A

Loss in connectivity among regions of the brain reward system in alcohol dependence.

Human brain mapping

Kuceyeski A, Meyerhoff DJ, Durazzo TC, Raj A

Bayesian algorithm using spatial priors for multiexponential T2 relaxometry from multiecho spin echo MRI.

Magnetic resonance in medicine

Kumar D, Nguyen TD, Gauthier SA, Raj A

T2 prep three-dimensional spiral imaging with efficient whole brain coverage for myelin water quantification at 1.5 tesla.

Magnetic resonance in medicine

Nguyen TD, Wisnieff C, Cooper MA, Kumar D, Raj A, Spincemaille P, Wang Y, Vartanian T, Gauthier SA

A pilot study of quantitative MRI measurements of ventricular volume and cortical atrophy for the differential diagnosis of normal pressure hydrocephalus.

Neurology research international

Moore DW, Kovanlikaya I, Heier LA, Raj A, Huang C, Chu KW, Relkin NR

The generation and validation of white matter connectivity importance maps.


Kuceyeski A, Maruta J, Niogi SN, Ghajar J, Raj A

A fast Edge-preserving Bayesian reconstruction method for Parallel Imaging applications in cardiac MRI.

Magnetic resonance in medicine

Singh G, Raj A, Kressler B, Nguyen TD, Spincemaille P, Zabih R, Wang Y

Visualization and segmentation of liver tumors using dynamic contrast MRI.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference

Raj A, Juluru K

A maximum likelihood approach to parallel imaging with coil sensitivity noise.

IEEE transactions on medical imaging

Raj A, Wang Y, Zabih R

Fast and stable bayesian image expansion using sparse edge priors.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society

Raj A, Thakur K

Bayesian parallel imaging with edge-preserving priors.

Magnetic resonance in medicine

Raj A, Singh G, Zabih R, Kressler B, Wang Y, Schuff N, Weiner M

Improved signal-to-noise ratio in parallel coronary artery magnetic resonance angiography using graph cuts based Bayesian reconstruction.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference

Singh G, Nguyen T, Kressler B, Spincemaille P, Raj A, Zabih R, Wang Y

Statistical aspects of parallel imaging reconstruction.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference

Raj A, Kressler B, Singh G, Zabih R, Wang Y