Paul A. Yushkevich, Ph.D.

faculty photo
Professor of Radiology
Department: Radiology

Contact information
Penn Image Computing and Science Laboratory
Richards Building, 6th Floor, D605
3700 Hamilton Walk
Philadelphia, PA 19104
Office: 215-746-6924
B.S. (Computer Science and Mathematics)
University of North Carolina at Charlotte, 1996.
M.S. (Computer Science)
University of North Carolina Chapel Hill, 2000.
Ph.D. (Computer Science)
University of North Carolina Chapel Hill, 2003.
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Description of Research Expertise

My research portfolio combines theoretical work on statistical shape characterization using a symmetry-based representation of shape with applied and translational research in multiple areas of biomedical image analysis. I am particularly interested in analysis techniques that are tailored to specific anatomical structures. My key work in this area involves automatic segmentation and morphometry of the hippocampal formation (HF) in magnetic resonance imaging (MRI). The HF plays a central role in memory function and is a site of early neurodegeneration in Alzheimer’s disease. In a broad effort to develop more detailed imaging-based biomarkers for Alzheimer’s disease, my team has developed a first of its kind detailed computational atlas of the HF from postmortem MRI microscopy. With NIH R01 funding, we are now integrating this atlas with histology, leveraging it for the analysis of the HF and its subfields in in vivo MRI, and evaluating MRI-derived subfield-specific as alternative imaging biomarkers in dementia. We recently published a pioneering technique for automatic segmentation of HF subfields in high-resolution, HF-focused T2-weighted in vivo MRI, showing excellent agreement with manual segmentation. Concurrently, we developed and evaluated a strategy for improving the accuracy of general-purpose segmentation techniques using machine learning as a corrective wrapper method. Other recent publications include a surface-based tract-specific strategy for diffusion MRI analysis, for which open-source software is currently being developed, and an automatic cardiac MRI segmentation method with an explicit prior on heart wall thickness.

Selected Publications

Wisse LEM, Ravikumar S, Ittyerah R, Lim S, Lane J, Bedard ML, Xie L, Das SR, Schuck T, Grossman M, Lee EB, Tisdall MD, Prabhakaran K, Detre JA, Mizsei G, Trojanowski JQ, Artacho-Pérula E, de Iñiguez de Onzono Martin MM, M Arroyo-Jiménez M, Muñoz Lopez M, Molina Romero FJ, P Marcos Rabal M, Cebada Sánchez S, Delgado González JC, de la Rosa Prieto C, Córcoles Parada M, Wolk DA, Irwin DJ, Insausti R, Yushkevich PA.: Downstream effects of polypathology on neurodegeneration of medial temporal lobe subregions. Acta Neuropathol Commun 9: 128, Jul 2021.

Yushkevich PA, López MM, Martin MMIO, Ittyerah R, Lim S, Ravikumar S, Bedard ML, Pickup S, Liu W, Wang J, Hung LY, Lasserve J, Vergnet N, Xie L, Dong M, Cui S, McCollum L, Robinson JL, Schuck T, de Flores R, Grossman M, Tisdall MD, Prabhakaran K, Mizsei G, Das SR, Artacho-Pérula E, Jiménez MADMA, Rabal MAPM, Romero FJM, Sánchez SC, González JCD, de la Rosa-Prieto C, Parada MC, Lee EB, Trojanowski JQ, Ohm DT, Wisse LEM, Wolk DA, Irwin DJ, Insausti R.: Three-dimensional mapping of neurofibrillary tangle burden in the human medial temporal lobe. Brain Jul 2021.

McCollum LE, Das SR, Xie L, de Flores R, Wang J, Xie SX, Wisse LEM, Yushkevich PA, Wolk DA; Alzheimer's Disease Neuroimaging Initiative.: Oh brother, where art tau? Amyloid, neurodegeneration, and cognitive decline without elevated tau. Neuroimage Clin 31: 102717, Jun 2021.

Wisse LEM, de Flores R, Xie L, Das SR, McMillan CT, Trojanowski JQ, Grossman M, Lee EB, Irwin D, Yushkevich PA, Wolk DA; Alzheimer’s Disease NeuroImaging Initiative.: Pathological drivers of neurodegeneration in suspected non-Alzheimer's disease pathophysiology. Alzheimers Res Ther 13: 100, May 2021.

Zimmerman CE, Khandelwal P, Xie L, Lee H, Song HK, Yushkevich PA, Vossough A, Bartlett SP, Wehrli FW.: Automatic Segmentation of Bone Selective MR Images for Visualization and Craniometry of the Cranial Vault. Acad Radiol Apr 2021.

Berron D, Vogel JW, Insel PS, Pereira JB, Xie L, Wisse LEM, Yushkevich PA, Palmqvist S, Mattsson-Carlgren N, Stomrud E, Smith R, Strandberg O, Hansson O.: Early stages of tau pathology and its associations with functional connectivity, atrophy and memory. Brain Mar 2021.

Wisse LEM, Chételat G, Daugherty AM, de Flores R, la Joie R, Mueller SG, Stark CEL, Wang L, Yushkevich PA, Berron D, Raz N, Bakker A, Olsen RK, Carr VA.: Hippocampal subfield volumetry from structural isotropic 1 mm(3) MRI scans: A note of caution. Hum Brain Mapp 42: 539-550, Feb 2021.

Rathore S, Mohan S, Bakas S, Sako C, Badve C, Pati S, Singh A, Bounias D, Ngo P, Akbari H, Gastounioti A, Bergman M, Bilello M, Shinohara RT, Yushkevich P, O'Rourke DM, Sloan AE, Kontos D, Nasrallah MP, Barnholtz-Sloan JS, Davatzikos C.: Multi-institutional noninvasive in vivo characterization of IDH, 1p/19q, and EGFRvIII in glioma using neuro-Cancer Imaging Phenomics Toolkit (neuro-CaPTk). Neurooncol Adv 2: iv22-iv34, Jan 2021.

Venet L, Pati S, Feldman MD, Nasrallah MP, Yushkevich P, Bakas S.: Accurate and Robust Alignment of Differently Stained Histologic Images Based on Greedy Diffeomorphic Registration. Appl Sci (Basel) 2021.

Klooster N, Humphries S, Cardillo E, Hartung F, Xie L, Das S, Yushkevich P, Pilania A, Wang J, Wolk DA, Chatterjee A.: Sensitive Measures of Cognition in Mild Cognitive Impairment. J Alzheimers Dis 2021.

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Last updated: 09/07/2021
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