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USC Mark and Mary Stevens Neuroimaging and Informatics Institute Newsletter / Summer 2020


The Genetic Architecture of the Human Cerebral Cortex

Neda Jahanshad, PhD

Neda Jahanshad, PhD, associate professor of neurology at the INI and Paul Thompson, PhD, associate director of the institute, led a massive international MRI and genetics collaboration that united more than 360 scientists from 184 institutions in what’s been called the “crown jewel” of the Enhancing Neuro Imaging Genetics through Meta-Analysis (ENIGMA) Consortium. The study, published in the journal Science in March, studied more than 50,000 people and found 306 genetic variants that influence brain structure.

Read more about their research or view the publication.

THC Exposure is Reflected in the Microstructure of the Cerebral Cortex and Amygdala of Young Adults

Ryan Cabeen, PhD

Ryan Cabeen, PhD, a postdoctoral fellow at the INI, and Institute Director Arthur W. Toga led a research team that explored associations between THC exposure and brain microstructure using data from the Human Connectome Project. They uncovered a relationship between exposure to THC and structural abnormalities in brain areas related to emotion regulation, decision making and salience processing.

View the publication and watch the Watch the 3D animation below based on the data collected.

New Findings on Alzheimer’s Disease

Judy Pa, PhD

Judy Pa, PhD, associate professor of neurology at the INI, and her team co-authored two studies of Alzhiemer’s disease in Neurobiology of Aging this spring. One investigation looked at a particular type of inflammatory marker known as tumor necrosis factor (TNF)-α, finding that higher levels of the marker were associated with lower functional connectivity in the brains of older adults. The other study explored the relationship between mitochondrial DNA and the risk of developing Alzheimer’s disease.

Read about functional connectivity or learn more about Alzheimer’s disease risk.

How Cognitive Intelligence is a Whole Brain Phenomenon

Paul Thompson, PhD

The INI’s Paul Thompson, PhD, and Neda Jahanshad, PhD, were part of an international collaboration through the ENIGMA Schizophrenia Working Group, which analyzed MRI scans and cognitive measures from 1,717 participants. The study shows that small differences in brain connectivity are associated with differences in general cognitive ability, or IQ.

Read about the group’s findings here.


COVID-19 Data Archive

Dominique Duncan, PhD, assistant professor of neurology at the INI, received a grant of more than $230,000 from NSF to build and launch a data archive for researchers studying COVID-19. COVID-ARC will leverage the institute’s experience in organizing, storing and disseminating biomedical data to rapidly unite researchers studying the disease caused by the novel coronavirus. The platform will enable researchers to store, share, visualize and analyze a variety of data types, including patient medical history, demographic information, symptoms, cognitive assessments, imaging data, electrophysiology recordings and more.

Exercising in Virtual Reality

Judy Pa, PhD, associate professor of neurology at the INI, received a five-year, $7 million grant from the National Institute on Aging to launch a phase 2 clinical trial of a virtual reality-based intervention for Alzheimer’s disease. NeuroRiderVR, a 16-week program for older adults with concerns about Alzheimer’s disease, combines physical and cognitive exercise to improve brain function in an effort to reduce the risk of developing the debilitating disease. Though both cognitive and physical exercise can be effective in managing Alzheimer’s, few studies have tested a hybrid intervention that combines the two approaches.

Functional Imaging of Alzheimer’s Disease

Kay Jann, PhD, assistant professor of research at the INI, and Danny JJ Wang, PhD, professor of neurology and radiology and director of imaging technology innovation at the INI, have received a five-year grant of more than $3.2 million from the National Institute on Aging to apply advanced fMRI technology to the study of Alzheimer’s disease. Hosung Kim, PhD, assistant professor of neurology at the INI, is a co-investigator on the grant. The goal of the project is to identify a noninvasive, economical imaging biomarker of neuronal injury in mild cognitive impairment (MCI) and Alzheimer’s disease.

Ultra-High Field Vascular Imaging

Lirong Yan, PhD, assistant professor of neurology at the INI, received $300,000 from the BrightFocus Foundation, a nonprofit organization that supports research on brain and eye diseases, to study the role of cerebrovascular diseases in Alzheimer’s, as well as vascular cognitive impairment and dementia. She and her team will use the institute’s ultra-high field 7Tesla MRI scanner to collect detailed images of very small blood vessels in the brain that are difficult to see with lower-resolution scanners.

Brain Health and Stroke Recovery

Sook-Lei Liew, PhD, assistant professor of neurology at the INI with joint appointments in occupational science and occupational therapy; biokinesiology and physical therapy; neurology; and biomedical engineering, received nearly $3.1 million from the National Institute of Neurological Disorders and Stroke to study how patients regain motor and sensory function following a stroke. She and her team will analyze existing data from the Enhancing Neuro Imaging Genetics through Meta-Analysis (ENIGMA) Stroke Recovery Working Group, which has collected the world’s largest retrospective data collection of stroke brain scans and sensorimotor behavior.

Ultra-High Field Imaging of Epilepsy Patients

Vishal Patel, MD, PhD, assistant professor of radiology at the INI, was one of two Keck School of Medicine faculty to receive a Baxter Foundation Fellowship Award of $100,000. He will use the institute’s ultra-high field 7Tesla MRI scanner to study regions of abnormal brain tissue that cause seizures in epilepsy patients. Ultimately, his findings may enable more individuals with epilepsy to undergo surgery that reduces seizures and improves overall quality of life.

A Deep Learning Algorithm for Diagnosing Sleep Apnea

Hosung Kim, PhD, assistant professor of neurology at the INI, received a one-year Technology Advancement Grant of approximately $50,000 from the USC Stevens Center for Innovation to study obstructive sleep apnea syndrome. Using a large dataset collected at a sleep clinic, Kim will develop a deep learning algorithm that can be integrated into portable sleep monitoring devices. That data can help physicians diagnose sleep apnea quickly and inexpensively.

Expanded Mapping of the Hippocampus

Michael Bienkowski, PhD, assistant professor of research at the INI, is part of a group working to flesh out maps of connectivity in the hippocampus. The team, led by Gianluca Lazzi, PhD, director of the USC Institute for Technology and Medical Systems Innovation, received an NIH R01 supplement to develop the connectomics of the hippocampus before and after peripheral neurostimulation.

Learn more about recent awards our faculty have earned

Training and Outreach

Virtual Conferences:


Scientific conferences look a little different these days—OHBM, the annual meeting of the Organization for Human Brain mapping, is one of the biggest events in the field of neuroscience—but this year it took place virtually. Researchers presented posters, attended keynote lectures and engaged with other scientists, all through an interactive online forum.

65 researchers from the INI presented their latest findings on brain aging, epilepsy, neural network mapping and more. At the end of July, our Global Alzheimer’s Association Interactive Network, a federated data platform that fosters cohort discover and collaboration, will recruit new users and data partners with a virtual booth at the 2020 Alzheimer’s Association International Conference.

NIIN Students Present Work at OHBM

Students in the INI’s Master of Science in Neuroimaging and Informatics (NIIN) program took part in a special opportunity this term: They analyzed diffusion MRI data collected by INI’s Farshid Sepehrband, PhD, Kay Jann, PhD, and Ryan Cabeen, PhD—and an abstract the students wrote was accepted to OHBM 2020. In June, they presented their poster at the virtual conference.

Watch an animated visualization of the corticospinal tract data.

View the poster

SMART-VR Cribs Project

USC’s SensoriMotor Assessment and Rehabilitation Training in Virtual Reality (SMART-VR) Center, co-directed by INI’s Sook-Lei Liew, PhD, and Judy Pa, PhD, postponed its annual symposium—but found a creative way to keep its community engaged and connected. In March, the center launched the #SMARTVRCribsChallenge—which uses the format of the early 2000s hit MTV show "MTV Cribs,” where celebrities gave behind-the-scenes tours of their homes—to give viewers an inside look at VR-equipped labs.

Take a virtual tour of Dr. Liew’s lab and see how she uses VR for stroke rehabilitation.

Virtual Tour of Stevens Hall for Neuroimaging

We’re spending less time at the institute lately—and we miss our world-class research facilities. Luckily, the INI’s Dr. Sook-Lei Liew helped us film and launch a virtual tour of Stevens Hall for Neuroimaging! You’ll get to explore the building, see a hologram of our director, Dr. Arthur W. Toga, sharing the INI’s vision, and experience a 7T MRI scan up close.

Download the USC SMART-VR app in the iOS or Android app store and select USC Stevens Neuroimaging and Informatics Institute. You can also learn more about the app here.

NiftyTorch Deep Learning Library

INI’s Farshid Sepherband, PhD, built and released NiftyTorch, a Python API for deploying deep learning in neuroimaging research. NiftyTorch allows researchers without an extensive machine learning or coding background to benefit from the emerging and powerful field of deep learning. Some of its key features include:

  • Pytorch Embedded End to End data-loading pipeline
  • Built-in Attention module to demographic data and other modalities or mask
  • Additional Loss Functions incorporated to easily use with any network
  • Automatic Hyperparameter tuning for each network
  • Easily customizable to use your own network
  • Multi-scale Training
  • Built-in classification networks
  • Built-in CNNs units such as Bottleneck, BinaryActivation

Learn more and view demos on how to use NiftyTorch

Literature Review on Posttraumatic Epilepsy

Rachael Garner, a research assistant at LONI in the lab of Dominique Duncan, PhD, was first author on a literature review of posttraumatic epilepsy (PTE), which develops following a traumatic brain injury. The paper outlines current research on PTE and priorities for future study. Garner and Duncan help lead the Informatics and Analytics Core of the EpiBioS4Rx project, an international multicenter collaboration to study animals and patients with TBI and PTE to aid future clinical trials of therapies to prevent epilepsy.

Read the review or learn more about EpiBioS4Rx.


2019 Highly Cited Researcher

INI Director Arthur W. Toga

INI Director Arthur W. Toga was named to the 2019 list of Highly Cited Researchers, compiled by Clarivate Analytics, which identifies scientists who are among the most influential in their respective fields. Researchers who make the list have authored numerous papers that rank in the top 1% of citations in their field over the past decade.

Newly Tenured Professors: Neda Jahanshad and Judy Pa

Two of INI’s outstanding faculty members were awarded tenure this spring. Neda Jahanshad, PhD, was promoted to associate professor of neurology, with a joint appointment in biomedical engineering at the Viterbi School of Engineering. Judy Pa, PhD, was also promoted to associate professor of neurology, with a joint appointment in the USC Dornsife College of Letters, Arts and Science’s department of psychology. Pa primarily studies Alzheimer’s disease, including exploring genetic risk for the condition and lifestyle interventions that may aid in prevention.

INI Professor Elected to Leadership Role in ISMRM Diffusion Study Group

Farshid Sepehrband, PhD

INI’s Farshid Sepehrband, PhD, was elected secretary of the International Society for Magnetic Resonance in Medicine’s (ISMRM) diffusion study group. The group’s mission is to facilitate the technological development, evaluation, and clinical application of diffusion MRI.

Meet Our Featured Postdocs

Muye Zhu

Muye Zhu received her PhD in Neuroscience and MS in computer science from the University of California. Her research focuses on developing computational methods and tools to gain understanding of the structural connectome of the mammalian brain. In particular, she applies a combination of machine learning, numerical optimization and statistical methods to large microscopic imaging data of the brain to investigate the morphology and long-range connectivity of neuronal populations.

Julio Villalon

Julio Villalon received his medical doctorate from University of the North in Colombia. During his early career, he used magnetic resonance spectroscopy to study brain tumors. His graduate work focused on advanced Diffusion MRI (dMRI) techniques, such as DTI, tensor distribution function (TDF), constrained spherical deconvolution (CSD) and biophysical compartment models such NODDI. Currently, in his postdoctoral training, he is continuing to explore other quantitative MRI tools, such as myelin mapping techniques. These techniques will allow him to address questions about the deeper microstructure of the brain, such as the axonal diameter distribution, and aggregate g-ratio estimation.

Check back in the Fall to meet more of our postdocs.

INI In The News

Alzheimer’s Disease: Early Onset Prevention, Reducing Risk & Caring for Loved Ones
Judy Pa Presents NeuroRiderVR

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