Laboratory of Neuro Imaging

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Laboratory of Neuro Imaging
LONI logo
Director Arthur W. Toga
Faculty Paul Thompson
Location Los Angeles, California, USA
Affiliations University of Southern California

The Laboratory of Neuro Imaging (LONI) is a research laboratory located at the Mark and Mary Stevens Neuroimaging and Informatics Institute (INI) within the Keck School of Medicine of USC’s Department of Neurology. The laboratory conducts a wide variety of brain imaging studies of normal brain anatomy and function, development, aging, and disease. Historically, research at LONI has focused on design, development, validation and wide dissemination of software tools for use in understanding the relationships between brain structure and function across space, time and scale. In particular, work has been conducted toward the construction of multidimensional brain atlases seeking to promote computationally efficient representations of brain anatomy, function and physiology in a standardized 3D coordinate system. Brain imaging modalities include MRI, fMRI, Diffusion Tensor Imaging, Magnetic Resonance Spectroscopy, Positron Emission Tomography, Optical Intrinsic Signal, among other means for gathering spatially based neurophysiological signals.[1]


LONI’s foundations can be traced to the Washington University in St. Louis, where Founder and Director Arthur W. Toga held an assistant professor position in the Neurology department of the School of Medicine between 1980 and 1987. Toga officially founded LONI in 1983 within the School of Medicine’s McDonnell Center for Higher Brain Function.

In 1987, LONI moved to the David Geffen School of Medicine at the University of California, Los Angeles, where it thrived within the Department of Neurology for more than 25 years. At UCLA, LONI became a leader in building population-based and disease-specific digital brain atlases and databases.

In 2013, LONI moved to the University of Southern California and was integrated into the newly launched Neuroimaging and Informatics Institute, later renovated and renamed the Mark and Mary Stevens Neuroimaging and Informatics Institute (INI) with a $50 million gift from the longtime USC benefactors[2]. A number of faculty members—Arthur W. Toga, Paul M. Thompson, Hong-Wei Dong, Yonggang Shi, Kristi Clark and John Van Horn—transitioned along with LONI to the new institute. In joining the Keck School of Medicine of USC, LONI gained access to a number of additional resources, including a brand-new Siemens 7T Terra MRI scanner, installed in 2017. [3]  

Partnerships and Affiliations[edit]

LONI is known for its highly collaborative national and international research projects, including the long-running Human Connectome Project [CITE] and the recently launched Epilepsy Bioinformatics Study for Antiepileptogenic Therapy (EpiBioS4Rx) [CITE]. Closer to home, LONI faculty collaborate with other researchers across USC and with the three other centers housed within the Mark and Mary Stevens Neuroimaging and Informatics Institute (INI):


Imaging Genetics Center (IGC): Led by INI’s Associate Director Paul M. Thompson, the IGC aims to understand how genes determine brain structure and function. The center uses Diffusion Weighted Imaging to map connectivity within the brain and actively develops technical and mathematical tools to study how the brain changes in disorders and diseases such as autism, HIV, schizophrenia and traumatic brain injury. Thompson and the IGC co-founded the Enhancing Neuro Imaging Genetics through Meta-Analysis (ENIGMA) Consortium, which analyses brain scans of more than 50,000 people around the world in big data studies. Focusing on the interaction between brain health and genetics, this collaborative group studies 22 brain diseases in 37 countries around the world, and has released some of the largest neuroimaging studies of multiple disorders including bipolar disorder, schizophrenia and epilepsy[4].

Center for Image Acquisition (CIA): Launched in 2016, the CIA uses state-of-the-art technologies and analytical approaches to collect and optimize images of the human brain, sharing the tools developed with the larger scientific community. The CIA houses two of the world’s most advanced Magnetic Resonance Imaging (MRI) scanners, the Siemens Prisma 3T and the Siemens Terra 7T—the latter was the first of its kind installed in North America, and contains a powerful magnet that allows researchers and clinicians to image the brain in ultra-high resolution. In addition to imaging technology, the CIA is also equipped with a dedicated supercomputing system. Its personnel work in tandem with the Laboratory of Functional MRI Technology, led by Danny JJ Wang, director of Imaging Technology Innovation at INI.

Center for Integrative Connectomics (CIC): Launched in 2017 and led by Hong-Wei Dong, professor of neurology at the Keck School of Medicine of USC, the CIC absorbed the Mouse Connectome Project, which has traced more than 2,000 pathways within the mouse brain. The center is developing a detailed connectivity map of the mammalian brain in an effort to understand the neural networks underlying health and disease, including neurological conditions such as autism, Alzheimer’s disease, Parkinson’s disease and Huntington’s disease. In 2017, the center joined the BRAIN Initiative Cell Census Network with a $19 million grant[5], where it will lead the neuroanatomy analysis and assist with connectivity and transcriptome analyses aimed at characterizing and classifying neurons in the mouse brain.

Labs and Groups

Laboratory of Functional MRI Technology (LOFT): LOFT leads the institute in developing tools for neuroimaging, creating specialized software to collect images at high spatial and temporal resolutions, including special parameters for vascular imaging and neuromodulation studies. The laboratory is led by Danny JJ Wang, director of Imaging Technology Innovation at the institute and professor of neurology at the Keck School of Medicine of USC.[6]

Connectivity and Network Development Laboratory (CANDL): Led by Kristi Clark, assistant professor of neurology at the Keck School of Medicine of USC, CANDL aims to understand how the networks of the human brain develop and respond to experiences, with an emphasis on the hippocampus. The laboratory works on methods development (including phenome wide-association studies; in vivo imaging techniques; and ex-vivo imaging), normal brain development studies and research on neurodevelopmental disorders, such as dyslexia and childhood obesity.

Neuroplasticity and Neurorehabilitation Laboratory (NPNL): NPNL is housed within the USC Chan Division of Occupational Science and Occupational Therapy and led by Sook-Lei Liew, assistant professor with joint appointments in the USC Division of Biokinesiology and Physical Therapy, the Keck School of Medicine of USC’s Department of Neurology and the USC Viterbi School of Engineering. The goal of NPNL is to enhance neural plasticity in order to improve the quality of life of a wide population of individuals, especially those recovering from stroke. The lab uses brain-computer interfaces, noninvasive brain stimulation, neuroimaging, behavioral techniques and virtual reality to accomplish this goal. It has published one of the largest stroke imaging datasets, Anatomical Tracings of Lesion After Stroke (ATLAS)[7] and recently launched the Rehabilitation Environment using the Integration of Neuromuscular-based Virtual Enhancements for Neural Training (REINVENT)[8], a low-cost virtual reality brain-computer interface for patients who have suffered severe strokes. REINVENT received a special jury recognition for innovative use of VR room-scale technology at the 2016 SXSW Film Awards.[9]


The Laboratory of Neuro Imaging has deployed a comprehensive infrastructure for conducting advanced neuroimaging and brain mapping research. This infrastructure is based on the following types of resources:

  • Software: LONI faculty and staff work to develop efficient computational algorithms and software for the quantitative mapping of brain structure and function.
  • Scientific Data Workflows: the development of process oriented algorithms and meta-algorithms for assessing neuroimaging and other biologically relevant data sets. See LONI Pipeline for overview. See also discussions of Scientific Data Provenance.
  • Databases: The LONI Image Database was developed to provide a flexible and effective interfaces for managing, archival and protection of neuroimaging data.
  • Computational resources: Through a collection of complementary NIH grant mechanisms, LONI has sought to provide high-end computational servers, storage and networking facilities, which include Grid server, Gigabit network, Data Immersive Visualization Environment (DIVE) as well as brain tissue preparation, genetics, and microscopy laboratory space.


Examples of the brain mapping research conducted at LONI include:

Alzheimer's disease: Investigating structural, functional, metabolic and pathological changes triggered by Alzheimer's disease. LONI research focuses on characterizing the timecourse of pathology in the AD brain.

  • Alzheimer’s Disease Neuroimaging Initiative (ADNI): ADNI is a global effort to develop biomarkers, treatments or prevention strategies for Alzheimer’s disease through research collaboration and data sharing. Clinical, imaging, genetic and behavioral data from this multisite longitudinal study are housed within LONI’s Image and Data Archive.
  • Global Alzheimer’s Association Interactive Network (GAAIN): The Global Alzheimer’s Association Interactive Network (GAAIN) advances research into the causes, prevention and treatment of Alzheimer’s and related neurodegenerative diseases through a global cooperative of sharing, investigation and discovery. The first open-access federated AD data discovery platform of its kind, the GAAIN platform allows researchers to find genetic, imaging, clinical and other data collected across many studies and perform preliminary analyses, while allowing providers to maintain ultimate control of their data.
  • Other Alzheimer’s research at LONI includes cognitive and physical interventions in virtual reality; metabolic risk assessment; mouse models; research into the vascular basis of dementia; gender differences; role of the brain stem; and connectivity mapping.

Epilepsy Bioinformatics Study for Antiepileptogenic Therapy (EpiBioS4Rx): EpiBioS4Rx is a five-year NIH-funded collaboration that unites researchers from USC, UCLA, University of Melbourne, University of Eastern Finland, and the Albert Einstein College of Medicine. The project seeks to prevent or cure posttraumatic epilepsy. LONI’s primary role in the study involves the harmonization and processing of data.[10]

Parkinson’s disease: LONI is a key contributor to the Parkinson’s Progression Marker’s Initiative (PPMI), the Michael J. Fox Foundation’s flagship biomarker study, which seeks to identify biomarkers of Parkinson’s disease. The study includes a shared database where researchers can access a repository of longitudinal data from more than 1,000 participants at 33 clinical sites across the United States, Europe, Israel and Australia.

Enhancing Neuro Imaging Genetics through Meta-Analysis (ENIGMA): The ENIGMA Consortium, co-founded by Paul M. Thompson, performs some of the largest-ever studies of the human brain, analyzing brain scans of more than 50,000 people worldwide. This collaborative group studies 22 brain diseases in 37 countries, focusing on the interaction between brain health and genetics. ENIGMA has published some of the largest-ever neuroimaging studies of schizophrenia, major depression, bipolar disorder, epilepsy and obsessive-compulsive disorder.[11]

Human Connectome Project (HCP): The HCP is a multiyear multisite collaboration that aims to provide an unparalleled compilation of neural data and an interface to graphically navigate this data. HCP researchers are mapping the brain’s major pathways, circuits, regions, and functions. One of the project’s two consortia comprises LONI and the Martinos Center for Biomedical Imaging at Massachusetts General Hospital; the two centers are responsible for acquiring and processing imaging data, as well as developing novel algorithms for analysis and graphical means for interactively navigating brain connectivity.[12]

Mouse Connectome Project (MCP): The MCP, funded by NIH, aims to create a complete mesoscale connectivity atlas of the mouse brain and to generate its global neural networks. Using fluorescent dyes as tracers and novel computational informatics tools for analysis, the project has already provided researchers with a better understanding of how various brain structures organize into networks and communicate with one another. The MCP team includes neuroanatomists, computer scientists, and web programmers.[13] Ongoing activities include:

  • Atlasing of the C57BL/6J mouse brain
  • Neuronal white matter tract tracing in mice

Normal brain development and neurodevelopmental disorders: LONI development efforts have focused on assessing structural brain changes by mapping anatomical growth and pruning associated with both normal and abnormal brain development during infancy, childhood and adolescence.

Additional ongoing projects explore:

  • Schizophrenia: Mapping heritability and effect of risk genes on structural features in the brain
  • Optical Intrinsic Signal Imaging: LONI contributes to the mapping of the brain by measuring intrinsic activity-related changes in tissue reflectance.
  • Mathematical modeling
  • Neuroscience databasing, for instance in the LONI Image and Data Archive
  • Applications of Grid computing in the neurosciences

Recent Findings[edit]

APOE ε4 allele and Alzheimer’s disease: Using data from nearly 58,000 participants via the Global Alzheimer’s Association Interactive Network (GAAIN), LONI researchers Arthur W. Toga, Scott Neu and Judy Pa reexamined the link between age, gender and Alzheimer’s disease. Caucasian men and women with the allele were equally likely to develop the disease, except for the decade between the ages of 65 and 75, when women have an increased risk. This finding has reversed the long-standing view that women have a higher risk of developing Alzheimer’s at any age, and is relevant to future Alzheimer’s research and clinical interactions. The study was published in the Journal of the American Medical Association Neurology in August 2017.[14]

7T MRI and Cushing’s disease: LONI researchers Meng Law and Arthur W. Toga, along with Keck School of Medicine of USC neurosurgeon Gabriel Zada, administered the first 7T MRI scan of a Cushing’s patient in the United States[15]. The disease is characterized by pituitary microadenomas, which are often impossible to visualize with 1.5T or 3T MRI scans. Law, Toga and Zada were able to successfully visualize the tumor at 7T; the patient subsequently received surgery and is in remission. The case was published in the Journal of Neurosurgery in March 2018.[16]

Training and Outreach[edit]

LONI is engaged in regular outreach and training efforts, including hosting seminars and ongoing programs for high school, undergraduate and graduate students as well as post-docs and visiting scientists.

Master of Science in Neuroimaging and Informatics (NIIN): This premier master’s program, run by LONI and the INI, teaches students about brain structure and function, neuroimaging and the associated informatics. Students complete hands-on MRI training with the institute’s state-of-the-art scanners and develop expertise in computational methods for processing, analyzing and mining brain imaging data. The one-year program prepares students for careers in biomedicine, and graduates of the program continue on to medical school, competitive PhD programs or jobs in the industry.

Big Data to Knowledge programs (funded by the NIH BD2K initiative)[17]: The Big Data for Discovery Science Center (BDDS) is composed of leaders in biomedical imaging, computer science, genetics and proteomics. BDDS aims to accelerate data-driven knowledge discovery, provide an innovative array of training and assist leaders with managing and delivering large-scale biomedical projects. The Training Coordinating Center (TCC) provides tools and programs to assist in the education and training of big data biomedical scientists. TCC hosts an weeklong annual seminar, the Data Science Innovation Lab[18]; oversees the “RoAD TRIP” mentorship program and compiles and maintains the Educational Resource Discovery Index (ERuDIte) of educational content, including more than 10,000 videos, documents, assignments, books and courses about biomedicine and data science.


Arthur W. Toga is the director of LONI and the associate director of the USC Mark and Mary Stevens Neuroimaging and Informatics Institute. He is also a provost professor of ophthalmology, neurology, radiology, engineering and psychiatry and the behavioral sciences at the Keck School of Medicine of USC and the Ghada Irani Chair in neuroscience. Toga received his PhD from St. Louis University and has performed decades of groundbreaking research on neuroimaging, informatics, brain structural and functional mapping and brain atlasing. He has also helped answer some of the fundamental questions about eye disease and its relationship to central visual processing.[19]

Paul M. Thompson is the associate director of the USC Mark and Mary Stevens Neuroimaging and Informatics Institute, the director of the Imaging Genetics Center and professor of ophthalmology, neurology, radiology, engineering and psychiatry and the behavioral sciences at the Keck School of Medicine of USC. He received his PhD in neuroscience from UCLA, and has performed key research on the genetic, mathematical, computer science and clinical aspects of neuroimaging and brain mapping. Thompson directs the worldwide ENIGMA consortium and has published some of the largest studies of brain diseases such as HIV, schizophrenia and depression.[20]

See also[edit]


  1. ^ "USC Stevens Hall for Neuroimaging officially opens its doors - USC News". Retrieved 2018-04-05. 
  2. ^ Gordon, Larry. "USC brain research institute gets $50-million gift". Retrieved 2018-04-05. 
  3. ^ "Photo Gallery: USC Stevens Hall Installs the First Next-Generation 7T MRI Machine in North America". Retrieved 2018-04-05. 
  4. ^ "The world's largest set of brain scans are helping reveal the workings of the mind and how diseases ravage the brain". Science | AAAS. 2018-01-23. Retrieved 2018-04-05. 
  5. ^ "Brain cell study at USC gets $19 million National Institutes of Health grant - USC News". Retrieved 2018-04-05. 
  6. ^ "Leader in brain imaging joins USC Stevens Neuroimaging and Informatics Institute | Keck School of Medicine of USC". Retrieved 2018-04-05. 
  7. ^ "Anatomical Tracings of Lesions After Stroke (ATLAS)". Retrieved 2018-04-05. 
  8. ^ "How Virtual Avatars Help Stroke Patients Improve Motor Function". PCMAG. Retrieved 2018-04-05. 
  9. ^ "'Baby Driver,' 'Mr. Roosevelt' Top SXSW Audience Award Winners". Retrieved 2018-04-05. 
  10. ^ "$21.7 million spurs USC research on how epilepsy develops - USC News". Retrieved 2018-04-05. 
  11. ^ "The world's largest set of brain scans are helping reveal the workings of the mind and how diseases ravage the brain". Science | AAAS. 2018-01-23. Retrieved 2018-04-05. 
  12. ^ "Mapping the Human Connectome". The Scientist. Retrieved 2018-04-05. 
  13. ^ "Mouse Connectome Project Archives - Huntington's Disease News". Huntington's Disease News. Retrieved 2018-04-05. 
  14. ^ Neu, Scott C.; Pa, Judy; Kukull, Walter; Beekly, Duane; Kuzma, Amanda; Gangadharan, Prabhakaran; Wang, Li-San; Romero, Klaus; Arneric, Stephen P. (2017-10-01). "Apolipoprotein E Genotype and Sex Risk Factors for Alzheimer Disease". JAMA Neurology. 74 (10). doi:10.1001/jamaneurol.2017.2188. ISSN 2168-6149. 
  15. ^ "USC's 7 Tesla MRI scanner first to identify Cushing's disease in US patient". Health Imaging. Retrieved 2018-04-05. 
  16. ^ Law, Meng; Wang, Regina; Liu, Chia-Shang J.; Shiroishi, Mark S.; Carmichael, John D.; Mack, William J.; Weiss, Martin; Wang, Danny J. J.; Toga, Arthur W. (2018-03-23). "Value of pituitary gland MRI at 7 T in Cushing's disease and relationship to inferior petrosal sinus sampling: case report". Journal of Neurosurgery: 1–5. doi:10.3171/2017.9.JNS171969. ISSN 0022-3085. 
  17. ^ "Big Data to Knowledge | NIH Common Fund". Retrieved 2018-04-05. 
  18. ^ "USC-led data science workshop coaches and connects early-career researchers". HSC News. Retrieved 2018-04-05. 
  19. ^ "LinkedIn: Arthur W. Toga". 
  20. ^ "LinkedIn: Paul M. Thompson". 

External links[edit]

Coordinates: 34°4′2″N 118°26′36″W / 34.06722°N 118.44333°W / 34.06722; -118.44333