Imaging Research for Neurodevelopment

Imaging Research for Neurodevelopment

Led by Dr. Duan Xu, the Imaging Research for Neurodevelopment Lab at UCSF focuses on early detection of abnormal development in newborns. To achieve this goal, the researchers in Dr. Xu's lab develop dedicated MRI hardware, pulse sequences, and postprocessing techniques. These methods are then applied to the Premri, Bamri, and Cardiac cohorts to further elucidate neurodevelopment of the neonatal brain:



Currently there is no way to predict developmental outcomes in babies that suffer brain injury as a result of prematurity. The goal of this study is to see if we can identify a relationship between the findings on a baby's MRI scan and his or her long term neurological and developmental outcome.


This study explores hypoxic-ischemic brain injury in term new born infants. Hypoxic Ischemia Encephalopathy is a type of injury caused by lack of oxygen and/or blood supply which can occur before or during birth.


The focus of this study is to determine if the aforementioned techniques can help detect brain injury in babies undergoing surgery for congenital heart disease.


Our group is working with the Hyperpolarized Technology Resource Center to employ advanced C13 spectroscopy to study the metabolism of brain injury in rodents.


Compact 7T

Imaging for Neurodevelopment is partnering with GE and the Mayo Clinic to develop and test the next big development in advanced brain imaging: Lightweight, Compact, Low-Cryogen Head-Only 7T MRI. Delivering powerful imaging capability in a small footprint, this technology represents a tremendous step towards bringing high-field imaging to more clinical and research settings.

Machine Learning

Can machine learning approaches improve how we gather, learn and predict with our infant MRI data? Our group is working to implement the latest advances in machine learning powered image reconstruction, processing and analysis.


Structural Baby ConnectomeStructural Baby Connectome

The goal of this project is to establish a framework for assessing structural connectivity in the newborn brain at any stage of development, starting with premature neonates, and to characterize structural networks in different clinical populations. Main challenges include: data quality assurance, automated parcellation of the cortical surface, and proper analysis of network properties using graph theoretic analysis.

Contact: Olga Tymofiyeva

Oxygenation and Perfusion StudyOxygenation and Perfusion Study

This project aims to modify and apply existing ASL techniques to study neonatal cerebral perfusion to better characterize infants with Hypoxic Ischemic Encephalopathy. An additional goal is to further develop alternative MRI techniques to assess the oxygenation in the brain of a newborn and fetus.

Contact: Xin Liu

MRSI SpectroscopySpectroscopy

Studies have illustrated prognostic value in determining metabolite ratios between Lactate (Lac), N-acetyl aspartate (NAA), and Choline (CHO) from newborn infants. The goal of this project is to study neonates with signs of HIE by looking at the metabolite ratio differences between Normal and Abnormal outcome groups.  We also perform longitudinal comparisons to determine changes in metabolite ratio across outcome groups.

fMRI - NeonatalFunctional Baby Connectome

The goal of the project is to apply functional MRI technique based on BOLD mechanism to detect brain networks in babies. In order to do so, we detect temporal correlation between BOLD signals in different brain regions. In newborns, the so-called "resting state" fMRI is performed to detect the coherent spontaneous neuronal activity within a brain network.


  • Tymofiyeva O, Hess CP, Ziv E, Tian N, Bonifacio SL, McQuillen PS, Ferriero DM, Barkovich AJ, Xu D. Towards the "Baby Connectome": Mapping the Structural Connectivity of the Newborn Brain. PLoS ONE. 2012 (in press).
  • Xu D, Bonifacio SL, Charlton NN, Vaughan PC, Lu Y, Ferriero DM, Vigneron DB, Barkovich AJ. MR spectroscopy of normative premature newborns. J Magn Reson Imaging. 2011 Feb;33(2):306-311.
  • Xu D, Lee MC, Carballido-Gamio J, Barkovich MJ, Majumdar S, Vigneron DB, Nelson SJ. Quantitative analysis of spatial distortions of diffusion techniques at 3T. Magn Reson Imaging. 2010 Apr;28(3):451-454.
  • Tymofiyeva O, Hess CP, Ziv E, Lee PN, Glass HC, Ferriero DM, Barkovich AJ, Xu D. A DTI-based template-free cortical connectome study of brain maturation. PLoS ONE
  • Xu D, Cunningham CH, Chen AP, Li Y, Kelley DAC, Mukherjee P, Pauly J, Nelson SJ, Vigneron DB. Phased Array 3-D MR Spectroscopic Imaging of the Brain at 7 Tesla. Magn Reson Imaging. 2008 Nov;26(9):1201-1206.
  • Xu D, Chen AP, Cunningham C, Osorio JA, Nelson SJ, Vigneron DB. Spectroscopic imaging of the brain with phased-array coils at 3.0 T. Magn Reson Imaging. 2006 Jan;24(1):69-74.
  • Xu D, Henry RG, Mukherjee P, Carvajal L, Miller SP, Barkovich AJ, Vigneron DB. Single-shot fast spin-echo diffusion tensor imaging of the brain and spine with head and phased array coils at 1.5 T and 3.0 T. Magn Reson Imaging. 2004 Jul;22(6):751-759.


Duan Xu, PhD
Assistant Professor in Residence
[email protected]

Dr. Duan Xu is an Assistant Professor in Residence at UCSF's Department of Radiology and Biomedical Imaging.

Olga Tymofiyeva, PhD
Assistant Professional Researcher
[email protected]

Dr. Olga Tymofiyeva has worked in UCSF Radiology & Biomedical Department since May 2010. She holds her degrees in Physics (PhD, University of Wuerzburg, Germany) and Electrical Engineering (MSc, Karlsruhe University of Applied Sciences, Germany and BSc, NTUU "KPI", Kyiv, Ukraine). Dr. Tymofiyeva's current research interest lies in using MRI to study normal and abnormal brain development, as well as the effects of interventions:

Shujuan Fan, MBBS, MEd, PhD
Postdoctoral Scholar
[email protected]

Dr. Shujuan Fan joined our Imaging Research for Neurodevelopment lab in Aug, 2017. She was trained in clinical medicine (MBBS, 2005) and applied psychology (Med, 2008) at Shandong University (Jinan, China), and received her PhD in Biomedical Imaging at Dept. of Electrical and Electronic Engineering, The University of Hong Kong (Hong Kong, 2013). Dr. Fan’s current major research interest is using hyper polarized 13C MR to study brain metabolism during normal development and neonatal injuries such as ischemic stroke.

Yiran Chen, BSc
Graduate Student
[email protected]

Yiran Chen graduated with a BS degree in Physics from Welseyan College. Her current research includes post-processing of newborn images acquired by magnetic resonance imaging to investigate brain microstructures and functions during maturation. She is also involved in technical development to improve images qualities.

Justin P. Yuan, BSc
Assistant Specialist
[email protected]

Justin P. Yuan is an Assistant Specialist at UCSF Radiology & Biomedical Imaging. He obtained his BS in Physiology & Neuroscience from UC San Diego. His research interests are in the usage of MRI to characterize adolescent brain changes and the reliability of such measures.


Trevor Flynn, BA
Staff Research Associate
[email protected]

Trevor Flynn joined the Xu Lab in June 2013 after receiving his B.A. in Neuroscience from Pomona College in 2013. Trevor's interests include brain mapping and improving how MRI data is collected and processed for special experimental paradigms. In the Xu Lab Trevor collects and processes MRI data from infants in the Bamri, Premri, and Cardiac studies and investigates the variability of functional connectivity in these populations.



Artan Kaso, PhD
Postdoctoral Scholar
[email protected]



Liz Phillips, BSc
Former Junior Specialist
[email protected]

Liz Phillips graduated with a BA in Biology (Minor: Chemistry) from the University of Utah, where she was involved in pre-clinical research of stem cell treatments for kidney disease and diabetes for seven years, and clinical research using PET/CT to detect brown adipose tissue for two years. She joined the Xu Lab in January 2015, where her research includes the post-processing of spectroscopic data acquired in preterm newborns to study metabolic changes over the course of development. Her research interests included pediatric imaging, cancer imaging, and improving the data quality of MRI scans. Liz is currently pursuing an MD degree.

Hosung Kim, PhD
Former Postdoctoral Scholar
[email protected]

Dr. Hosung Kim developed various analytic frameworks (e.g., cortical morphometry, VBM, DBM and structural network analysis) for the assessment of brain structures in healthy controls and pathological conditions that often present anatomical variations implying the hypothesized pathophysiology.  He joined the Xu Lab in April 2014, where he expands his skill-set to the analysis of fetal/neonatal brain MRIs. He is an awardee of the 2014-2015 Banting Fellowships of Canada. Dr. Hosung Kim is currently an Assistant Professor of Neurology at the USC Keck School of Medicine.

Jiaolong Cui, PhD
Former Postdoctoral Scholar
[email protected]

Dr. Cui received his Ph.D degree in Biomedical Engineering from the University of Hong Kong in 2013. He worked as postdoctoral fellow in McLean hospital, Harvard Medical School from 2013-2014. He came to UCSF as a postdoctroal researcher in Dr. Xu's group in September 2014. His research interests were focused on using advanced MRI techniques, e.g. diffusion tensor imaging and functional MRI, to investigate the brain structural and functional maturation in newborns. Jialong is currently a member of the technical staff at Oracle.

Xin Liu, PhD
Former Postdoctoral Scholar

Xin Liu was a postdoctoral researcher in Dr. Xu's group from 2011-2014. He received his Ph.D. in Medical Physics in 2011 from the Center for Advanced Imaging Research (UCAIR) at the University of Utah, Salt Lake City, Utah. His research focused on MRI applications to detect the perfusion and oxygenation of the neonatal brain.

Patricia Lee, BSc
Former Staff Research Associate

Patricia Lee was a Staff Research Associate from 2011-2013. Her research interests were in longitudinally characterizing metabolite concentrations of hypoxic-ischemic brain injury in vivo using NMR Spectroscopy. She is currently pursuing an MD degree.


Yu Zhang, MD
Former Visiting Postdoctoral Scholar

Yu Zhang is a PhD Candidate of Orthopaedic Surgery in Jilin University of China who was a Visiting Postdoctoral Scholar in UCSF Radiology & Biomedical Department since from Dec 2011-2013. His research interests were in fMRI.


Nan Tian, MSc
Former Junior Engineer

Nan Tian received his BS and MS from Case Western Reserve University in Biomedical Engineering. His research interests were in developing a coil and MRI compatible incubator for CHDMRI, PREMRI, and BAMRI neonates. He was in Dr.Xu's lab October 2009-2012.


Jae-Seung Kim, PhD
Former Visiting Research Scientist

Dr. Kim is currently acting as a Principal Engineer in the Multimedia R&D Team of Samsung Electronics. He was a Visiting Research Scientist in Dr. Xu's lab from July 2011-2012.


Charles Vaughan, BSc, MPH
Former Staff Research Associate

Charlie is currently pursuing a career in Public Health and Medicine. He was a Staff Research Associate in the Xu lab from 2009-2010.