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.