Nelson Lab People

Jason Crane

Crane, JasonDirector of Informatics and Software
[email protected]



Manager Scientific Software Development

Undergraduate Education

BA Chemistry, Brandeis University 

Graduate Education

PhD Chemistry, University of California Berkeley

Role in the lab

Design and development of software systems for data analysis and management.

Current project

My current efforts are focused on development of the open-source SIVIC software package for analysis and visualization of MR spectroscopy data.

Recent Publication

Ozturk-Isik E., Chen A.P., Crane J.C., Bian W., Xu D. Han E.T., Chang S.M., Vigneron D.B., Nelson S.J. 3D Sensitivity Encoded Ellipsoidal MR Spectroscopic Imaging of Gliomas at 3T. J. Magnetic Resonance Imaging, 27(9) 1249-1257, (2009). (pdf)

Crane J.C., Nelson S.J., Erberich S.G. Service Oriented Architecture for Secure and Rapid Access to Distributed DICOM Medical Images Using HealthGrid Technology:  A Globus MEDICUS Plug-In for OsiriX PACS. (Invited to Radiographics, 2008).

Hu S., Lustig M., Chen A.P., Crane J.C., Kerr A., Kelley D.A.C., Hurd R., Kurhanewicz J., Nelson S.J., Pauly J.M., D.B. Vigneron D.B. Compressed Sensing for Resolution Enhancement of Hyperpolarized C-13 Flyback 3D-MRSI. Journal of Magnetic Resonance, 192(2) 258-264, (2008). (pdf)

Li Y., Chen A.P., Crane J.C., Chang S.M., Vigneron D.B., Nelson S.J. Three-dimensional, J-resolved H-1 magnetic resonance spectroscopic imaging of volunteers and patients with brain tumors at 3 T. Magnetic Resonance in Medicine, 58(5) 886-892 (2007). (pdf)

Li Y., Osorio J.A., Ozturk-Isik E., Chen A.P., Xu D., Crane J.C., Cha S., Chang S., Berger M.S., Vigneron D.B., Nelson S.J. Considerations in applying 3D PRESS H-1 brain MRSI with an eight-channel phased-array coil at 3 T. Magnetic Resonance Imaging, 24(10), 1295-1302 (2006). (pdf)

Crane J.C., Crawford F.W., Nelson J. Grid Enabled Magnetic Resonance Scanners for Near Real-Time Medical Image Processing, Journal of Parallel and Distributed Computing, 66(12), 1524-1533 (2006). 

Ozturk E, Crane JC, Chang SM, Berger MS, Nelson SJ.  Unaliasing Lipid Contamination for MR Spectroscopic Imaging of Gliomas at 3T Using Sensitivity Encoding (SENSE). Magn Reson. Med. 55(5), 1164-1169 (2006). (pdf)

Adam Elkhaled

Elkhaled, AdamPost-doctoral Fellow
ad[email protected]



Undergraduate Education

UC San Diego, Bioengineering

Graduate Education

UC Berkeley/ UC San Francisco Joint Graduate Group in Bioengineering

Role in the lab

Ex vivo proton high-resolution magic angle spinning (1H HR-MAS) spectroscopic characterization of infiltrating glioma as a means of discerning relevant disease biomarkers

Development of in vivo whole-brain short-echo 1H MRS acquisitions

Analysis of serially-acquired MRS patient data

Current project

Implementation of an in vivo Carr-Purcell-Meiboom-Gill (CPMG)-based PRESS sequence optimized for the detection of myo-inositol at 3T, with application for distinguishing treatment effect (reactive astrogliosis) from tumor in patients with recurrent GBM

Recent Publications

A. Elkhaled, L. Jalbert, A. Constantin, H. Yoshihara, R. Srinivasan, S.M. Chang, S. Cha, and S.J. Nelson. Characterization of Metabolites in Infiltrating Gliomas using Ex vivo 1H HR-MAS Spectroscopy. NMR in Biomedicine  27(5): 578-593, 2014.

A. Elkhaled, L. Jalbert, J. Phillips, H. Yoshihara, R. Srinivasan, G. Bourne, S.M. Chang, S. Cha,   and S.J. Nelson. Magnetic Resonance of 2-Hydroxyglutarate in IDH1-Mutated Low-Grade Gliomas. Sci Transl Med. 4, 116ra5, 2012

Yan Li

Li, YanAssistant Researcher
[email protected]


Undergraduate Education

Bachelor of Medicine, Shanghai Second Medical University, Shanghai, China

MSc, Biochemistry, McGill University, QC, Canada

PhD, Bioengineering, UCSF/UC Berkeley Joint Graduate Group in Bioengineering, San Francisco, CA, USA

Role in the lab

Conducting research

Current project

Developing and implementing an optimal acquisition parameters and quantification methods for Magnetic Resonance Spectroscopic Imaging (MRSI) at 7 Tesla in patients with gliomas.

Recent Publications

Li Y., Lupo J.M., Polley M.Y., Crane J.C., Bian W., Cha S., Chang S.M., Nelson S.J., Serial Analysis of imaging parameters in patients with newly diagnosed Glioblastoma Multiforme. Neuro-Oncology, accepted with minor revision, 2010. 

Xu D., Cunningham C.H., Chen A.P., Li Y., Kelly D.A.C., Mukherjee P., Pauly J.M., Nelson S.J., Vigneron D.B., Phased array 3D MR spectroscopic imaging of the brain at 7 T. Magn Reson Imaging, 2008; 26(9):1201-1206. (pdf)

Li Y., Srinivasan R., Ratiney H., Lu, Y., Chang S., Nelson, S.J., Comparison of T1 and T2 metabolite relaxation times in gliomas and normal brain at 3 T. J. Magn Reson Imaging. 2008; 28(2):342-350. (pdf)

Li Y., Chen A.P., Crane J.C., Change S.M., Vigneron D.B., Nelson S.J., Three-dimensional J-resolved H-1 magnetic resonance spectroscopic imaging of volunteers and patients with brain tumors at 3 T. Magn Reson Med. 2007; 58(5):886-892. (pdf)

Li Y., Osorio J.A., Ozturk-Isik E., Chen, A.P., Xu D., Crane J.C., Cha S., Chang S.,  Berger M.S., Vigneron D.B., Nelson S.J., Considerations in applying 3-D PRESS H-1 brain MRSI with an eight-channel phased-array coil at 3 T. Magn Reson. Imaging.  2006; 24(10):1295-1302 (pdf)

Beck Olson

Olson, Beck

Programmer Analyst IV
[email protected]


Undergraduate Education

BS Physics with Specialization in Computational Physics

Role in the lab

Help to maintain the lab's software base and to develop new software for processing, analysis, visualization, and management of imaging data. 

Current projects

  • SIVIC: An Extensible Open-Source DICOM MR  Spectroscopy Software Framework and Application Suite. (
  • Cerebro: The Nelson Lab's Research Database.

II Woo Park

Park, Il Woo

Postdoctoral Scholar
[email protected]


Undergraduate Education

UC Berkeley, Bioengineering

Graduate Education

UC San Francisco/UC Berkeley Joint Graduate Group in Bioengineering

Role in the lab

Maintaining and managing animal-related protocols and studies

Processing and analyzing 13C clinical data

Mentoring undergraduate and graduate students 

Current project

Development of an early biomarkers for MGMT activity and response to Temozolomide treatment using DNP-Hyperpolarized 13C MR Spectroscopic Imaging

Recent Publications

Park I, Chen AP, Zierhut ML, Ozturk-Isik E, Vigneron DB, Nelson SJ. Implementation of 3 T Lactate-Edited 3D 1H MR Spectroscopic Imaging with Flyback Echo-Planar Readout for Gliomas Patients. Ann Biomed Eng. 2010 Jul 23. [Epub ahead of print] (pdf)

Park I, Larson P, Zierhut ML, Hu S, Bok R, Ozawa T, VandenBerg SR, Kurhanewicz J, Vigneron DB, James CD, Nelson SJ. Hyperpolarized 13C MR Metabolic Imaging: Application to Brain Tumors. Neuro Oncol. 2010 Feb;12(2):133-44. (pdf)

Zierhut ML, Yen Y-F, Chen AP, Bok R, Albers MJ, Zhang V, Tropp J, Park I, Vigneron DB, Kurhanewicz J, Hurd RE, Nelson SJ. Kinetic Modeling of Hyperpolarized 13C1-Pyruvate Metabolism in Normal Rat Kidneys and TRAMP Mice. J Magn Reson. 2010 Jan;202(1):85-92. (pdf)

Zierhut ML, Ozturk-Isik E, Chen AP, Park I, Vigneron DB, Nelson SJ. 1H spectroscopic imaging of human brain at 3 Tesla: comparison of fast three-dimensional magnetic resonance spectroscopic imaging techniques. J Magn Reson Imaging. 2009 Sep;30(3):473-80. (pdf)

Yen Y-F, Kohler SJ, Chen A, Tropp J, Bok R, Zhang V, Albers M, Zierhut ML, Park I, Nelson SJ, Vigneron D, Kurhanewicz J, Hurd RE. Imaging Considerations for In Vivo 13C Metabolic Mapping Using Hyperpolarized 13C-pyruvate. Magn Reson Med. 2009 Jul;62(1):1-10. (pdf)

Park I, Tamai G, Lee MC, Chuang CF, Chang SM, Berger MS, Nelson SJ, Pirzkall A. Patterns of Recurrence Analysis in newly diagnosed GBM following 3D Conformal Radiation Therapy with respect to Pre-RT MR Spectroscopic Findings. Int J Radiat Oncol Biol Phys. 2007 Oct 1;69(2):381-9. (pdf)

Maryam Vareth

Vareth, MaryamResearch Data Analyst
[email protected]



 Undergraduate Education

Electrical Engineering and Computer Science, University of California Berkeley

Graduate Education

Electrical Engineering and computer Science, University of California Berkeley

Bioengineering, University of California, Berkeley and San Francisco (Joint Graduate Group)

Role in the lab

Data Analyst

Current project 

Design and development of techniques for acquisition, reconstruction, post-processing and quantitative analysis of multi-channel, phased array detectors for high field Magnetic Resonance Spectroscopy imaging (MRSI) with the goal of improving the sensitivity and specificity of the data obtained for characterizing human disease.