Refaat Gabr
Department of electrical and Computer Engineering,

Johns Hopkins University, Baltimore, MD 21218. 

Tel: 443-287-1918

Email: gabr@jhu.edu

 

 

refaat.JPG

Welcome to my home page
I am a PhD student at the Department of Electrical and Computer Engineering at Johns Hopkins University. I work with Prof. Paul Bottomley at the Division of Magnetic Resonance, Department of Radiology, School of Medicine, Johns Hopkins University. My research interests are in magnetic resonance spectroscopy (MRS) and magnetic resonance imaging (MRI) methodologies.

 

Education
Cairo University, Giza, Egypt
B.Sc. in Biomedical Engineering, May 2000
Cairo University, Giza, Egypt
M.Sc. in Biomedical Engineering, 2000- 2003
Johns Hopkins University, Baltimore, MD, USA
MSE. in Electrical and Computer Engineering, 2004- 2006
Johns Hopkins University, Baltimore, MD, USA
PhD student, Electrical and Computer Engineering department, 2004-present

Expected to graduate in 2009

Resarch Intersts:

I am interested in MRS quantifications techniques and pre- and post-processing strategies to enhance the signal to noise ratio (SNR) in cardiac proton and phosphorus spectroscopy.  Accurate measurement of chemical exchange rates in saturation transfer MRS, fast imaging of the MR relaxation parameters, cardiac MRI and cardiac muscle energy metabolism are hot research areas I am currently engaged in.  I am also interested in image reconstruction methods in MRI/MRS, like gridding, partial k-space methods, dynamic imaging, parallel imaging, and suppression of ringing, motion and off-resonance artifacts.  Areas where I do not have much experience but I am looking forward to work in include diffusion weighted and diffusion tensor imaging, MR microscopy, multidimensional MRS and their applications in MRI/MRS.

 

Research Experience
Research Assistant (2004-present), Department of Electrical and Computer Engineering and the Department of Radiology, Johns Hopkins University, Baltimore, MD.  I joined the magnetic resonance research group working under the supervision of Dr. Paul Bottomley.  My research focuses on improved method for doing saturation transfer MRS to quantify energy metabolism in the heart.  The following are the research studies I participated in:

·         CircleFit: A quantification techniques for 1D spectra that quantifies the complex spectrum by fitting the real-imaginary trajectory in the complex plane of a Lorentzian peak to a circle.  An energy descent optimization of the fit error leads to a set of recursive equations that implement the circle-fitting algorithm.  By fitting the complex spectrum, there is no need for phasing.  In addition, baseline is fitted be a smooth model-free active contour (paper published in JMR).

·         Constructive averaging:  In this work, a method of combining multiple acquisitions of single voxel MRS data, is presented and analyzed.  The method phase-correct each acquisition for phase variation caused by motion.  A method for phase estimation and correction is theoretically analyzed and is shown to agree with single voxel acquisitions in the human leg and heart (paper published in MRM).

·         Off-resonance correction:  Saturation transfer MRS often suffers from errors due to spillover irradiation that affects the accuracy of the calculated reaction rates.  Because existing formulae for calculating reaction rates show biased estimates, we have developed a correction formula that reverses the systematic errors in existing formulae based on numerical simulation of the Bloch-McConnell equations.  The new correction formula successfully reduces the error in the estimates of the reaction rate constants (paper to appear in JMR).

·         Dynamic range in MRI:  In this study, the practical dynamic range of the MR signal is measured in clinical MRI exams.  We also explore the factors affecting the dynamic range in MRI and study the feasibility of fiber-optic links  for MRI signal transmission in terms of dynamic range (a manuscript in preparation).

·         Cardiac energy metabolism:  In this study we measure the energy balance in the heart by MRI and MRS.  Mechanical work done by the heart is measured by cardiac MRI and the chemical energy supply measured by MRS (work in progress).

 

Research Assistant (2000-2003), Department of Biomedical Engineering, Cairo University, Giza, Egypt.   My research focused on magnetic resonance image reconstruction techniques. This included gridding, partial data reconstruction, dynamic imaging methods, and artifact suppression techniques. I worked under the supervision of Dr. Yasser Kadah.

 

Work Experience

·         Teaching Assistant, Cairo University, Giza, Egypt (2000-2004).

·         Design Engineer, Engineering Office for Integrated Projects, Cairo, Egypt (2002-2004)

Honors and Awards

·         Top of year 2000 graduation class (130 students) at the Systems and Biomedical Engineering Department, Cairo University, Giza, Egypt.

·         Listed in Marquis Who’s Who in the World (2007).

·         Received the E.K. Zaviosky Stipend from the International Society of Magnetic Resonance In Medicine (ISMRM) to attend its scientific meeting in Seattle, WA 2006

·         Received the International Society of Magnetic Resonance In Medicine (ISMRM) to attend the ISMRM Workshop on Data Processing for MR Spectroscopy and Imaging, Warrenton VA, 2006

Publications

Peer-reviewed Journal papers

1.      Refaat E. Gabr, Michael Schar, Arthur D. Edelstein,  Dara L. Kraitchman, Paul A. Bottomley, William Edelstein "MRI dynamic range and compatibility with signal transmission media", in preparation.

2.      Refaat E. Gabr, Robert G. Weiss, Paul A. Bottomley, "Correcting reaction rate measured by saturation transfer magnetic resonance spectroscopy " Journal of Magnetic Resonance, 191(2):248-258 2008.

3.      Refaat E. Gabr, Pelin Aksit, Paul A. Bottomley, Abou-Bakr M. Youssef, Yasser M. Kadah, "Deconvolution-Interpolation Gridding (DING): Accurate Reconstruction for Arbitrary k-space Trajectories" Magnetic Resonance in Medicine, 56(6):1182-1191. 2006 

4.      Refaat E. Gabr, Shashank Sathyanarayana, Michael Schär, Robert G. Weiss, Paul A. Bottomley, " On restoring motion-induced signal loss in single-voxel magnetic resonance spectra" Magnetic Resonance in Medicine, 56(4):754-60. 2006

5.      Refaat E. Gabr, Ronald Ouwerkerk and Paul A. Bottomley, "Quantifying in vivo MR spectra with circles" Journal of Magnetic Resonance, 179(1):152-63 2006.

6.      Yasser M. Kadah, Ahmed S. Fahmy, Refaat E. Gabr, Keith Heberlein, and Xiaoping Hu. "Progressive magnetic resonance image reconstruction based on iterative solution of a sparse linear system" Int J Biomed Imag, Vol. 2006, Article ID 49378, Pages 1-9 2006.

 

Conference papers/abstracts

1.      Refaat E. Gabr, Michael Schar, Arthur D. Edelstein, Paul A. Bottomley, William Edelstein , " MRI dynamic range: theory and measurement ", Proc. ISMRM 16 th Annual Meeting , Toronto, Canada, 2008.

2.      R. E. Gabr and P. A. Bottomley, " Improving the Circle Fitting (CFIT) Performance for MRS Data Quantification",  ISMRM Workshop on Data Processing for MR Spectroscopy and Imaging, Warrenton VA, 2006.

3.      R. E. Gabr, R. Ouwerkerk, P. A. Bottomley, "CFIT: A novel circle-fitting approach to spectral analysis", Proc. ISMRM 14 th Annual Meeting , Seattle, WA, 2006.

4.      R. E. Gabr, P. Aksit, P. A. Bottomley, A. M. Youssef, Y. M. Kadah, "Iterative Deconvolution-Interpolation Gridding", Proc. ISMRM 14 th Annual Meeting , Seattle, WA, 2006. 

5.      R. E. Gabr, M. Schär, S. Sathyanarayana, R. G. Weiss, P. A. Bottomley, "Predicting SNR gains from constructive averaging of proton spectra: theory and practice", Proc. ISMRM 14 th Annual Meeting , Seattle, WA, 2006.

6.      H. M. Ahmed, R. E. Gabr, K. Heberlein, X. Hu and Y. M. Kadah , "New strategy for simultaneous suppression of intra- and inter-slice motion" Proc. ISMRM 11 th Annual Meeting , Toronto, p. 1060, May 2003.

7.      Haitham M. Ahmed, Refaat E. Gabr, Abou-Bakr M. Youssef, Keith Heberlein, Xiaoping P. Hu and Yasser M. Kadah , "Combined intra- and inter-slice motion artifact suppression in magnetic resonance imaging" Proc. SPIE Medical Imaging 2003 , San Diego, February 2003.

8.      R. ElSayed*, T. A. Youssef, A. M. Badawi, "Localization of Face Features Using Pulse-Coupled Neural Network and Active Contour" IEEE, International Conference on Industrial Electronics, Technology and Automation IETA2001

 

Membership

·         ISMRM student member since 2006

·         ASBEB: Arab society of biomedical engineering and biotechnology 2005