1. No category

BIOGRAPHICAL SKETCH
Provide the following information for the Senior/key personnel and other significant contributors.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.
NAME
POSITION TITLE
Berkin Bilgic
Postdoctoral Research Fellow
eRA COMMONS USER NAME (credential, e.g., agency login)
BBILGIC
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and
residency training if applicable.)
DEGREE
INSTITUTION AND LOCATION
MM/YY
FIELD OF STUDY
(if applicable)
Bogazici University, Turkey
B.S.
06/08
Electrical and
Electronics Engineering
Bogazici University, Turkey
B.S.
06/08
Physics
Massachusetts Institute of Technology, MA
S.M.
02/10
Electrical Engineering
and Computer Science
Massachusetts Institute of Technology, MA
Ph.D.
02/13
Electrical Engineering
and Computer Science
Postdoctoral
02/13 to
date
Massachusetts General Hospital, MA
Medical Imaging/
Neuroscience
A. Personal Statement
My research focuses on the development of novel data acquisition and reconstruction methods that increase
the efficiency of MRI through the combination of MR physics, signal processing, and numerical optimization. By
fully harnessing the hardware capabilities of MR scanners, I aim to develop accelerated protocols that will help
us study the human physiology in finer detail than previously possible. I am pursuing this goal on two fronts:
1) Develop WAVE-CAPI acquisition/reconstruction for highly accelerated imaging.
Modern MR scanners are equipped with multiple receivers that are sensitive to signals arising from their
vicinity. Such difference in sensitivity can be used for reconstructing images from sub-sampled acquisitions,
thereby reducing the scan time. Due to physical limits of multi-channel receivers, pushing the acceleration
factor beyond 3 through conventional methods degrades the image quality. I am developing the Wave-CAIPI
technique that enables 10-fold acceleration with low image artifact and noise amplification penalties.
Wave-CAIPI has already been incorporated into the 3D gradient echo (GRE) acquisition sequence, which is
the main protocol used for Quantitative Susceptibility Mapping (QSM) and Susceptibility Weighted Imaging
(SWI). These modalities allow investigation of the magnetic susceptibility of the brain tissue, and facilitate
monitoring neurodegenerative diseases. Wave-CAIPI allows full-brain imaging at 1 mm isotropic voxel size in
two minutes with retained SNR values close to 100%. Since it requires no additional hardware, I will be able
to disseminate this method to any scan site by distributing the software.
2) Investigate white matter connectivity at high resolution through tissue susceptibility anisotropy.
The observed susceptibility of the brain tissue depends on the orientation of the head relative to the main
magnetic field. If susceptibility distribution is modeled as a tensor, it can be estimated by acquiring GRE data at
multiple orientations by rotating the head. This modality is termed Susceptibility Tensor Imaging (STI), and
requires data collected at 12 or more head positions. I aim to optimize a 1-minute whole-brain GRE exam at
1.5 mm isotropic resolution through Wave-CAIPI acceleration, thereby enabling a 12-minute STI exam. This
will render STI clinically feasible for the first time, which has been limited to research studies so far.
B. Research and/or Professional Experience:
Employment
02/07 – 06/07
Student Assistant, Bogazici University, Turkey
Supervisor: Prof. Taylan Akdogan
06/07 – 08/07
01/09 – 01/10
02/10 – 06/10
02/10 – 02/13
02/13 to date
Research Intern, Institute for Quantum Optics & Quantum Information (IQOQI), Austria
Supervisor: Prof. Anton Zeilinger
Research Assistant, Massachusetts Institute of Technology, Cambridge, MA
Supervisor: Prof. Berthold K. P. Horn
Teaching Assistant, Massachusetts Institute of Technology, Cambridge, MA
Supervisor: Prof. William T. Freeman
Research Assistant, Massachusetts Institute of Technology, Cambridge, MA
Supervisor: Prof. Elfar Adalsteinsson
Research Fellow, A. A. Martinos Center for Biomedical Imaging, Charlestown, MA
Supervisor: Prof. Kawin Setsompop
Honors
2004
2004
2004-2008
2008
2008
2008-2009
2011-2012
2012
2012-2013
2013
2013
2014
2014
Ranked 1st among Class of 2004, Izmir Science High School
Ranked 56th out of 1.8 million candidates in the University Entrance Exam, Turkey
Prime Ministry Scholarship, Turkey
Ranked 1st in the Faculty of Engineering among Class of 2008, Bogazici University
Ranked 1st in the double major program among Class of 2008, Bogazici University
DuPont – MIT Presidential Fellowship
CIMIT – MIT Medical Engineering Fellowship
MICCAI Young Scientist Award Finalist
ISMRM Educational Stipend
ISMRM Magna Cum Laude Merit Award
ISMRM Summa Cum Laude Merit Award
ISMRM Power Poster Award for top 2% conference abstracts
ISMRM Summa Cum Laude Merit Awards for two abstracts
Professional Societies and Public Advisory Committees
Membership:
International Society of Magnetic Resonance in Medicine (ISMRM)
Medical Image Computing and Computer Assisted Intervention (MICCAI) Society
Reviewer:
Journals: NeuroImage, Magnetic Resonance in Medicine, Frontiers in Human Neuroscience, American
Journal of Neuroradiology, Journal of American Aging Association, IEEE Transactions on Image
Processing, IEEE Signal Processing Letters
Conferences: ISMRM 2012, MICCAI 2012 and 2013, International Workshop on MRI Phase Contrast &
Quantitative Susceptibility Mapping 2013, IEEE Conference on Intelligent Transportation Systems 2010
and 2011
C. Journal Publications
1. B. Bilgic, V.K. Goyal, E. Adalsteinsson; Multi-contrast Reconstruction with Bayesian Compressed Sensing;
Magnetic Resonance in Medicine 66.6 (2011): 1601-1615.
2. B. Bilgic, A. Pfefferbaum, T. Rohlfing, E.V. Sullivan, E. Adalsteinsson; MRI Estimates of Brain Iron
Concentration in Normal Aging Using Quantitative Susceptibility Mapping; NeuroImage 59.3 (2012): 26252635.
3. B. Bilgic, K. Setsompop, J. Cohen-Adad, A. Yendiki, L.L. Wald, E. Adalsteinsson;Accelerated Diffusion
Spectrum Imaging with Compressed Sensing using Adaptive Dictionaries; Magnetic Resonance in
Medicine 68.6 (2012): 1747-1754.
4. B. Bilgic, B. Gagoski, T. Kok, E. Adalsteinsson; Lipid Suppression in CSI with Spatial Priors and Highly
Undersampled Peripheral k-space; Magnetic Resonance in Medicine 69.6 (2013): 1501-1511
5. B. Bilgic, I. Chatnuntawech, K. Setsompop, S.F. Cauley, L.L. Wald, E. Adalsteinsson; Fast Diffusion
Spectrum Imaging Reconstruction with Trained Dictionaries; IEEE Transactions on Medical Imaging 32.11
(2013): 2022-2033
6. B. Bilgic, I. Chatnuntawech, A.P. Fan, K. Setsompop, S.F. Cauley, L.L. Wald, E. Adalsteinsson; Fast
Image Reconstruction with L2-Regularization; Journal of Magnetic Resonance Imaging, DOI:
10.1002/jmri.24365
7. A.P. Fan, B. Bilgic, L. Gagnon, T. Witzel, H. Bhat, B.R. Rosen, E. Adalsteinsson; Quantitative
Oxygenation Venography from MRI Phase; Magnetic Resonance in Medicine, DOI: 10.1002/mrm.24918
8. B. Bilgic, A.P. Fan, J.R. Polimeni, S.F. Cauley, M. Bianciardi, E. Adalsteinsson, L.L. Wald, K.
Setsompop; Fast Quantitative Susceptibility Mapping with L1-Regularization and Automatic Parameter
Selection; Magnetic Resonance in Medicine, DOI: 10.1002/mrm.25029
9. I. Chatnuntawech, B. Gagoski, B. Bilgic, S.F. Cauley, K. Setsompop, E. Adalsteinsson; Accelerated MRSI
Using Randomly Undersampled Spiral-Based k-Space Trajectories; submitted to Magnetic Resonance in
Medicine
10. S.F. Cauley, Y. Xi, B. Bilgic, J. Xia, E. Adalsteinsson, V.R. Balakrishnan, L. L. Wald, K. Setsompop; Fast
Reconstruction for Multi-channel Compressed Sensing Using a Hierarchically Semiseparable Solver;
Magnetic Resonance in Medicine, DOI: 10.1002/mrm.25222
11. B. Bilgic, B. Gagoski, S.F. Cauley, A.P. Fan, J.R. Polimeni, P.E. Grant, L.L. Wald, K. Setsompop; WaveCAIPI for Highly Accelerated 3D Imaging; accepted for publication in Magnetic Resonance in Medicine
D. Selected Conference Contributions (out of 32)
1. B. Bilgic, A.P. Fan, E. Adalsteinsson; Quantitative Susceptibility Map Reconstruction with Magnitude Prior;
International Society for Magnetic Resonance in Medicine 19th Scientific Meeting, Montreal, Canada, 2011,
p. 746. Oral Presentation
2. B. Bilgic, V.K. Goyal, E. Adalsteinsson; Joint Bayesian Compressed Sensing for Multi-contrast
Reconstruction; International Society for Magnetic Resonance in Medicine 19th Scientific Meeting,
Montreal, Canada, 2011, p. 71. Oral Presentation
3. B. Bilgic, B. Gagoski E. Adalsteinsson; Lipid Suppression in CSI with Highly-Undersampled Peripheral kspace and Spatial Priors; International Society for Magnetic Resonance in Medicine 20th Scientific
Meeting, Melbourne, Australia, 2012, p. 4455. Poster Presentation
4. B. Bilgic, E. Adalsteinsson; Joint Bayesian Compressed Sensing with Prior Estimate; International Society
for Magnetic Resonance in Medicine 20th Meeting, Melbourne, Australia, 2012, p. 75. Oral Presentation
5. B. Bilgic, K. Setsompop, J. Cohen-Adad, V. Wedeen, L. Wald, E. Adalsteinsson; Accelerated Diffusion
Spectrum Imaging with Compressed Sensing using Adaptive Dictionaries; 15th International Conference
on Medical Image Computing and Computer Assisted Intervention, 2012; LNCS 7512:1-9. Oral
Presentation
6. B. Bilgic, I. Chatnuntawech, A.P. Fan, E. Adalsteinsson; Regularized QSM in Seconds; International
Society for Magnetic Resonance in Medicine 21st Scientific Meeting, Salt Lake City, Utah, USA, 2013, p.
168. Oral Presentation
7. B. Bilgic, I. Chatnuntawech, K. Setsompop, S.F. Cauley, L.L. Wald, E. Adalsteinsson; Fast DSI
Reconstruction with Trained Dictionaries; International Society for Magnetic Resonance in Medicine 21st
Scientific Meeting, Salt Lake City, Utah, USA, 2013, p. 58. Oral Presentation
8. B. Bilgic, I. Chatnuntawech, K. Setsompop, S.F. Cauley, L.L. Wald, E. Adalsteinsson; Fast Regularized
Reconstruction Tools for QSM and DSI; ISMRM Workshop on Data Sampling & Image Reconstruction,
Sedona, Arizona USA, 2013. Oral Presentation
9. B. Bilgic, A.P. Fan, C. Eichner, J.R. Polimeni, M. Bianciardi, E. Adalsteinsson, L.L. Wald, K. Setsompop;
Fast Reconstruction for Regularized Quantitative Susceptibility Mapping; accepted to International Society
for Magnetic Resonance in Medicine 22nd Scientific Meeting, Milan, Italy. Oral Presentation
10. B. Bilgic, B. Gagoski, S.F. Cauley, A.P. Fan, J.R. Polimeni, P.E. Grant, L.L. Wald, K. Setsompop; Rapid
QSM Acquisition with Wave-CAIPI; accepted to International Society for Magnetic Resonance in Medicine
22nd Scientific Meeting, Milan, Italy. Power Poster Presentation
E. Research Support
Current Support
N/A
Completed Support
N/A