Bilkent Electromagnetic Tissue Property (EMTP) and Biomedical Resarch Group

EMTP and BCI Research Group

Current research activities of the Electromagnetic Tissue Property (EMTP) and Brain Computer Interface (BCI) Research Group are focused on two different main subjects. One of them is the development of non-invasive electrical properties (EPs) imaging techniques using magnetic resonance imaging (MRI) which can be used for diagnostic purposes (e.g. tumor characterization) and also estimation of local specific absorption rate (SAR) distribution. EMTP and BCI Research Group is also interested in the clinical applications of EMTP mapping methods. Another focus of EMTP and BCI Research Group is to obtain high performance (accuracy and information transfer rate (ITR)) in electroencephalography (EEG) based BCI applications which provide a new way of communication between human and machines by interpreting user's brain activity in order to understand his/her intention. This includes improving the existing methods and developing novel methods. EMTP and BCI Research Group is also interested in visual cortex models and realizing practical BCI prototypes.

In our lab,

We make electromagnetic modeling and simulations of the RF and gradient coils used in MRI and their interactions with the tissue. Using these simulations, we work on developing EMTP mapping methods i.e. algorithms, and also on novel RF coil designs. We have developed the Full cr-MREPT and the Phase based cr-MREPT algorithms which have been found to be robust against internal boundary artifacts observed in other algorithms

Offline EEG analysis of one of our studies

We make offline EEG data analysis, work on BCI paradigms and Jansen-Rit Visual Cortex model and realize practical BCI prototypes.

For the experiments,

We use the 3T MRI scanner located at UMRAM in Bilkent University.

64 channel MR Compatible EEG System in UMRAM

We use 16 channel openBCI board with Ultracortex Mark III "Supernova" headset located in the Biomedical Lab and the 64 channel MR Compatible EEG System located at UMRAM in Bilkent University.

Detailed information about our studies and the ongoing projects can be found in Research and Publications.

Research

EMTP Studies

Magnetic Resonance Electrical Impedance Tomography (MREIT)

Magnetic Resonance Electrical Properties Tomography (MREPT)

Phantom experiment using 3T
MR scanner in UMRAM

Experimental result for the
conductivity (S/m) using cr-MREPT

Electromagnetic Modeling and Analysis of Tissue and MRI RF coils

Head model in a birdcage coil and electrical properties (conductivity and dielectric permittivity) of a head model in axial, coronal, and sagittal planes.

3D conductivity maps of a head
model in a birdcage coil model

3D RF magnetic field inside a head
model in a birdcage coil at 7T

BCI Studies

The outline of the activities that are in the scope of our research is:

Studies on c-VEP Paradigm
- Finding optimum input sequences that will generate separable EEG response
- Finding the optimum screen refresh rate for better information transfer rate
- Using the Jansen-Rit model to develop a new classification method
Studies on P300 Paradigm
- Fitting parametric curves to P300 waveforms to develop a new classification method
Developing a new hybrid paradigm in which P300 and c-VEP stimuli are presented simultaneously

An Example P300 Waveform
(Amiri et al. 2013)

An Illustration of cVEP Paradigm
(Kapeller et al. 2014)

Realizing a practical, asynchronous and portable BCI prototype that employs few (3) targets
- Using sinusoidal SSVEP stimuli with a novel decision method
- Using cVEP stimuli with a novel decision method
- Developing methods for monitoring the effects of attention level, mental fatigue and blinking artifacts
Validating the Jansen-Rit model of the visual cortex with recorded data in response to SSVEP and cVEP stimuli

Single Column Jansen-Rit Visual Cortex Model - Extended by Spiegler (Spiegler et al. 2010, Jansen, Rit 1995)

- Amiri, Setare, Ahmed Rabbi, Leila Azinfar, and Reza Fazel-Rezai. "A Review of P300, SSVEP, and Hybrid P300/SSVEP Brain- Computer Interface Systems." Brain-Computer Interface Systems - Recent Progress and Future Prospects (2013): n. pag. Web.

- Jansen, Ben H., and Vincent G. Rit. "Electroencephalogram and Visual Evoked Potential Generation in a Mathematical Model of Coupled Cortical Columns." Biological Cybernetics 73.4 (1995): 357-66. Web.

- Kapeller, Christoph, Kyousuke Kamada, Hiroshi Ogawa, Robert Prueckl, Josef Scharinger, and Christoph Guger. "An Electrocorticographic BCI Using Code-based VEP for Control in Video Applications: A Single-subject Study." Frontiers in Systems Neuroscience 8 (2014): n. pag. Web.

- Spiegler, Andreas, Stefan J. Kiebel, Fatihcan M. Atay, and Thomas R. Knösche. "Bifurcation Analysis of Neural Mass Models: Impact of Extrinsic Inputs and Dendritic Time Constants." NeuroImage 52.3 (2010): 1041-058. Web.

Some Ongoing and Completed Research Projects

Development of New Methods to Obtain High Performance in Electroencephalography based Brain-Computer Interfaces, TUBITAK116E153, Principal Investigator: Yusuf Ziya Ider
High Accuracy and Fast Magnetic Resonance Electrical Properties Tomography, TUBITAK114E522, Principal Investigator: Yusuf Ziya Ider, 01/04/2015-01/04/2018.
Clinical Adaptation, Further Development, and Determination of Clinical Indications of Convection-Reaction Equation based Magnetic Resonance Electrical Properties Tomography for the Diagnosis and Follow-Up of Brain Diseases

Magnetic Resonance Electrical Properties Tomography (MREPT), TUBITAK111E090, Principal Investigator: Yusuf Ziya Ider, 01/09/2011-28/02/2014.
Magnetic Resonance Electrical Impedance Tomography (MREIT) and Magnetic Resonance Current Density Imaging (MRCDI), TUBITAK107E260, Principal Investigator: Yusuf Ziya Ider, 01/02/2008-31/07/2011

Publications

2022

M. Kaan ÇAN , Y. Ziya IDER, “Bias Correction for Phase-Based cr-MREPT Using Low Resolution B1+ Magnitude”, Proceedings of QMRLUCCA: Workshop on MR phase, Magnetic Susceptibility and Electrical Properties Mapping, Lucca, Italy, 16-19 October 2022.
Yusuf Ider, “crEPT, gEPT, DBar, divergence methods: assumptions and implementation” (invited lecture), ”, Proceedings of QMRLUCCA: Workshop on MR phase, Magnetic Susceptibility and Electrical Properties Mapping, Lucca, Italy, 16-19 October 2022.

2021

Cemre Ariyurek, Bilal Tasdelen, Yusuf Ziya Ider and Ergin Atalar, (2021) “SNR Weighting for Shear Wave Speed Reconstruction in Tomoelastography”, NMR in Biomedicine, 2021;34:e4413, https://doi.org/10.1002/nbm.4413.
Safa Ozdemir , Efe Ilicak , Carmen Stutz , Mara Berger , Jascha Zapp , Lothar R. Schad , Yusuf Z. Ider , and Frank G. Zöllner, “Fast 3D Undersampled Bloch-Siegert based B Mapping for use in MREPT”, Proc. Intl. Soc. Mag. Reson. Med. 29th Annual Meeting (2021): 3780.

2020

Muhammad Nabi Yasinzai and Yusuf Ziya İder, “New approach for designing cVEP BCI stimuli based on superposition of edge responses”, IOP Publishing, Biomed. Phys. Eng. Express 6 (2020) 045018 https://doi.org/10.1088/2057-1976/ab98e7 The initial version of this paper is published in Cornell University arXiv as M. N. Yasinzai, Y. Z. Ider, “New Approach for Designing cVEP BCI Stimuli Based on Superposition of Edge Responses”, 2 April 2020, arXiv:2004.06766v1
Yusuf Ziya Ider and Merve Nur Akyer, “Properties and implementation issues of phase based cr-MRECT for conductivity imaging”, Proc. Intl. Soc. Mag. Reson. Med. 28th Annual Meeting (2020): 3190.
Cemre Ariyurek, Yusuf Ziya Ider, and Ergin Atalar, “Improving the SNR and Correcting the Bias in Elastograms in Helmholtz Inversion for MR Elastography”, Proc. Intl. Soc. Mag. Reson. Med. 28th Annual Meeting (2020): 3312.

2019

Yiğit Tuncel, Toygun Başaklar and Yusuf Ziya Ider, “A model based investigation of the period doubling behavior in human steady-state visual evoked potentials”, IOP Publishing, Biomed. Phys. Eng. Express 5 (2019) 045030 https://doi.org/10.1088/2057-1976/ab2d0b
Toygun Başaklar , Yiğit Tuncel and Yusuf Ziya Ider, “Effects of high stimulus presentation rate on EEG template characteristics and performance of c-VEP based BCIs”, IOP Publishing, Biomed. Phys. Eng. Express 5 (2019) 035023, https://doi.org/10.1088/2057-1976/ab0cee
Gokhan Ariturk and Yusuf Ziya Ider, “B1+ phase retrieval for non-quadrature radio frequency excitation and its preliminary application in MR-EPT”, IOP Publishing Phys. Med. Biol. 64 (2019) 02NT02 (11pp) https://doi.org/10.1088/1361-6560/aaf7be, accepted on 11 December 2018, published on 11 January 2019
Yusuf Ziya Ider and Celik Boga, “Inverse problem approach to cr-MREPT”, Proc. Intl. Soc. Mag. Reson. Med. 27th Annual Meeting (2019): 5052.
Safa Ozdemir and Yusuf Ziya Ider, “Estimation of transceive phase via LORE-GN algorithm and its use in MREPT”, Proc. Intl. Soc. Mag. Reson. Med. 27th Annual Meeting (2019): 5052.
Cemre Ariyurek , Bilal Tasdelen , Alireza Sadeghi-Tarakameh , Yusuf Ziya Ider , and Ergin Atalar, “Analysis and Maximization of SNR in MR Elastography Inversion”, Proc. Intl. Soc. Mag. Reson. Med. 27th Annual Meeting (2019): 3962.
Yusuf Ziya Ider, “Convection-reaction Electrical Properties Tomography”, Proceedings of 2nd International Workshop on MR-based Electrical Properties Tomography (IMEP2019), March 13-16 2019, Utrecht, The Netherlands

2018

Safa Ozdemir S, Yusuf Ziya Ider, “bSSFP phase correction and its use in magnetic resonance electrical properties tomography”, Magn Reson Med. 2019;81:934–946, https://doi.org/10.1002/mrm.27446, accepted on 12 June 2018.
Gulşah Yıldız and Yusuf Ziya Ider, "Use of dielectric padding to eliminate low convective field artifact in cr‐MREPT conductivity images". Magn Reson Med. 2019;81:3168–3184. https://doi.org/10.1002/mrm.27648, accepted on 5-12-2018
Y. Tuncel, T. Basaklar, Y. Z. Ider, "Period Doubling Behavior in Human Steady State Visual Evoked Potentials", IOP Publishing, Biomed. Phys. Eng. Express 4 (2018) 025024, https://doi.org/10.1088/2057-1976/aaa78f
G. Ariturk, Y. Z. Ider, “Optimal Multichannel Transmission for Improved cr-MREPT", IOP Publishing, Phys. Med. Biol. 63 (2018) 045001 (14pp), https://doi.org/10.1088/ 1361-6560/aaa732, accepted on 12-1-2018
Suleman Aijaz Memon, Abdul Waheed, Toygun Başaklar and Yusuf Ziya Ider, “Low-Cost Portable 4-Channel Wireless EEG Data Acquisition System for BCI Applications”, TIPTEKNO18 Tıp teknolojileri Kongresi, 8-10 Kasım 2018, Gazi Magosa, KKTC, To be published in IEEE Xplore.
Toygun Başaklar, Yusuf Ziya İder, ve Tuncel Yiğit, “Effects of High Stimulus Presentation Rate on c-VEP based BCIs”, TIPTEKNO18 Tıp teknolojileri Kongresi, 8-10 Kasım 2018, Gazi Magosa, KKTC, To be published in IEEE Xplore.
Yusuf Ziya Ider, Celik Boga, and Gulsah Yildiz, "Spatial resolution of Full cr-MREPT: 2D and 3D evaluation", Proceedings of Joint Annual Meeting ISMRM-ESMRMB, Paris, 16-21 June 2018, 5098
Safa Ozdemir and Yusuf Ziya Ider, “bSSFP Phase Correction and its use in MREPT”, Proceedings of Joint Annual Meeting ISMRM-ESMRMB, Paris, 16-21 June 2018, 5089
Gulsah Yildiz and Yusuf Ziya Ider, "LCF Artifact Elimination in cr-MREPT using Phased-Array Receive Coil", Proceedings of Joint Annual Meeting ISMRM-ESMRMB, Paris, 16-21 June 2018, 5093
Cemre Ariyurek, Bilal Tasdelen, Eric Barnhill, Arif Sanli Ergun, Yusuf Ziya Ider, and Ergin Atalar, "Usage of Octahedral Shear Strain Weights in the Inversion of Multifrequency MR Elastography", Proceedings of Joint Annual Meeting ISMRM-ESMRMB, Paris, 16-21 June 2018, 1076

2017

Oran OF, Ider YZ. "Feasibility of conductivity imaging using subject eddy currents induced by switching of MRI gradients." Magnetic Resonance in Medicine, 77:1926-1937 (2017), DOI 10.1002/mrm.26283

2016

Gurler N, Ider YZ, "Gradient-based electrical conductivity imaging using MR phase", Magnetic Resonance in Medicine, 2016 (early view) doi:10.1002/mrm.26097
Gurler N, Ider YZ, "Generalized Phase based Electrical Conductivity Imaging", ISMRM24(2016):2991
Gurler N, Oran OF, Keklikoglu HD, Ider YZ, "Application of Generalized Phase based Electrical Conductivity Imaging in the Subacute Stage of Hemorrhagic and Ischemic Strokes", ISMRM24(2016):2994
Ariturk G, Gurler N, Ider YZ, "Investigation and Reduction of the Effects of Gibbs Ringing in SSFP Phase Based MR-EPT", ISMRM24(2016):2995

2015

Gurler N, Ider YZ, "Numerical Methods and Software Tools for Simulation, Design, and Resonant Mode Analysis of Radio Frequency Bİrdcage Coils used in MRI", Concepts in Magnetic Resonance Part B, 45(1), p.13-32, Feb 2015 doi:10.1002/cmr.b.21279
Ider YZ, Gurler N, Oran OF, "Faz temelli manyetik rezonans elektriksel iletkenlik tomografisinin gürültü performansı", TMRD 2015, Ankara
Oran OF, Gurler N, Ider YZ, "Feasibility of conductivity imaging based on slice selection and readout gradient induced eddy-currents", ISMRM23(2015): 0930
Gurler N, Oran OF, Ider YZ, "Combination of Multichannel Receive Data for Local cr-MREPT", ISMRM23(2015): 3298

2014

Hafalir FS, Oran OF, Gurler N, and Ider YZ, "Convection-Reaction Equation Based Magnetic Resonance Electrical Properties Tomography (cr-MREPT), Medical Imaging, IEEE Transactions on , 33(3), p.777-793, Mar 2014 doi:10.1109/TMI.2013.2296715
Turk EA, Ider YZ, Ergun AS, and Atalar E, (2014), Approximate Fourier domain expression for Bloch–Siegert shift. Magn Reson Med. doi:10.1002/mrm.25104
Oran OF, Gurler N, Ider YZ, “A Simple Point-Wise Formula for Double Excitation MREPT Suitable for Reconstructing Boundaries”, ISMRM22(2014): 3250
Gurler N, Oran OF, Ider YZ, “cr-MREPT Using Multichannel Receive Coil”, ISMRM22(2014): 3247
Ariyurek C, Ider YZ., Gurler N, Ozdemir S, Emek A, Ergun AS, Atalar E, “Modes of Shear Waves in Brain MR Elastography”, ISMRM22(2014): 4270

2013

Oran OF, Hafalir FS, Gurler N, Ider YZ, “Convection-Reaction Equation based Low-Frequency Conductivity Imaging Using Readout Gradient Induced Eddy Currents”, ISMRM21(2013): 4188
Gurler N, Hafalir FS, Oran OF, Ider YZ, “A New Accurate FEM Based Optimization Method for Birdcage Coil Design at High Field Strength”, ISMRM21(2013): 2807
Hafalir FS, Oran OF, Gurler N, Ider YZ, “Magnetic Resonance Electrical Properties Tomography (MREPT) based on the Solution of the Convection-Reaction Equation”, ISMRM21(2013): 4187

2012

Oran OF, Ider YZ, "Magnetic resonance electrical impedance tomography (MREIT) based on the solution of the convection equation using FEM with stabilization",Phys. Med. Biol. 57 5113 doi:10.1088/0031-9155/57/16/5113
Turk EA., Kopanoglu E., Guney S., Bugdayci KE., Ider YZ., Erturk V.B., Atalar E., "A Simple Analytical Expression for the Gradient Induced Potential on Active Implants During MRI," Biomedical Engineering, IEEE Transactions on , vol.59, no.10, pp.2845,2851, Oct. 2012 doi: 10.1109/TBME.2012.2212190
Gurler N, Ider YZ.,“FEM based Design and Simulation Tool for MRI Birdcage Coils including Eigenfrequency Analysis”, COMSOL Conference Europe 2012, Milan, 2012

2011

Gürler N, Ider YZ, “Alçak Geçiren Kuş Kafesi Tipi Manyetik Rezonans Görüntüleme (MRG) RF Sargısının Tasarımı, Modellenmesi ve Benzetimi için bir Yazılım Aracı”, Tıp Teknolojileri Ulusal Kongresi ve 16. Biyomedikal Mühendisliği Toplantısı, Antalya, 2011
Hafalir FS, Oran OF, Ider YZ, “Hızlı Manyetik Rezonans Elektriksel Empedans Tomografi (MREET) için Spin-Eko Ekoplanar Görüntüleme (SEEPI) Darbe Dizinlerinin Kullanılması”, Tıp Teknolojileri Ulusal Kongresi ve 16. Biyomedikal Mühendisliği Toplantısı, Antalya, 2011

2010

Ider YZ, Birgul O, Oran OF, Arikan O, Hamamura MJ and Muftuler LT, "Fourier transform magnetic resonance current density imaging (FT-MRCDI) from one component of magnetic flux density", Phys. Med. Biol. 55 3177, 2010 doi:10.1088/0031-9155/55/11/013
Ider YZ, Oran OF, "3D FT-MRCDI: Phantom Experiments", Proceedings of Workshop on MR-based Impedance Imaging, co-sponsored by IEEE EMBS and ISMRM, Seoul, Korea, 2010
Oran OF, Ider YZ, "Triangular mesh based MREIT", Proceedings of Workshop on MR-based Impedance Imaging, co-sponsored by IEEE EMBS and ISMRM, Seoul, Korea, 2010
Cantas MR, Ider YZ, "Modified sensitivity matrix method for 3D MREIT", Proceedings of Workshop on MR-based Impedance Imaging, co-sponsored by IEEE EMBS and ISMRM, Seoul, Korea, 2010