All Projects

All Projects 

Project Title: Development of diagnostic products that can demonstrate genetic, metabolic and histopathologic features of glial brain tumors as non-invasive with magnetic resonance imaging

Funded by Tübitak 1003 Grants (2017-2020) 

Principal Investigator: Alp Dinçer

Co-Investigators: Esin Öztürk Işık, Koray Özduman, Alpay Özcan, Özge Can

Researchers:  Ayhan Gürsan, Korhan Polat, Cansu Akın Levi, Hande Halilibrahimoğlu, Seda Keskin

Project Summary: The aim of this project is to combine multimodal MR information for applying machine learning methodologies with the aim of differentiating glioblastoma types. For this purpose, the MR, genetic and metabolomic data obtained from a prospective cohort will be analyzed and machine learning methods will be developed for predicting survival rate by only using the MR data. The genetic and metabolomic data obtained from biopsy will be included in the ground truth information.

Keywords: Glioma, Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy, Genomics, Metabolomics, Machine Learning.


Project Title: 1H Bilateral, Flexible Breast RF Coil Design for Magnetic Resonance Imaging Systems 

Funded by: Tübitak 1001 Grants (2017-2019) 

Principal Investigator: Korkut Yeğin

Co-Investigators: Esin Öztürk Işık

Researchers:  Başak Bayrambaş, Büşra Kahraman

Project Summary: The main aim of this study is to design 1H bilateral, flexible breast RF coil for magnetic resonance imaging systems and to develop a software for analysis of breast MR images obtained with this coil.

Keywords: Breast, RF coil, magnetic resonance imaging.


Project Title: Determination of Multimodality Magnetic Resonance Imaging Based Biomarkers for Mild Cognitive Impairment in Parkinson Disease

Funded by Tübitak 1001 Grants (2015-2018) 

Principal Investigator: Esin Öztürk Işık

Co-Investigators: Tamer Demiralp, Hakan Gürvit, Başar Bilgiç, Haşmet Hanağası, Aziz Uluğ, Erdem Tüzün

Researchers:  Ani Kıçik, Dilek Betül Arslan, Sevim Cengiz, Gökçe Hale Hatay, Ozan Genç, Muhammed Yıldırım, Kardelen Eryürek

Project Summary: The main aim of this study to develop biomarkers that would indicate the presence of mild cognitive imparment (MCI) in Parkinson disease (PD) and the probability of its’ evolution into dementia by evaluating the findings from multimodality structural, metabolic, and functional MR imaging of patients diagnosed with PD-MCI or cognitively intact Parkinson’s disease, and healthy controls.

Keywords: Parkinson disease, mild cognitive impairment, neuropsychological evaluation, magnetic resonance imaging, genetics, machine learning.


Project Title: Investigation of the Human Brain Metabolism in-vivo in Chronic Liver Failure Using Magnetic Resonance Spectroscopic Editing Techniques

Funded by Boğaziçi University BAP Grants (2015-2018) 

Principal Investigator: Esin Öztürk Işık

Co-Investigators:  Bahattin Hakyemez, Emre Ökeer, Tuba Erürker Öztürk, Aylin Bican Demir

Researcher:  Gökçe Hale Hatay

Project Summary: The main objective of this study is to understand the metabolic changes in the brain that occur due to minimal hepatic encephalopathy, and define metabolic biomarkers that can help in the diagnosis of this disorder.

Keywords: Biocomputing, Signal Processing, MR spectroscopic imaging, Minimal hepatic encephalopathy.


Project Title: Feasibilty Study of Obtaining High-Resolution Spectroscopy Images Using Data Fusion Techniques

Funded by Royal Society Newton Mobility Grants (2016-2017) 

Investigators: Esin Öztürk Işık / Maria Valdes-Hernandez

Project Summary: The main objective of this study is to develop a pipeline to increase the resolution of magnetic resonance spectroscopy images to provide the international scientific and research community a technique to study tissue microstructure and metabolic changes in neurological diseases, and increase research output by optimising tissue characterisation complementing the information from multimodal and multispectral magnetic resonance imaging with the application of this technique.

Keywords: MR spectroscopic imaging, Cancer, Deep-Learning, Convolutional Neural Network, Signal Processing and Analysis.


Completed Projects 

Project Title: Accelerated Phosphorus MR Spectroscopic Imaging of Brain Tumors at 3T using Compressed Sensing

Funded by Tübitak 3501 Career Development Grants  (2012-2014) 

Principal Investigator: Esin Öztürk Işık

Co-Investigator:  Bahattin Hakyemez

Researcher: Gökçe Hale Hatay

Project Summary: Phosphorus magnetic resonance spectroscopic imaging (31P-MRSI) is a non-invasive MR spectroscopic imaging technique that detects the phosphorus containing metabolites of the brain. 31P MRSI provides in-vivo quantitative information about the energy metabolism, oxygen state and pH within a given region of interest. Although, phosphorus magnetic resonance spectroscopic imaging provides vast information, it has not been widely used in the clinical settings yet. One of the major reasons of this problem is the low MR signal of phosphorus, because phosphorus is 15 times less abundant in the body than proton, and its gyromagnetic ratio is less than half of that of proton’s (1H=42.58 MHz/T, 31P=17.2 MHz/T). It is possible to average out multiple phosphorus signal acquisitions to get a higher signal to noise ratio (SNR), but this would result in longer scan times. Faster phosphorus MR spectroscopic imaging techniques should be devised to enable a wider use of 31P-MRSI. In this study, we aimed to implement compressed sensing technique for fast phosphorus magnetic resonance spectroscopic imaging.

Keywords: Phosphorus MR Spectroscopic Imaging, Compressed Sensing, Human Brain, 3T.


Project Title: Phosphorus MR Spectroscopic Imaging of Brain Tumors at 3T (31P_SPECTRA_3T)

Funded by FP7 Marie Curie International Reintegration Grants  (IRG) (2010-2014) 

Principal Investigator: Esin Öztürk Işık

Project Summary:  The previous studies have shown phosphorus metabolite level differences between the brain tumors and healthy brain tissue. When the brain tissue gets ischemic, ATP production comes from hydrolysis of PCr catalyzed by creatine kinase leading to a reduction of PCr:-ATP ratio in 31P MRSI and the breakdown of glycogen to lactic acid which can be observed as the lactate peak in 1H spectra. Pi also increases at ischemia due to increased ATP hydrolysis that is not matched by ATP synthesis leading to a Pi/PCr increase.

Phosphorus MRSI has some major advantages over proton spectroscopic imaging. First, the phosphorus spectroscopy does not require any water suppression and it does not have any lipid contamination problems. Second, although the detection of lactate peak with 1H spectroscopy requires special spectral editing schemes due to the overlapping lipid resonances, 31P spectra can readily display the PCr, Pi, and ATP peaks that can give an assessment of the ischemic state. Tumor growth is associated with both an increased cell membrane synthesis and a higher degradation of cell membranes. Although both membrane synthesis and degradation are evaluated by observing the changes in a single Cho peak in 1H MR spectroscopy, these pathways can be differentiated using 31P MR spectroscopy.

Despite the advantages of 31P-MRSI, it has not been widely used for clinical applications at lower field strengths. The wider availability of high field scanners and multi-channel radiofrequency (RF) surface coils have increased the sensitivity and accuracy of MR imaging and spectroscopy of brain tumors through higher signal-to-noise ratio (SNR) and improved spectral resolution. Increased spectral dispersion at high field results in less overlap between different peaks and simplifies the appearance of the spectrum. Phosphorus MR spectroscopic imaging highly benefits from high field strength with a resulting increase in SNR, better definition of Pi peak, better separation of PC, PE, GPC and GPE peaks, and better estimation of pH values.

The goal of this project is to apply phosphorus magnetic resonance spectroscopic imaging accurately at high field 3T scanners to add new information regarding the characteristics of brain tumors and produce a new metric that estimates the aggressiveness of a brain tumor using 31P MRSI peak intensities.

Keywords: Phosphorus MR Spectroscopic Imaging, Human Brain, 3T