Onur Kocak

Dr. Onur Kocak

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Research Focus & Metrics

Academic Career Length

4Years (2023-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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14 August 2023 in Symmetry
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Journal Article
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OEOsman EROGUL
Osman EROGUL
ZTZiya Telatar
Ziya Telatar
OKOnur Kocak
Onur Kocak
In this study, an automated medical decision support system is presented to assist physicians with accurate and immediate brain tumor detection, segmentation, and volume estimation from MRI which is very important in the success of surgical operations and treatment of brain tumor patients. In the proposed approach, first, tumor regions on MR images are labeled by an expert radiologist. Then, an automated medical decision support system is developed to extract brain tumor boundaries and to calculate their volumes by using multimodal MR images. One advantage of this study is that it provides an automated brain tumor detection and volume estimation algorithm that does not require user interactions by determining threshold values adaptively. Another advantage is that, because of the unsupervised approach, the proposed study realized tumor detection, segmentation, and volume estimation without using very large labeled training data. A brain tumor detection and segmentation algorithm is introduced that is based on the fact that the brain consists of two symmetrical hemispheres. Two main analyses, i.e., histogram and symmetry, were performed to automatically estimate tumor volume. The threshold values used for skull stripping were computed adaptively by examining the histogram distances between T1- and T1C-weighted brain MR images. Then, a symmetry analysis between the left and right brain lobes on FLAIR images was performed for whole tumor detection. The experiments were conducted on two brain MRI datasets, i.e., TCIA and BRATS. The experimental results were compared with the labeled expert results, which is known as the gold standard, to demonstrate the efficacy of the presented method. The performance evaluation results achieved accuracy values of 89.7% and 99.0%, and a Dice similarity coefficient value of 93.0% for whole tumor detection, active core detection, and volume estimation, respectively.

4 July 2023 in Diagnostics
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Ziya Telatar
OKOnur Kocak
Onur Kocak
OEOsman EROGUL
Osman EROGUL
Temporal lobe epilepsy, a neurological disease that causes seizures as a result of excessive neural activities in the brain, is the most common type of focal seizure, accounting for 30–35% of all epilepsies. Detection of epilepsy and localization of epileptic focus are essential for treatment planning and epilepsy surgery. Currently, epileptic focus is decided by expert physician by examining the EEG records and determining EEG channel where epileptic patterns begins and continues intensely during seizure. Examination of long EEG recordings is very time-consuming process, requires attention and decision can vary depending on physician. In this study, to assist physicians in detecting epileptic focus side from EEG recordings, a novel deep learning-based computer-aided diagnosis system is presented. In the proposed framework, ictal epochs are detected using long short-term memory network fed with EEG subband features obtained by discrete wavelet transform, and then, epileptic focus identification is realized by using asymmetry score. This algorithm was tested on EEG database obtained from the Ankara University hospital. Experimental results showed ictal and interictal epochs were classified with accuracy of 86.84%, sensitivity of 86.96% and specificity of 89.68% on Ankara University hospital dataset, and 96.67% success rate was obtained on Bonn EEG dataset. In addition, epileptic focus was identified with accuracy of 96.10%, sensitivity of 100% and specificity of 93.80% by using the proposed deep learning-based algorithm and university hospital dataset. These results showed that proposed method can be used properly in clinical applications, epilepsy treatment and surgical planning as a medical decision support system.

6 September 2025 in Symmetry
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OKOnur Kocak
Onur Kocak
The aim of this study is to analyze the signal generated in the brain for a specific motor task and to identify the region where it occurs. For this purpose, electroencephalography (EEG) signals were divided into delta, theta, alpha, and beta frequency sub-bands, and feature extraction was performed by looking at the time-frequency characteristics of the signals belonging to the obtained sub-bands. The epoch corresponding to motor imagery or action and the signal source in the brain were determined by power spectral density features. This study focused on a hand open–close motor task as an example. A machine learning structure was used for signal recognition and classification. The highest accuracy of 92.9% was obtained with the neural network in relation to signal recognition and action realization. In addition to the classification framework, this study also incorporated advanced preprocessing and energy analysis techniques. Eye blink artifacts were automatically detected and removed using independent component analysis (ICA), enabling more reliable spectral estimation. Furthermore, a detailed channel-based and sub-band energy analysis was performed using fast Fourier transform (FFT) and power spectral density (PSD) estimation. The results revealed that frontal electrodes, particularly Fp1 and AF7, exhibited dominant energy patterns during both real and imagined motor tasks. Delta band activity was found to be most pronounced during rest with T1 and T2, while higher-frequency bands, especially beta, showed increased activity during motor imagery, indicating cognitive and motor planning processes. Although 30 s epochs were initially used, event-based selection was applied within each epoch to mark short task-related intervals, ensuring methodological consistency with the 2–4 s windows commonly emphasized in the literature. After artifact removal, motor activity typically associated with the C3 region was also observed with greater intensity over the frontal electrode sites Fp1, Fp2, AF7, and AF8, demonstrating hemispheric symmetry. The delta band power was found to be higher than that of other frequency bands across T0, T1, and T2 conditions. However, a marked decrease in delta power was observed from T0 to T1 and T2. In contrast, beta band power increased by approximately 20% from T0 to T2, with a similar pattern also evident in gamma band activity. These changes indicate cognitive and motor planning processes. The novelty of this study lies in identifying the electrode that exhibits the strongest signal characteristics for a specific motor activity among 64-channel EEG recordings and subsequently achieving high-performance classification of the corresponding motor activity.

23 January 2024 in Biomedical Engineering / Biomedizinische Technik
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Journal Article
Closed access
OKOnur Kocak
Onur Kocak
CFCansel Ficici
Cansel Ficici
HFHikmet Firat
Hikmet Firat
ZTZiya Telatar
Ziya Telatar
Objectives: Diagnosing the sleep apnea can be critical in preventing the person having sleep disorder from unhealthy results. The aim of this study is to obtain a sleep apnea scoring approach by comparing parametric and non-parametric power spectral density (PSD) estimation methods from EEG signals recorded from different brain regions (C4–M1 and O2–M1) for transient signal analysis of sleep apnea patients. Methods: Power Spectral Density (PSD) methods (Burg, Yule–Walker, periodogram, Welch and multi-taper) are examined for the detection of apnea transition states including pre-apnea, intra-apnea and post-apnea together with statistical methods. Results: In the experimental studies, EEG recordings available in the database were analyzed with PSD methods. Results showed that there are statistically significant differences between parametric and non-parametric methods applied for PSD analysis of apnea transition states in delta, theta, alpha and beta bands. Moreover, it was also revealed that PSD of EEG signals obtained from C4–M1 and O2–M1 channels were also found statistically different as proved by classification using the K-nearest neighbour (KNN) method. Conclusions: It was concluded that not only applying different PSD methods, but also EEG signals from different brain regions provided different statistical results in terms of apnea transition states as obtained from KNN classification.

9 November 2024 in Diagnostics
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Ziya Telatar
OEOsman EROGUL
Osman EROGUL
OKOnur Kocak
Onur Kocak
Background/Objectives: In this study, a medical decision support system is presented to assist physicians in epileptic focus detection by correlating MRI and EEG data of temporal lobe epilepsy patients. Methods: By exploiting the asymmetry in the hippocampus in MRI images and using voxel-based morphometry analysis, gray matter reduction in the temporal and limbic lobes is detected, and epileptic focus prediction is realized. In addition, an epileptic focus is also determined by calculating the asymmetry score from EEG channels. Finally, epileptic focus detection was performed by associating MRI and EEG data with a decision tree. Results: The results obtained from the proposed algorithm provide 100% overlap with the physician’s finding on the EEG data. Conclusions: MRI and EEG correlation in epileptic focus detection was improved compared with physicians. The proposed algorithm can be used as a medical decision support system for epilepsy diagnosis, treatment, and surgery planning.

3 June 2025 in Diagnostics
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Journal Article
Open access
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OKOnur Kocak
Onur Kocak
CFCansel FICICI
Cansel FICICI
İlknur Ezgi Doğanİlknur Ezgi Doğan
İlknur Ezgi Doğan
ZTZiya Telatar
Ziya Telatar
NPNIHAN OZUNLU PEKYAVAS
NIHAN OZUNLU PEKYAVAS
Objectives: In healthy young adults, thoracic kyphosis can be attributed to a number of factors, including a sedentary lifestyle, stress, poor posture, activity and daily habits, muscle pain, fatigue, and anxiety. In regard to clinical diagnosis and evaluation methods, high-cost radiological measurements and a variety of non-radiological clinical methods are employed. In this study, a decision support system that performs automatic thoracic kyphosis angle measurements has been developed with the objective of avoiding exposure of the human body to radiation and reducing the time required for measurements. Methods: The features were determined with reference to the thoracic kyphosis measurements that were manually marked by the expert on the subjects. The kyphosis angle was calculated by automatically identifying the T1 and T12 points through image segmentation using a convolutional neural network (CNN), which is a type of deep learning algorithm. Results: Intra-class consistency of ICC > 0.95 (p < 0.05) and internal consistency reliability of Cronbach’s α = 0.947 are obtained. Conclusions: The results demonstrate that the proposed algorithm exhibits high intra-class consistency and high internal consistency reliability to provide an automated thoracic kyphosis angle measurement system.