Browsing by Author "Soyak, Refik"

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Citation - WoS: 13
Citation - Scopus: 15
Channel Attention Networks for Robust Mr Fingerprint Matching
(IEEE-Inst Electrical Electronics Engineers Inc, 2022) Soyak, Refik; Navruz, Ebru; Ersoy, Eda Ozgu; Cruz, Gastao; Prieto, Claudia; King, Andrew P.; Unay, Devrim
Objective: Magnetic Resonance Fingerprinting (MRF) enables simultaneous mapping of multiple tissue parameters such as T1 and T2 relaxation times. The working principle of MRF relies on varying acquisition parameters pseudo-randomly, so that each tissue generates its unique signal evolution during scanning. Even though MRF provides faster scanning, it has disadvantages such as erroneous and slow generation of the corresponding parametric maps, which needs to be improved. Moreover, there is a need for explainable architectures for understanding the guiding signals to generate accurate parametric maps. Methods: In this paper, we addressed both of these shortcomings by proposing a novel neural network architecture (CONV-ICA) consisting of a channel-wise attention module and a fully convolutional network. Another contribution of this study is a new channel selection method: attention-based channel selection. Furthermore, the effect of patch size and temporal frames of MRF signal on channel reduction are analyzed by employing a channel-wise attention. Results: The proposed approach, evaluated over 3 simulated MRF signals, reduces error in the reconstruction of tissue parameters by 8.88% for T1 and 75.44% for T2 with respect to state-of-the-art methods. Conclusion: It is demonstrated that channel attention mechanism helps to focus on informative channels and fully convolutional network extracts spatial information achieve the best reconstruction performance. Significance: As a consequence of improvement in fast and accurate manner, presented work can contribute to make MRF appropriate for clinical use.
Citation - Scopus: 7
Classification of Healthy Siblings of Bipolar Disorder Patients From Healthy Controls Using Mri
(IEEE, 2019) Cigdem, Ozkan; Soyak, Refik; Aydeniz, Burhan; Oguz, Kaya; Demirel, Hasan; Kitis, Omer; Eker, Cagdas
Three Dimensional magnetic resonance imaging (3D-MRI) has been utilized to classify patients with neuroanatomical abnormalities apart from healthy controls (HCs). The studies on the diagnosis of Bipolar Disorder (BD) focuses also on the unaffected relatives of BD patients in order to examine the heritable resistance factors associated with the disorder. Hence, the comparison of Healthy Siblings of Bipolar Disorder patients (HSBDs) and HCs is also required owing to the high heritability of BD. In this paper, the classification of 27HSBDs from 38HCs has been studied by using 3D-MRI and Computer-Aided Detection (CAD). The pre-processing of 3D-MRI data is performed by taking advantage of Voxel-Based Morphometry (VBM) and the structural deformations in the Gray Matter (GM) and White Matter (WM) are obtained by using a general linear model. The model is configured by using a two sample t-test technique and Total Intracranial Volume (TIV) as a covariate. The altered voxels between data groups are considered as Voxel of Interests (VOIs) and the 3D masks are generated for GM and WM tissue probability maps. The Relief-F algorithm is utilized to rank the features and a Fisher Criterion (FC) method is considered to determine the number of top-ranked discriminative features. The performances of Support Vector Machines (SVM) and the Naive Bayes (NB) algorithms are compared on the classification of HSBD and HC. The experiments are performed for GM-only, WM-only, and their combinations. The experimental results indicate that the changes between the brain regions of HSBD and HC might provide information on the heritable factors associated with the BD. Additionally, it is concluded that using the combination of GM and WM tissue probability map provides better results than considering them, separately. Finally, it is obtained that the classification accuracy of SVM on HSBD and HC comparison is better than that of NB.
Citation - WoS: 1
Citation - Scopus: 3
Effects of Covariates on Classification of Bipolar Disorder Using Structural Mri
(IEEE, 2019) Cigdem, Ozkan; Horuz, Erencan; Soyak, Refik; Aydeniz, Burhan; Sulucay, Aysu; Oguz, Kaya; Demirel, Hasan
Three-Dimensional Magnetic Resonance Imaging (3D-MRI) and Computer-Aided Detection (CAD) have been widely studied in the detection and diagnosis of neuroanatomical abnormalities, including bipolar disorder (BD). Pre-processing of 3D-MRI scans plays an important role in post-processing. In this study, Voxel-Based Morphometry (VBM) is used to compare the morphological differences at the grey matter (GM) and white matter (WM) of BD subjects versus healthy controls (HCs). The effects of using different covariates (i.e. total intracranial volume (TIV), age, sex, and their combinations) on classification of BDs from HCs have been investigated for GM-only, WM-only, and their combination. 3D masks for GM and WM are generated separately by using local differences between BPs and HCs and the two sample t-test method. Principle component analysis based dimensionality reduction and support vector machine with Gaussian kernel are employed for classification of 26 BDs and 38 HCs obtained from Ege University, School of Medicine, Department of Psychiatry. The results indicate that using only TIV as a covariate provides more robust results for BD classification compared to other covariate combinations. Furthermore, the combination of GM and WM improves classification performance. The highest classification accuracies obtained for GM, WM, and their combination are 70.30%, 79.70%, and 82.80% respectively.