İlgi alanları

Sürdürülebilir Kalkınma Amaçları

• 9
• 1

• MakaleYalnız künye2026/r/gumushane/10587
  Comparison of automated subcortical segmentation methods: VolBrain vs. 3D Slicer in brain volumetry

  Acer, Niyazi; Palanci, Ozgur; Ipekten, Funda; Erdogan, Furkan Mert; Yarar, Burhan; Ozyasar, Ali Faruk

  Objective:Accurate volume measurements of subcortical brain structures are essential in neuroimaging studies. This study aimed to compare two automated segmentation algorithms, 3D Slicer and VolBrain, for subcortical brain volumetry. Method:Subcortical volume measurements obtained using 3D Slicer and VolBrain were compared using the Neurofeedback Skull-stripped (NFBS) dataset. Statistical analyses included the coefficient of determination (R2) and Bland-Altman (B-A) plots. Volumetric measurements from both tools were evaluated across multiple subcortical brain regions. Results:Strong agreement was observed for the caudate nucleus, thalamus, and hippocampus, while notable discrepancies were identified in the amygdala, globus pallidus, and nucleus accumbens. Both constant and proportional systematic errors were detected in certain regions, with greater variability observed in 3D Slicer measurements. Intraclass Correlation Coefficient (ICC) analysis demonstrated weak agreement for the accumbens and amygdala, and moderate agreement for the hippocampus and thalamus, highlighting region-specific differences in performance Conclusion:Both VolBrain and 3D Slicer are effective tools for subcortical brain volumetry. VolBrain provides a fully automated workflow, whereas 3D Slicer allows greater flexibility through detailed corrections. Method selection should be guided by research objectives, regions of interest, and image quality. Further validation across diverse datasets is warranted to improve clinical applicability, particularly in regions showing lower agreement.

  • 
  İncele
• MakaleAçık Erişim2026/r/gumushane/19396
  Nöroanatomi Eğitimini Geliştirmek İçin Difüzyon MRI Analizi ile Birlikte Traktografi Yazılımının Kullanılması: Bir Nöroanatomi Eğitim Çalışması

  Palancı, Özgür; Aygün, Tayfun; Keskin, Arif; Salbacak, Ahmet; Kazancı, Necip Furkan

  Amaç: Bu çalışma, geleneksel nöroanatomi eğitimine ek olarak DSI Studio yazılımı kullanılarak yapılan segmentasyon ve traktografi eğitiminin tıp öğrencilerinin akademik başarısı üzerindeki etkisini değerlendirmeyi amaçlamıştır. Gereç ve Yöntemler: Çalışma, gönüllü ikinci sınıf tıp öğrencileriyle yapılmıştır. Traktografi eğitimine katılan öğrenciler çalışma grubunu (n=32), katılmayanlar ise kontrol grubunu (n=40) oluşturmuştur. Her iki gruba da eğitim öncesi ve sonrası 23 maddelik çoktan seçmeli bir bilgi testi uygulanmıştır. Eğitim içeriği nöronal yapılar, DTI/DSI'nin temel prensipleri, Brodmann alanları, beyaz madde organizasyonunun görselleştirilmesi ve üç boyutlu traktografi uygulamalarını içermiştir. Veriler SPSS 27.0 kullanılarak analiz edilmiş ve istatistiksel anlamlılık düzeyi p<0,05 olarak belirlenmiştir. Bulgular: Her iki grupta da son test puanları ön test puanlarından anlamlı derecede yüksek bulunmuştur (p<0,001). Bununla birlikte, çalışma grubu kontrol grubuna kıyasla anlamlı derecede daha yüksek son test puanları elde etmiştir (p=0,044). Çalışma grubunda ön test sonrası fark (öğrenme kazanımı) da daha büyüktü (p=0,013). Gruplar arasındaki öğrenme kazanımı için etki büyüklüğü orta düzeydeydi. Sonuç: DSI Studio ile gerçekleştirilen segmentasyon ve traktografi uygulamaları, nöroanatomik yapıların üç boyutlu incelenmesini ve değerlendirmesini sağlayarak nöroanatomi eğitiminde akademik performansı artırır. Bu tür yazılımların tıp eğitimine entegrasyonu, özellikle karmaşık anatomik yapıları içeren konularda öğrenme sürecini kolaylaştırabilir.

  • 
  • 
  İncele
• MakaleYalnız künye2026/r/gumushane/16295
  Contralateral DTI-ALPS index as a prognostic biomarker in IDH-wildtype glioblastoma: integrating extent of resection and sex-stratified analyses

  Aygün, Tayfun; Keskin, Arif; Palanci, Ozgur; Öztanir, Mustafa Namik; Yücel, Nurullah; Hekimoglu, Gulam

  Aim This study aimed to evaluate the independent prognostic value of the contralateral DTI-ALPS index in IDH-wildtype glioblastoma, incorporating tumor morphometry, extent of resection, and sex-stratified analyses within a multivariable framework.Methods A retrospective analysis was performed on 153 IDH-wildtype glioblastoma patients from the publicly available UPENN-GBM dataset. Contralateral DTI-ALPS was calculated using DSI Studio via manual ROI placement; tumor morphometry was derived from expert-annotated segmentation labels using 3D Slicer. Survival analyses included Kaplan-Meier estimation, multivariable Cox regression, time-dependent ROC, restricted cubic spline, and sequential C-index comparison with likelihood-ratio testing.Results The contralateral DTI-ALPS index independently predicted overall survival after adjustment for age, sex, tumor volume, and GTR status (HR = 0.405, 95% CI: 0.227-0.725, p = 0.002). Each one standard deviation increase in DTI-ALPS was associated with a 24.2% reduction in mortality risk. GTR >= 90% (HR = 0.651, p = 0.017) and age (HR = 1.021, p = 0.007) also retained independent significance. DTI-ALPS significantly improved model discrimination beyond age alone (C-index: 0.625 -> 0.653 -> 0.668; likelihood-ratio test p = 0.002). Time-dependent AUC reached 0.741 at 6 months. ALPS-based stratification was more pronounced in the subtotal resection subgroup. Sex-stratified analyses showed numerically stronger associations in females, but formal interaction testing did not confirm effect modification. In an exploratory MGMT subset (n = 57), DTI-ALPS did not retain independent significance after MGMT adjustment.Conclusion The contralateral DTI-ALPS index may provide complementary prognostic information beyond established clinical predictors in IDH-wildtype glioblastoma; however, given the incomplete MGMT methylation data and ongoing methodological debate regarding the biological validity of DTI-ALPS, these findings should be considered exploratory. Prospective validation in cohorts with complete molecular and treatment data is required.

  • 
  İncele
• MakaleAçık Erişim2026/r/gumushane/12137
  Fully automated 3D volumetric analysis of masticatory muscles in a pediatric population: A CT-based normative morphometric study

  Kanber Uzun, Özlem; Ertemoğlu Öksüz, Canan; Kalkışım, Şahi Nur; Palancı, Özgür; Yıldırım, Yusuf İslam

  The masticatory muscles play a fundamental role in craniofacial growth and development, yet normative volumetric data encompassing all four muscles across the full pediatric age range remain poorly characterized. The aim of this study was to establish age- and sex-specific normative reference values for the volumetric development of masticatory muscles in a normal pediatric population (0–17 years) using a fully automated 3D segmentation method. This retrospective, cross-sectional study included 258 normal pediatric individuals stratified into four age groups based on biomechanical milestones (0–5, 6–9, 10–13, and 14–17 years). Bilateral volumes of the masticatory muscles were automatically calculated using TotalSegmentator in the 3D Slicer environment. Two-way analysis of variance and Bonferroni post-hoc tests were applied. All muscles showed significant volume increases with age (p < 0.001), with the masseter demonstrating the greatest increase (199%). No sex differences were observed in 0–5 years; significant male-favoring differentiation began from 6 to 9 years. The temporalis muscle exhibited a biphasic sex differentiation pattern, with no significant difference at 10–13 years despite significance at 6–9 and 14–17 years. The highest sex-related effect sizes were observed in the pterygoid muscles (medial pterygoid ηp² = 0.176; lateral pterygoid ηp² = 0.160). Bilateral asymmetry analyses revealed left-sided favoring in the masseter, a lateralization trend in the temporalis (exploratory), right-sided favoring in the medial pterygoid, and sex-specific lateralization in the lateral pterygoid. These findings provide a large-scale CT-based normative reference for pediatric masticatory muscles, demonstrating muscle-specific volumetric patterns and variable sex differentiation, with normative ranges supporting clinical decision-making in dentistry, craniofacial surgery, and pediatric radiology.

  • 
  İncele
• MakaleAçık Erişim2026/r/gumushane/12133
  Cortical thickness and volume alterations in patients with high myopia: a magnetic resonance imaging study

  Aydin, Emre; Palanci, Ozgur

  Background: The retina and optic nerve are integral components of the visual system and maintain direct anatomical and functional connections with the brain. Both structures are markedly affected in high myopia (HM). Accordingly, characterizing brain structural alterations associated with HM may provide important insights into its underlying neurobiological mechanisms. Using brain magnetic resonance imaging (MRI), this study aimed to evaluate regional gray matter (GM) and white matter (WM) volume changes, their relative percentages, and cortical thickness alterations in individuals with HM. Methods: High-resolution structural MRI, together with visual acuity (VA), intraocular pressure (IOP), refractive error, axial length (AL), and anterior chamber depth (ACD), was used to compare 30 adults with HM and 22 healthy controls (HC). Regional brain volumes and cortical thickness were analyzed in the fusiform gyrus (FuG), inferior temporal gyrus (ITG), middle temporal gyrus (MTG), superior temporal gyrus (STG), and occipital subregions including the calcarine cortex (Calc), cuneus (Cun), lingual gyrus (LiG), inferior occipital gyrus (IOG), middle occipital gyrus (MOG), and superior occipital gyrus (SOG). Results: Compared with HCs, HM patients demonstrated significant volumetric increases in the ITG and MTG regions (all p < 0.05), with the left ITG remaining significant after false discovery rate (FDR) correction. No significant volumetric differences were observed in the fusiform or occipital regions. In contrast, cortical thickness analyses revealed significant thinning in the fusiform gyrus and bilateral occipital subregions, including the calcarine cortex, cuneus, lingual gyrus, and middle occipital gyrus (p = 0.000–0.026, FDR-corrected). Cortical thickness in the fusiform and occipital regions showed negative correlations with AL and ACD and positive correlations with spherical equivalent. Conclusions: High myopia is associated with region-specific brain structural alterations, characterized by volumetric increases in temporal regions and cortical thinning in fusiform and occipital areas, indicating that HM-related neuroanatomical changes extend beyond the ocular system to involve central nervous system structures. Trial registration: Not applicable.

  • 
  İncele
• MakaleAçık Erişim2025/r/gumushane/12410
  Volumetric and microstructural changes in the Hippocampus and cingulum in children with west syndrome

  PALANCI, Özgür; KAMAŞAK, Tülay; AYDIN KASAP, Zeliha; EYÜBOĞLU, İlker; DİLBER, Beril; CANSU, Ali

  Purpose: We aimed to investigate structural changes in the hippocampus using automated segmentation techniques to evaluate the anatomy and function of the hippocampus in patients with West syndrome (WS). Methods: The study included 48 participants (24 with WS and 24 healthy controls) aged 0‐4 years. Automated segmentation methods were used to measure hippocampal volume and evaluate diffusion tensor imaging (DTI) parameters such as fractional anisotropy (FA) and mean diffusivity (MD). Bonferroni correction was applied for multiple comparisons, setting the adjusted significance threshold at p < 0.0033. Results: Children with WS exhibited significantly reduced total hippocampal volume and diminished volumes in the CA2–CA3, CA4-dentate gyrus (CA4-DG), and SR-SL-SM regions compared to healthy controls (padj <0.0033). After correction, no significant differences were found in the CA1 and subiculum regions (padj >0.0033). Although initial comparisons between ongoing WS and seizure-controlled WS suggested increased volumes in several hippocampal regions in the seizure-controlled group, these differences did not remain significant after adjustment and must be interpreted with caution. Notably, patients with seizure-controlled WS displayed larger hippocampal volumes, higher FA, and lower MD values, indicating a possible link between seizure activity and structural alterations. Additionally, DTI analysis of the cingulum revealed lower FA and higher MD values in WS patients, suggesting compromised microstructural integrity. Conclusions: These findings emphasize the potential role of hippocampal alterations in the pathophysiology of WS and suggest that DTI parameters may serve as useful measures for monitoring disease progression and treatment response.

  • 
  İncele
• MakaleAçık Erişim2023/r/gumushane/20338
  Migrenli Hastalarda volBrain Yöntemi ile Serebellumun Hacimsel Analizi

  Özyaşar, Ali Faruk; Eyuboglu, Ilker; Çakmakl, Vildan; Alioglu, Zekeriya; Palancı, Özgür; Erten, Kübra

  Migren, geniş bir semptom yelpazesine sahip tekrarlayan bir baş ağrısı sendromudur. Migren tanısı çoğunlukla baş ağrısının özellikleri ve diğer semptomlar dikkate alınarak geriye dönük olarak konur. Migren baş ağrısının nasıl başladığı ve hangi beyin bölgelerinde meydana geldiği yeterince bilinmemektedir. Beyin sapı çekirdeklerinin uyarılabilirliğindeki değişikliklerin endojen ağrı mekanizmalarını etkilediği ve trigeminovasküler yapıların tek taraflı tutulumunun migren gelişiminde etkili mekanizmalar olduğu bilinmektedir. Migren hastalığında serebellumun rolünü anlamak, sinirbilimde oldukça yeni bir konudur. Çalışmamıza 19 Migren Hastası (MH) ve 14 Sağlıklı Kontrolör (SK) katıldı. Serebellumun hacimsel analizi için otomatik beyin hacmi hesaplama yöntemi olan volbrain ceres yöntemi kullanılmış ve beyincik yapılarının hacimleri elde edilmiştir. Verilerin analizinde SPSS 22.0 programı kullanılmış ve anlamlılık düzeyi p<0.05 olarak kabul edilmiştir. MH crus I, Crus II, lobus VIIB VIIIA, VIIIB ve IX'un gri madde hacimlerinde önemli bir artış var. Hastalık süresi ve atak sıklığına göre serebellum yapıları incelendiğinde serebellum, crusII, lobül VIIB ve lobül VIIIA'nın gri cevher hacimlerinde anlamlı artış saptandı. Bu bölgeler, saldırı frekansı ile pozitif bir korelasyon gösterdi. Sonuç olarak posterior serebellar yapılar, atakların sıklığı ve hastalığın süresi ile örtüşen bir aktivite göstermektedir. Beyincikte hacimsel veya fonksiyonel değişiklikler migren ağrısının patofizyolojisinde etkili olduğunu gösterir..

  • 
  İncele
• MakaleAçık Erişim2023/r/gumushane/20200
  Evaluation of White Matter and Cerebellum Structures of Essential Tremor and Parkinson's Patients by Diffusion Tensor Imaging and Volbrain Method

  Özyaşar, Ali Faruk; Eyuboglu, Ilker; Çakmakl, Vildan; Alioglu, Zekeriya; Palancı, Özgür; Köktürk, Elif Gökçen

  Essential tremor (ET) and Parkinson's disease (PD) are the two most commonly encountered tremor disorders in movement disorders. Diffusion tensor imaging (DTI) is one of the best in vivo ways of mapping white matter pathways in the human brain. The aim of our study was to investigate diffusion variables and cerebellum volume in ET and PD using parcellation methods. Our study included 20 ET, 20 PD and 20 healthy controls. Fraction Anisotropy (FA) and Mean Diffusivity (MD) values were obtained with DTI, while the volume of each lobe of the cerebellum was obtained with T1 images. One-way ANOVA was used for intergroup analysis and Scheffe test was used for post-hoc analysis. Significant differences were found in the diffusion values of the pedunculus cerebellaris, fornix stria, superior longitudinal fasciculus, sagittal stratum, cerebral pedunculus, tapatum and thalamus of ET and PD. Lobule V, Lobule IX, Lobule X volumes of the cerebellum showed significant differences between the groups. Stria thermialis shows involvement of mesolimbic dopaminergic system in PD and it is thought that disruption of strial networks leads to changes in the activity of cerebellar networks and reveals the role of the cerebellum in tremor. It is obvious that cerebellar thalamocortical pathways are affected in Parkinson's disease. In Parkinson's disease, patients should be evaluated for visual processing, conceptualisation, postural instability and gait disturbance to clarify the diagnosis or to differentiate from essential tremor.

  • 
  İncele
• MakaleYalnız künye2018/r/gumushane/13072
  Volume calculation of brain structures in migraine disease by using mristudio

  Palancı, Özgür; Kalaycıoğlu, Ahmet; Acer, Niyazi; Eyüpoğlu, İlker; Çakmak, Vildan A.

  Migraine is a neurological disorder that is known as headache and accompanies attacks of neurological and gastrointestinal symptoms and prevents daily life activities of the person. In the literature, the volume changes of many structures in the brain have been investigated using brain magnetic resonance images (MRI) of migraine patients, but it has not yet been investigated whether there is a comprehensive and detailed volume change involving all the structures of the brain. The purpose of this study is to examine the brain structures in a wide range and to determine in which regions the volume changes. In this study, 25 healthy subjects and 25 migraine patients were included in the study. SPSS 15.0 program was used for statistical analysis. The Mristudio was used in our study when we examined the volumes of migraine patients and brain structures of healthy individuals. Statistically significant volume changes were found in the volumes of structures found in the brain frontal, parietal, occipital, temporal lobes. Volumetric changes were assessed in terms of duration of illness and frequency of attacks. In conclusion, our study is compatible with migraine pathophysiology. Structural changes in the brain are thought to be a risk factor for migraine. The evidence on the relationship of regional gray matter volumetric change detected in migraine is unclear. We believe that this ambiguity is caused by the method used.

  • 
  İncele