Dogu Baran Aydogan

University of Eastern Finland | UEF · A.I. Virtanen Institute for Molecular Sciences

While tractography is widely used in brain imaging research, its quantitative validation is highly difficult. Many fiber systems, however, have well-known topographic organization which can even be quantitatively mapped such as the retinotopy of visual pathway. Motivated by this previously untapped anatomical knowledge, we develop a novel tractogra...

Tractography is a powerful technique capable of non-invasively reconstructing the structural connections in the brain using diffusion MRI images, but the validation of tractograms is challenging due to lack of ground truth. Owing to recent developments in mapping the mouse brain connectome, high-resolution tracer injection-based axonal projection m...

We propose a new technique to clean outlier tracks from fiber bundles reconstructed by tractography. Previous techniques were mainly based on computing pair-wise distances and clustering methods to identify unwanted tracks, which relied heavy upon user inputs for parameter tuning. In this work, we propose the use of topological information in track...

Quantifying the connectivity of material microstructures is important for a wide range of applications from filters to biomaterials. Currently, the most used measure of connectivity is the Euler number, which is a topological invariant. Topology alone, however, is not sufficient for most practical purposes. In this study, we use our recently introd...

We propose a novel feature for binary images that provides connectivity information by taking into account the proximity of connected components and cavities. We start by applying the Euclidean distance transform and then we compute the contour tree. Finally, we assign the normalized algebraic connectivity of a contour tree derivative as a feature...

Transcranial magnetic stimulation (TMS) is a powerful tool for non-invasive brain stimulation, with versatile applications in research, diagnostics, and the treatment of psychiatric and neurological disorders. Currently, TMS is administered the same way to all individuals, resulting in inconsistent treatment outcomes. To increase its effectiveness,...

Neuromodulation is based on the principle that brain stimulation produces plastic changes in cerebral circuitry. Given the intersubject structural and functional variability, neuromodulation has a personalized effect in the brain. Moreover, because of cerebral dominance and interhemispheric functional and structural differences in the same individu...

Transcranial magnetic stimulation (TMS) is a powerful tool for non-invasive brain stimulation, with versatile applications in research, diagnostics, and the treatment of psychiatric and neurological disorders. Currently, TMS is administered the same way to all individuals, resulting in inconsistent treatment outcomes. To increase its effectiveness,...

Topographic organization stands as an important characteristic of the brain (Patel, Kaplan, and Snyder 2014; Wedeen et al. 2012). Tractography studies have highlighted this principle in the sensory and motor systems (Aydogan and Shi 2018; Lee, Lee, and Han 2016). Gradients have been used to describe spatial changes in connectivity patterns (Margul...

Transcranial magnetic stimulation (TMS) is a powerful tool for non-invasive brain stimulation, with applications ranging from research to diagnostics to treatment of psychiatric and neurological disorders. Currently, TMS is applied the same way to all individuals without personalization, leading to inconsistent treatment outcomes [1]. One way to pe...

Motivation: Whole brain tractography is highly challenging, and it is prone to false positive streamlines despite the use of Anatomically Constraint Tractography (ACT). Goal(s): This study aims to reduce implausible streamlines in tractograms by introducing a novel refinement approach, thereby enhancing the accuracy of white matter connectivity an...

Motivation: The currently available tools to describe changes in structural connectivity preclude an in-depth topography study of the brain's white matter. We sought to quantify the degree of change in structural connectivity through the mathematical notion of directional derivatives. Goal(s): To define and compute the directional derivatives of...

Neuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, vis...

Thalamocortical pathways are considered crucial in the sensorimotor functioning of children with cerebral palsy (CP). However, previous research has been limited by non-specific tractography seeding and the lack of comparison between different CP subtypes. We compared limb-specific thalamocortical tracts between children with hemiplegic (HP, N = 15...

We have studied the effects of manual quality control of brain Magnetic Resonance Imaging (MRI) images processed with Freesurfer. T1 images of first episode psychosis patients (N=60) and healthy controls (N=41) were inspected for gray matter boundary errors. The errors were fixed, and the effects of error correction on brain volume, thickness, and...

Neuroscience research has expanded dramatically over the past 30 years by advancing standardization and tool development to support rigor and transparency. Consequently, the complexity of the data pipeline has also increased, hindering access to FAIR (Findable, Accessible, Interoperabile, and Reusable) data analysis to portions of the worldwide res...

Neuroscience research has expanded dramatically over the past 30 years by advancing standardization and tool development to support rigor and transparency. Consequently, the complexity of the data pipeline has also increased, hindering access to FAIR data analysis to portions of the worldwide research community. brainlife.io was developed to reduce...

Estimating structural connectivity from diffusion-weighted magnetic resonance imaging is a challenging task, partly due to the presence of false-positive connections and the misestimation of connection weights. Building on previous efforts, the MICCAI-CDMRI Diffusion-Simulated Connectivity (DiSCo) challenge was carried out to evaluate state-of-the-...

The analysis of motor evoked potentials (MEPs) generated by transcranial magnetic stimulation (TMS) is crucial in research and clinical medical practice. MEPs are characterized by their latency and the treatment of a single patient may require the characterization of thousands of MEPs. Given the difficulty of developing reliable and accurate algori...

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a...

Background: State-of-the-art navigated transcranial magnetic stimulation (nTMS) systems can display the TMS coil position relative to the structural magnetic resonance image (MRI) of the subject's brain and calculate the induced electric field. However, the local effect of TMS propagates via the white-matter network to different areas of the brain,...

Background: Transcranial magnetic stimulation (TMS) of the dorsolateral prefrontal cortex (DLPFC) is an established treatment for major depressive disorder (MDD). Recent attempts to improve TMS efficacy by individually targeting DLPFC subregions that are functionally connected to the subgenual cingulate cortex (sgACC) appear promising. However, sg...

Brain-state-dependent stimulation of the brain is an exciting and very promising new approach for research and treatment of psychiatric and neurological disorders. The phase of electroencephalographic (EEG) signal has been shown to affect corticospinal responses, e.g., to transcranial magnetic stimulation (TMS). Because EEG has limited sensitivity...

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in...

Limitations in the accuracy of brain pathways reconstructed by diffusion MRI (dMRI) tractography have received considerable attention. While the technical advances spearheaded by the Human Connectome Project (HCP) led to significant improvements in dMRI data quality, it remains unclear how these data should be analyzed to maximize tractography accu...

File formats that store the results of computational tractography were typically developed within specific software packages. This approach has facilitated a myriad of applications, but this development approach has generated insularity within software packages, and has limited standardization. Moreover, because tractography file formats were devel...

Along tract statistics enables white matter characterization using various diffusion MRI (dMRI) metrics. These diffusion models reveal detailed insights into white matter microstructural changes with development, pathology, and function. Here, we aim at assessing the clinical utility of dMRI metrics along the corticospinal tract, investigating whet...

Gliomas that infiltrate networks and systems, such as the motor system, often lead to substantial functional impairment in multiple systems. Network-based statistics (NBS) allow to assess local network differences and graph theoretical analyses enable investigation of global and local network properties. Here, we used network measures to characteri...

Studying white matter connections with tractography is a promising approach to understand the development of different brain processes, such as proprioception. An emerging method is to use functional brain imaging to select the cortical seed points for tractography, which is considered to improve the functional relevance and validity of the studied...

Limitations in the accuracy of brain pathways reconstructed by diffusion MRI (dMRI) tractography have received considerable attention. While the technical advances spearheaded by the Human Connectome Project (HCP) led to significant improvements in dMRI data quality, it remains unclear how these data should be analyzed to maximize tractography accu...

White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same in...

White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same in...

Along tract statistics enables white matter characterization using various diffusion MRI (dMRI) metrics. Here, we applied a machine learning (ML) method to assess the clinical utility of dMRI metrics along corticospinal tracts (CST), investigating whether motor glioma patients can be classified with respect to their motor status. The ML-based analy...

Gliomas that infiltrate networks and systems, such as the motor system, often lead to substantial functional impairment in multiple systems. Network-based statistics (NBS) allow to 25 assess local network differences (1) and graph theoretical analyses (2) enable investigation of global and local network properties. Here, we used network measures to...

Tumors infiltrating the motor system lead to significant disability, often caused by corticospinal tract injury. The delineation of the healthy-pathological white matter (WM) interface area, for which diffusion magnetic resonance imaging (dMRI) has shown promising potential, may improve treatment outcome. However, up to 90% of white matter (WM) vox...

White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same in...

Tumors infiltrating the motor system lead to significant disability, often caused by corticospinal tract injury. The delineation of the healthy-pathological white matter (WM) interface area, for which diffusion magnetic resonance imaging (dMRI) has shown promising potential, may improve treatment outcome. However, up to 90% of white matter (WM) vox...

Tractography is an important technique that allows the in vivo reconstruction of structural connections in the brain using diffusion MRI. Although tracking algorithms have improved during the last two decades, results of validation studies and international challenges warn about the reliability of tractography and point out the need for improved al...

White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segmentation protocols and techniques. This can result in different reconstructions of the same in...

Transcranial magnetic stimulation (TMS) is a non-invasive brain stimulation technique that is widely used in both research and clinical settings. However, state-of-the-art TMS guidance systems do not leverage the valuable structural connectivity in real-time applications. This is mainly due to the limitations of tractography which has been increasi...

Synopsis We present results from IronTract, the first challenge to evaluate tractography on the two-shell diffusion scheme of the Human Connectome Project (HCP). Accuracy was evaluated by comparison to tracer injections in the same macaque brains as the diffusion data. Training and validation datasets involved different injection sites. We observed...

Real-time information about the structural connections in the brain would be highly valuable when performing navigated transcranial magnetic stimulation (nTMS). This information can be obtained using diffusion MRI (dMRI) based tractography that can extract major structural connections in the brain, in-vivo and non-invasively. However, this has been...

Tractography is a powerful technique that reveals structural connections of the brain, in vivo, using diffusion magnetic resonance imaging (dMRI). Real-time information about these connections would be highly valuable when performing navigated transcranial magnetic stimulation (nTMS). Two main reasons have prevented the adoption tractography in nTM...

Tracking algorithms have remarkably improved during the last two decades. However, multiple validation studies warn about the reliability and reproducibility of results, and point out to the need for better algorithms. In propagation based tracking, connections are typically modeled as piece-wise linear segments. In this work, we propose a novel pr...

Purpose: Fiber tracking with diffusion weighted magnetic resonance imaging has become an essential tool for estimating in vivo brain white matter architecture. Fiber tracking results are sensitive to the choice of processing method and tracking criteria. Phantom studies provide concrete quantitative comparisons of methods relative to absolute groun...

Diffusion MRI fiber tractography is widely used to probe the structural connectivity of the brain, with a range of applications in both clinical and basic neuroscience. Despite widespread use, tractography has well-known pitfalls that limits the anatomical accuracy of this technique. Numerous modern methods have been developed to address these shor...

Diffusion MRI fiber tractography is widely used to probe the structural connectivity of the brain, with a range of applications in both clinical and basic neuroscience. Despite widespread use, tractography has well-known pitfalls that limits the anatomical accuracy of this technique. Numerous modern methods have been developed to address these shor...

Topographic regularity is an important biological principle in brain connections that has been observed in various anatomical studies. However, there has been limited research on mathematically characterizing this property and applying it in the analysis of in vivo connectome imaging data. In this work, we propose a general mathematical model of to...

Topographic regularity of axonal connections is commonly understood as the preservation of spatial relationships between nearby neurons and is a fundamental structural property of the brain. In particular the retinotopic mapping of the visual pathway can even be quantitatively computed. Inspired from this previously untapped anatomical knowledge, w...

Diffusion MRI (dMRI) based tractography is a unique, indispensable in-vivo technique to study the structural connectivity of the brain. However the reliability of the results has recently been heavily disputed, which underlines the need to go beyond the currently available algorithms. In this work we present a novel walker based fiber tractography...

Cortico-striato-thalamo-cortical (CSTC) loops (or circuits or networks) are thought to play critical roles in the pathophysiology of several brain disorders such as Tourette syndrome, depression, Parkinson's syndrome and addiction. In particular the abnormal neural activity in the CSTC circuits are thought to implicate obsessive-compulsive disorder...

The preservation of the spatial relationships among axonal pathways has long been studied and known to be critical for many functions of the brain. Being a fundamental property of the brain connections, there is an intuitive understanding of topographic regularity in neuroscience but yet to be systematically explored in connectome imaging research....

Topographical organization is an integral property of brain's neural pathways. In this work we propose a novel approach to quantify the topographic preservation of fiber bundles obtained using dMRI based tractography. For that we used the well known organization of the somatosensory pathway. In our study we compared the tractograms obtained using o...

Millions of people worldwide suffer from fragility fractures, which cause significant morbidity, financial costs and even mortality. The gold standard to quantify structural properties of trabecular bone is based on the morphometric parameters obtained from μCT images of clinical bone biopsy specimens. The currently used image processing approaches...

Microscaffolds play a crucial role in cell culturing. They can be designed and produced in different ways depending on the applications and materials used. The cell medium (fluid) transports the cells into the microscaffold and is an effective factor for cell growth and stimulation. The architecture of microscaffolds influences fluid flow character...

Traditional scaffold fabrication methods used in tissue engineering enable only limited control over essential parameters such as porosity, pore size and pore interconnectivity. In this study, we designed and fabricated five different types of three-dimensionally interconnected, highly porous scaffolds with precise control over the scaffold charact...

There is a growing need in medical image processing to analyze segmented objects. In this study we are interested in analyzing morphological properties of complex structures such as the trabecular bone. Although, there are various shape description approaches proposed in the literature, there is not an adequate method to represent foreground object...

A micro-computed tomography (μ-CT) image analysis was used in the micro-structural analysis of self-reinforced bioabsorbable osteoconductive composites. The composites studied were known to have a porous structure, but the total porosity of these composites had not been measured due to lack of interconnected pores. The micro-structure of the compos...