Publications

Simona Leserri, Dogu Baran Aydogan (2024). Studying topographic organization of the brain with directional derivatives of connectivity. ISMRM.

Joonas Laurinoja, Umair Hassan, Christoph Zrenner, Matilda Makkonen, Mikko Nyrhinen, Pantelis Lioumis, Fa-Hsuan Lin, Risto Ilmoniemi, Dogu Baran Aydogan (2024). Preliminary investigation of BOLD dependence on EEG–TMS using a closed-loop TMS–EEG–fMRI setup. ISMRM.

Joonas Laurinoja, Umair Hassan, Christoph Zrenner, Matilda Makkonen, Mikko Nyrhinen, Pantelis Lioumis, Fa-Hsuan Lin, Risto Ilmoniemi, Dogu Baran Aydogan (2024). Preliminary investigation of BOLD dependence on EEG–TMS using a closed-loop TMS–EEG–fMRI. OHBM.

Milan Hájek, Ulrich Flögel, Adriana a S. Tavares, Lucia Nichelli, Aneurin Kennerley, Thomas Kahn, Jurgen J Futterer, Aikaterini Firsiori, Holger Grüll, Nandita Saha, Felipe Counago, Dogu Baran Aydogan, Others (2024). MR beyond diagnostics at the ESMRMB annual meeting: MR theranostics and intervention. Magnetic Resonance Materials in Physics, Biology and Medicine.

Simona Leserri, Dogu Baran Aydogan (2024). HARP: Hierarchical anatomical refinement of pathways in tractography. ISMRM.

Gabriel Girard, Dogu Baran Aydogan, Stamatios N Sotiropoulos (2024). Chapter 14. Probabilistic tractography. Handbook of Diffusion MR Tractography.

Soichi Hayashi, Bradley A. Caron, Anibal Sólon Heinsfeld, Sophia Vinci-Booher, Brent McPherson, Daniel N. Bullock, Giulia Bertò, Guiomar Niso, Sandra Hanekamp, Daniel Levitas, Kimberly Ray, Anne MacKenzie, Lindsey Kitchell, Josiah K. Leong, Filipi Nascimento-Silva, Serge Koudoro, Hanna Willis, Jasleen K. Jolly, Derek Pisner, Taylor R. Zuidema, Jan W. Kurzawski, Kyriaki Mikellidou, Aurore Bussalb, Christopher Rorden, Conner Victory, Dheeraj Bhatia, Dogu Baran Aydogan, Fang-Cheng F. Yeh, Franco Delogu, Javier Guaje, Jelle Veraart, Steffen Bollman, Ashley Stewart, Jeremy Fischer, Joshua Faskowitz, Maximilien Chaumon, Ricardo Fabrega, David Hunt, Shawn McKee, Shawn T. Brown, Stephanie Heyman, Vittorio Iacovella, Amanda F. Mejia, Daniele Marinazzo, R. Cameron Craddock, Emanuele Olivetti, Jamie L. Hanson, Paolo Avesani, Eleftherios Garyfallidis, Dan Stanzione, James Carson, Robert Henschel, David Y. Hancock, Craig A. Stewart, David Schnyer, Damian O. Eke, Russell A. Poldrack, Nathalie George, Holly Bridge, Ilaria Sani, Winrich A. Freiwald, Aina Puce, Nicholas L. Port, Franco Pestilli (2024). brainlife.io: A decentralized and open source cloud platform to support neuroscience research. Nature methods.

Simona Leserri, Dogu Baran Aydogan (2024). Analyzing Brain Topography Via Directional Derivatives of Connectivity. OHBM.

Dogu Baran Aydogan, Victor H. Souza, Renan H. Matsuda, Pantelis Lioumis, Risto J. Ilmoniemi (2023). Real-time tractography-assisted neuronavigation for TMS. bioRxiv.

Tuukka T. Raij, Emma Komulainen, Dogu Baran Aydogan, Siina Pamilo, Erkki Isometsä, Tommi Raij (2023). Depression core network-based individualized targeting for transcranial magnetic stimulation. Brain Stimulation.

Matthias Eisenmann, Annika Reinke, Vivienn Weru, Minu D Tizabi, Fabian Isensee, Tim J Adler, Sharib Ali, Vincent Andrearczyk, Marc Aubreville, Ujjwal Baid, Others (2023). Why is the winner the best?. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition.

Gabriel Girard, Jonathan Rafael-Patiño, Raphaël Truffet, Dogu Baran Aydogan, Nagesh Adluru, Veena a Nair, Vivek Prabhakaran, Barbara B Bendlin, Andrew L Alexander, Sara Bosticardo, Others (2023). Tractography passes the test: Results from the diffusion-simulated connectivity (disco) challenge. NeuroImage.

Dogu Baran Aydogan, Victor Hugo Souza, Pantelis Lioumis, Risto J. Ilmoniemi (2023). Targeting networks of the brain with real-time tractography-based TMS neuronavigation. Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation.

Boshra Shams, Peter Vajkoczy, Thomas Picht, Lucius S Fekonja, Dogu Baran Aydogan (2023). Mapping and visualization of white matter deformation in glioma patients using deep learning. OHBM.

Julia Jaatela, Dogu Baran Aydogan, Timo Nurmi, Jaakko Vallinoja, Helena Mäenpää, Harri Piitulainen (2023). Limb-specific thalamocortical tracts are impaired differently in hemiplegic and diplegic subtypes of cerebral palsy. Cerebral Cortex.

Vesa Vahermaa, Dogu Baran Aydogan, Tuukka Raij, Reetta-Liina Armio, Heikki Laurikainen, Jari Saramäki, Jaana Suvisaari (2023). FreeSurfer 7 quality control: Key problem areas and importance of manual corrections. NeuroImage.

Diego Milardovich, Victor H Souza, Ivan Zubarev, Sergei Tugin, Jaakko O Nieminen, Claudia Bigoni, Friedhelm C Hummel, Juuso T Korhonen, Dogu Baran Aydogan, Pantelis Lioumis, Others (2023). DELMEP: a deep learning algorithm for automated annotation of motor evoked potential latencies. Scientific Reports.

Boshra Shams, Peter Vajkoczy, Thomas Picht, Lucius S Fekonja, Dogu Baran Aydogan (2023). Deep neural network based visualization of white matter deformation in glioma patients. Annual Meeting of the German Society for Neurosurgery (DGNC).

Risto J. Ilmoniemi, Jaakko O. Nieminen, Aino E. Nieminen, Lari M. Koponen, Heikki Sinisalo, Victor H. Souza, Juuso T. Korhonen, Pantelis Lioumis, Olli-Pekka Kahilakoski, Dogu Baran Aydogan (2023). Connecting to brain networks using multi-channel TMS and EEG. Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation.

Olli-Pekka Kahilakoski, Heikki Sinisalo, Jaakko O. Nieminen, Kim Valén, Kyösti Alkio, Dogu Baran Aydogan, Roberto Guidotti, Dubravko Kičić, Renan Matsuda, Ana Soto, Victor H. Souza, Timo Roine, Risto J. Ilmoniemi (2023). Accurate and precise digital real-time control of transcranial magnetic stimulation. Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation.

Joonas Laurinoja, Umair Hassan, Mikko Nyrhinen, Matilda Makkonen, Pantelis Lioumis, Fa-Hsuan Lin, Christoph Zrenner, Risto Ilmoniemi, Dogu Baran Aydogan (2023). Accuracy of eeg-phase estimation for closed-loop brain stimulation inside the mri device. Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation.

Elena Ukharova, Pantelis Lioumis, Aino E. Tervo, Jaakko O. Nieminen, Ida Granö, Dogu Baran Aydogan, Tuomas P. Mutanen, Victor H. Souza, Matteo Fecchio, Mario Rosanova, Et Al (2022). Whole-brain structural connectivity affects TMS–EEG signal propagation. Abstracts of the 32nd International Congress of Clinical Neurophysiology (ICCN) of the IFCN.

Julia Jaatela, Dogu Baran Aydogan, Timo Nurmi, Jaakko Vallinoja, Harri Piitulainen (2022). Identification of proprioceptive thalamocortical tracts in children: comparison of fMRI, MEG, and manual seeding of probabilistic tractography. Cerebral Cortex.

Chiara Maffei, Gabriel Girard, Kurt G. Schilling, Dogu Baran Aydogan, Nagesh Adluru, Andrey Zhylka, Ye Wu, Matteo Mancini, Andac Hamamci, Alessia Sarica, Et Al (2022). Insights from the IronTract challenge: Optimal methods for mapping brain pathways from multi-shell diffusion MRI. NeuroImage.

Boshra Shams, Ziqian Wang, Timo Roine, Dogu Baran Aydogan, Peter Vajkoczy, Christoph Lippert, Thomas Picht, Lucius S. Fekonja (2022). Machine learning-based prediction of motor status in glioma patients using diffusion MRI metrics along the corticospinal tract. Brain Communications.

Lucius S. Fekonja, Ziqian Wang, Alberto Cacciola, Timo Roine, D. Admin, Darius Mewes, Sebastian Vellmer, Peter Vajkoczy, Thomas Picht (2022). Network analysis shows decreased ipsilesional structural connectivity in glioma patients. Communications Biology.

Dogu Baran Aydogan (2022). Fiber coupling (FICO) measure using anisotropic smoothing of track orientation density images for tractogram filtering. Proceedings of the 29th Annual Meeting of ISMRM. London.

Matthias Eisenmann, Annika Reinke, Vivienn Weru, Minu Dietlinde Tizabi, Fabian Isensee, Tim J. Adler, Patrick Godau, Veronika Cheplygina, Michal Kozubek, Sharib Ali, Et Al (2022). Biomedical image analysis competitions: The state of current participation practice. arXiv preprint arXiv:2212.08568.

Jelle Veraart, Daan Christiaens, Erpeng Dai, Luke J. Edwards, Vladimir Golkov, Siawoosh Mohammadi, Kurt G. Schilling, Mohammad Hadi Aarabi, Benjamin Ades-Aron, Nagesh Adluru, Et Al (2022). A data-driven variability assessment of brain diffusion MRI preprocessing pipelines. Proceedings of the 29th Annual Meeting of ISMRM. London.

Jovan Hutton Pulitzer, Henry Joseph Legere Iii, Nicholas Solter, Dogu Baran Aydogan (2021). System and method for digital remote primary, secondary, and tertiary color calibration via smart device in analysis of medical test results.

Kurt G. Schilling, François Rheault, Laurent Petit, Colin B. Hansen, Vishwesh Nath, Fang-Cheng Yeh, Gabriel Girard, Muhamed Barakovic, Jonathan Rafael-Patino, Thomas Yu, Et Al (2021). Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?. NeuroImage.

Dogu Baran Aydogan, Victor H. Souza, Pantelis Lioumis, Risto J. Ilmoniemi (2021). Towards real-time tractography-based TMS neuronavigation. Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation.

Olli-Pekka Kahilakoski, Juuso T. Korhonen, Victor H. Souza, Roberto Guidotti, Dogu Baran Aydogan, Tuomas P. Mutanen, Ana M. Soto, Jaakko O. Nieminen, Dubravko Kičić, Timo Roine (2021). Software architecture for closed-loop multi-locus transcranial magnetic stimulation. Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation.

Dogu Baran Aydogan, Yonggang Shi (2021). Parallel Transport Tractography. IEEE Transactions on Medical Imaging.

Chiara Maffei, Gabriel Girard, Kurt G. Schilling, Dogu Baran Aydogan, Nagesh Adluru, Andrey Zhylka, Ye Wu, Matteo Mancini, Andac Hamamci, Alessia Sarica, Et Al (2021). New insights from the IronTract challenge: Simple post-processing enhances the accuracy of diffusion tractography. Proceedings of the 28th Annual Meeting of ISMRM. Online.

Lucius S. Fekonja, Ziqian Wang, Dogu B. Aydogan, Timo Roine, Melina Engelhardt, Felix R. Dreyer, Peter Vajkoczy, Thomas Picht (2021). Detecting Corticospinal Tract Impairment in Tumor Patients With Fiber Density and Tensor-Based Metrics. Frontiers in Oncology.

Dogu Baran Aydogan (2020). Visualization of uncertainty in tractograms using ROC-based transfer functions for real-time TMS applications. Proceedings of the 27th Annual Meeting of ISMRM. Online.

Vishwesh Nath, Kurt G. Schilling, Prasanna Parvathaneni, Yuankai Huo, Justin A. Blaber, Allison E. Hainline, Muhamed Barakovic, David Romascano, Jonathan Rafael-Patino, Matteo Frigo, Vesna Prčkovska, Et Al (2020). Tractography reproducibility challenge with empirical data (TraCED): The 2017 ISMRM diffusion study group challenge. Journal of Magnetic Resonance Imaging.

Chiara Maffei, Gabriel Girard, Kurt G. Schilling, Nagesh Adluru, Dogu Baran Aydogan, Andac Hamamci, Fang-Cheng Yeh, Matteo Mancini, Ye Wu, Alessia Sarica (2020). The IronTract challenge: Validation and optimal tractography methods for the HCP diffusion acquisition scheme. Proceedings of the 27th Annual Meeting of ISMRM. Online.

Dogu Baran Aydogan, Victor Hugo Souza, Risto J Ilmoniemi (2020). Processing of structural and diffusion MRI for real-time tractography-based nTMS. The 6th Annual Brain Stimulation and Imaging Meeting.

Pantelis Lioumis, Dogu Baran Aydogan, Risto J Ilmoniemi, Aki Laakso (2019). Real-time diffusion MRI-based tractography guided TMS speech cortical mapping. 11th Annual Meeting of the Society for the Neurobiology of Language.

Kurt G. Schilling, Vishwesh Nath, Colin Hansen, Prasanna Parvathaneni, Justin Blaber, Yurui Gao, Peter Neher, Dogu Baran Aydogan, Yonggang Shi, Mario Ocampo-Pineda, Et Al (2019). Limits to anatomical accuracy of diffusion tractography using modern approaches. NeuroImage.

Dogu Baran Aydogan, Victor Hugo Souza, Risto J Ilmoniemi (2019). Diffusion MRI processing pipeline for real-time tractography-based nTMS. 11th International nTMS Symposium on nTMS in Neurosurgery and Neuromodulation.

Aarti Mishra, Gerson D. Hernandez, Claudia Lopez, Dogu Aydogan, Yonggang Shi, Meng Law, Lon S. Schneider, Roberta Diaz Brinton (2019). Blood-Based Inflammatory Biomarkers for Predicting Therapeutic Response in Regional Brain Volume Changes in Patients with Alzheimer's Disease. Alzheimer’s & Dementia.

Junyan Wang, Dogu Baran Aydogan, Rohit Varma, Arthur W. Toga, Yonggang Shi (2018). Modeling topographic regularity in structural brain connectivity with application to tractogram filtering. NeuroImage.

Dogu Baran Aydogan, Yonggang Shi (2018). Tracking and validation techniques for topographically organized tractography. NeuroImage.

Dogu Baran Aydogan, Russell Jacobs, Stephanie Dulawa, Summer L. Thompson, Maite Christi Francois, Arthur W. Toga, Hongwei Dong, James A. Knowles, Yonggang Shi (2018). When tractography meets tracer injections: a systematic study of trends and variation sources of diffusion-based connectivity. Brain Structure and Function.

Dogu Baran Aydogan, David Sean Thylur, Junyan Wang, Yuchun Tang, Janet Sobell, James A. Knowles, Yonggang Shi (2018). Automatic reconstruction of cortico-striato-thalamo-cortical loops with application to obsessive-compulsive disorder. Proceedings of the 26th Annual Meeting of ISMRM. Paris.

Dogu Baran Aydogan, Yonggang Shi (2018). A novel moving frame approach for topographically organized white matter fiber tractography. OHBM.

Dogu Baran Aydogan, Yonggang Shi (2017). Topography preserving tractography for mapping human brain pathways. Proceedings of the 25th Annual Meeting of ISMRM. Honolulu, Hawaii.

Junyan Wang, Dogu Baran Aydogan, Rohit Varma, Arthur W. Toga, Yonggang Shi (2017). Topographic Regularity for Tract Filtering in Brain Connectivity. Information Processing in Medical Imaging.

Dogu Baran Aydogan, Yonggang Shi (2016). Probabilistic Tractography for Topographically Organized Connectomes. Medical Image Computing and Computer-Assisted Intervention – MICCAI 2016.

Dogu Baran Aydogan, Yonggang Shi (2015). Track Filtering via Iterative Correction of TDI Topology. Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015.

Elli Käpylä, Tomáš Sedlačík, Dogu Baran Aydogan, Jouko Viitanen, František Rypáček, Minna Kellomäki (2014). Direct laser writing of synthetic poly(amino acid) hydrogels and poly(ethylene glycol) diacrylates by two-photon polymerization. Materials Science and Engineering: C.

Dogu Baran Aydogan, Jari Hyttinen (2014). Characterization of microstructures using contour tree connectivity for fluid flow analysis. Journal of The Royal Society Interface.

Dogu Baran Aydogan (2014). Contour tree connectivity and analysis of microstructures. Tampere University of Technology.

Dogu Baran Aydogan, Jari Hyttinen (2013). Contour tree connectivity of binary images from algebraic graph theory. 2013 IEEE International Conference on Image Processing.

Ashkan Bonabi, Dogu Baran Aydogan, Jari Hyttinen (2013). Simulation of Microporous Architecture's Effects on Fluid Flow Characteristics in Cell Seeding. 2013 UKSim 15th International Conference on Computer Modelling and Simulation.

Dogu Baran Aydogan, Niko Moritz, Hannu T. Aro, Jari Hyttinen (2013). Analysis of Trabecular Bone Microstructure Using Contour Tree Connectivity. Medical Image Computing and Computer-Assisted Intervention – MICCAI 2013.

Elli Käpylä, Dogu Baran Aydogan, Sanni Virjula, Sari Vanhatupa, Susanna Miettinen, Jari Hyttinen, Minna Kellomäki (2012). Direct laser writing and geometrical analysis of scaffolds with designed pore architecture for three-dimensional cell culturing. Journal of Micromechanics and Microengineering.

Dogu Baran Aydogan, Jari Hyttinen (2012). Binary image representation by contour trees. Medical Imaging 2012: Image Processing.

Sanna Salonen, Elli Käpylä, Dogu Baran Aydogan, Sari Vanhatupa, Minna Kellomäki, Susanna Miettinen (2012). Behaviour of human adipose stem cells in microstructured scaffolds. TERMIS World Congress.

T. Niemelä, D. B. Aydogan, M. Hannula, J. Hyttinen, M. Kellomäki (2011). Determination of bioceramic filler distribution and porosity of self-reinforced bioabsorbable composites using micro-computed tomography. Composites Part A: Applied Science and Manufacturing.

Elli Käpylä, Dogu Baran Aydogan, Sanna Turunen, Jari Hyttinen, Minna Kellomäki (2011). Picosecond laser-induced polymerization of highly porous microscaffolds. 24th European Conference on Biomaterials.

Kati Juuti-Uusitalo, PA Giorgetti, Dogu Baran Aydogan, Markus Hannula, Heli Skottman, Jari Hyttinen (2011). Comparison Of Local Binary Pattern And Dual Tree Complex Wavelet Texture Analysis Approaches On The Assessment Of Human Embryonic Stem Cell Derived Retinal Pigment Epithelial Cell Culture Maturity. ARVO/ISIE Imaging Conference.

Dogu Baran Aydogan, Markus Hannula, Anne Rajala, Aliisa Pälli, Suvi Haimi, Minna Kellomäki, Jari Hyttinen (2011). Analysis of biomaterial scaffold fiber thickness for assessing cell attachment. 24th European Conference on Biomaterials.

Niina Ahola, Kaarlo Paakinaho, Laura Tirkkonen, Suvi Haimi, Dogu Baran Aydogan, Sanni Toropainen, Jari Hyttinen, Minna Kellomäki (2011). Advanced Osteopromotive Scaffolds for Bone Tissue Engineering: Supercritical Fluid Processing and Cellular Response with Human Adipose Stem Cells. Functional Materials, Scientific day for young researchers.

Tiiu Niemelä, Dogu Baran Aydogan, Markus Hannula, Jari Hyttinen, Minna Kellomäki (2010). Distribution of the bioceramic particles in the self-reinforced polylactide composites: a micro-CT study. 23rd European Conference on Biomaterials.

Dogu Baran Aydogan, Markus Hannula, Niko Moritz, Erkki Levänen, Jari Hyttinen (2010). Analysis of multiple resolution μ-CT image sets for pore-size distribution estimation. World Congress on Medical Physics and Biomedical Engineering, September 7 - 12, 2009, Munich, Germany.

Dogu Baran Aydogan, Markus Hannula, Tiiu Niemelä, Minna Kellomäki, Jari Hyttinen (2010). 3D shape analysis of filler particles in the Self-reinforced Polylactide Composites. 23rd European Conference on Biomaterials.

Dogu Baran Aydogan, Markus Hannula, Tuukka Arola, Prasun Dastidar, Jari Hyttinen (2009). 2D texture based classification, segmentation and 3D orientation estimation of tissues using DT-CWT feature extraction methods. Data & Knowledge Engineering.

Dogu Baran Aydogan, Markus Hannula, Niko Moritz, Erkki Levänen, Jari Hyttinen (2009). Pore-size distribution estimation using multiple resolution µ-CT image sets. Scan Balt Forum and Biomaterials Days.

Dogu Baran Aydogan, Markus Hannula, Niko Moritz, Erkki Levänen, Jari Hyttinen (2009). Pore analysis of materials and tissues for characterization and diagnosis. Tissue Engineering Symposium.

Dogu Baran Aydogan, Markus Hannula, Minna Kellomäki, Jari Hyttinen (2009). Pore analysis of biomaterials and tissues for characterization and diagnosis. Scan Balt Forum and Biomaterials Days.

Alper Cömert, Markku Honkala, Dogu Baran Aydogan, Antti Vehkaoja, Jarmo Verho, Jari Hyttinen (2009). Comparison of Different Structures of Silver Yarn Electrodes for Mobile Monitoring. 4th European Conference of the International Federation for Medical and Biological Engineering.

Antti Vehkaoja, Jarmo Verho, Alper Comert, Dogu Baran Aydogan, Merja Perhonen, Jukka Lekkala, Jouko Halttunen (2008). System for ECG and heart rate monitoring during group training. 2008 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Dogu Baran Aydogan, Markus Hannula, Tuukka Arola, Prasun Dastidar, Jari Hyttinen (2008). Texture based classification and segmentation of tissues using DT-CWT feature extraction methods. 2008 21st IEEE International Symposium on Computer-Based Medical Systems.

Dogu Baran Aydogan, M. Hannula, T. Arola, P. Dastidar, J. Hyttinen (2008). Comparison of DT-CWT Based Rotation Variant and Invariant Methods on Tissue Characterization. 14th Nordic-Baltic Conference on Biomedical Engineering and Medical Physics.