About Neurominer CZ

Welcome to Neurominer.CZ, a cutting-edge neuroimaging lab where the intersection of Computational Biology, Neuroscience, Biomedical Engineering, and Biophysics converge to yield transformative research. Founded in 2007, our lab has been a hub for both academic and pedagogical excellence, under the leadership of Assoc. Prof. Daniel Schwarz, Ph.D.

Our research

Our research primarily focuses on neuroimaging and machine learning techniques to address pressing questions in neuroscience and biomedical engineering. Over the years, we have supervised an array of academic theses, including projects on mathematical modeling in MRI, and metaheuristic optimization methods. Our findings don't just live in the lab; they form the basis of coursework in Computational Biology at Masaryk University and Biomedical Engineering & Bioinformatics at Brno University of Technology.

Pedagogical Commitment

In addition to our research, we have a strong commitment to education. Our lab has been instrumental in organizing summer schools focused on interdisciplinary approaches to neuroscientific and biomedical research. These educational endeavors go hand-in-hand with our mission to guide the next generation of scientists.

Projects

In this post, you will find short summaries of some of our major projects.

• 2023-2025: ELICIT: New strategies in processing of multi-echo fMRI data;  
  co-PI --- Czech Science Foundation (GAČR): GA23-06957S
• 2017-2020: NEUROMINER: unveiling hidden patterns in neuroimaging data;  
  PI --- Ministry of Health of the Czech Republic (NV17-33136A)
• 2012-2015: Advanced Methods for Recognition of MR brain images for Computer Aided Diagnosis of Neuropsychiatric Disorders;  
  PI ---Ministry of Health of the Czech Republic (13359/4)
• 2009-2011: Modern pattern recognition methods for image data analysis in neuropsychiatric research;  
  PI ---Ministry of Health of the Czech Republic (10347/3)
• 2009-2011: Prediction of the initial phases of the schizophrenia using brain morphology imaging methods;  
  PI --- Ministry of Health of the Czech Republic (10347/3)
• 2007-2008: Nonlinear multimodal registration for automatic morphometry of MRI brain images based on anatomically constrained spatial deformations;  
  PI ---Czech Science Foundation (102/07/P263)

Papers

• Vyskovsky, R; Schwarz, D; Churova, V; Kasparek, T Structural MRI-Based Schizophrenia Classification Using Autoencoders and 3D Convolutional Neural Networks in Combination with Various Pre-Processing Techniques BRAIN SCIENCES 2022 https://doi.org/10.3390/brainsci12050615
• Jamarik, J; Vojtisek, L; Churova, V; Kasparek, T; Schwarz, D Identification of Laminar Composition in Cerebral Cortex Using Low-Resolution Magnetic Resonance Images and Trust Region Optimization Algorithm DIAGNOSTICS 2022 https://doi.org/10.3390/diagnostics12010024
• Churova, V; Vyskovsky, R; Marsalova, K; Kudlacek, D; Schwarz, D Anomaly Detection Algorithm for Real-World Data and Evidence in Clinical Research: Implementation, Evaluation, and Validation Study JMIR MEDICAL INFORMATICS 2021 https://doi.org/10.2196/27172
• Filip, P; Dufek, M; Mangia, S; Michaeli, S; Bares, M; Schwarz, D; Rektor, I; Vojtisek, L Alterations in Sensorimotor and Mesiotemporal Cortices and Diffuse White Matter Changes in Primary Progressive Multiple Sclerosis Detected by Adiabatic Relaxometry FRONTIERS IN NEUROSCIENCE 2021 https://doi.org/10.3389/fnins.2021.711067
• Vyskovsky, R; Schwarz, D; Kasparek, T Brain Morphometry Methods for Feature Extraction in Random Subspace Ensemble Neural Network Classification of First-Episode Schizophrenia NEURAL COMPUTATION 2019 https://doi.org/10.1162/neco_a_01180
• Dluhos, P; Schwarz, D; Cahn, W; van Haren, N; Kahn, R; Spaniel, F; Horacek, J; Kasparek, T; Schnack, H Multi-center machine learning in imaging psychiatry: A meta-model approach NEUROIMAGE 2017 https://doi.org/10.1016/j.neuroimage.2017.03.027
• Kůs, R; Schwarz, D Computer-aided Diagnostics of Schizophrenia: Comparison of Different Feature Extraction Methods ACTA POLYTECHNICA HUNGARICA 2017 https://doi.org/10.12700/APH.14.5.2017.5.12
• Janousova, E; Montana, G; Kasparek, T; Schwarz, D Supervised, Multivariate, Whole-Brain Reduction Did Not Help to Achieve High Classification Performance in Schizophrenia Research FRONTIERS IN NEUROSCIENCE 2016 https://doi.org/10.3389/fnins.2016.00392
• Popovici, V; Budinska, E; Capkova, L; Schwarz, D; Dusek, L; Feit, J; Jaggi, R Joint analysis of histopathology image features and gene expression in breast cancer BMC BIOINFORMATICS 2016 https://doi.org/10.1186/s12859-016-1072-z
• Janousova, E; Schwarz, D; Kasparek, T Combining various types of classifiers and features extracted from magnetic resonance imaging data in schizophrenia recognition PSYCHIATRY RESEARCH-NEUROIMAGING 2015 https://doi.org/10.1016/j.pscychresns.2015.03.004
• Schwarz, D; Kasparek, T Brain morphometry of MR images for automated classification of first-episode schizophrenia INFORMATION FUSION 2014 https://doi.org/10.1016/j.inffus.2013.02.002
• Dluhos, P; Schwarz, D; Kasparek, T Wavelet Features for Recognition of First Episode of Schizophrenia from MRI Brain Images RADIOENGINEERING 2014 https://hdl.handle.net/11012/36419
• Schwarz, D; Kasparek, T Comparison of Two Methods for Automatic Brain Morphometry Analysis RADIOENGINEERING 2011 https://hdl.handle.net/11012/56942
• Kasparek, T; Thomaz, CE; Sato, JR; Schwarz, D; Janousova, E; Marecek, R; Prikryl, R; Vanicek, J; Fujita, A; Ceskova, E Maximum-uncertainty linear discrimination analysis of first-episode schizophrenia subjects PSYCHIATRY RESEARCH-NEUROIMAGING 2011 https://doi.org/10.1016/j.pscychresns.2010.09.016
• Kasparek, T; Marecek, R; Schwarz, D; Prikryl, R; Vanicek, J; Mikl, M; Ceskova, E Source-Based Morphometry of Gray Matter Volume in Men With First-Episode Schizophrenia HUMAN BRAIN MAPPING 2010 https://doi.org/10.1002/hbm.20865
• Kasparek, T; Prikryl, R; Schwarz, D; Kucerova, H; Marecek, R; Mikl, M; Vanicek, J; Ceskova, E Gray matter morphology and the level of functioning in one-year follow-up of first-episode schizophrenia patients PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY 2009 https://doi.org/10.1016/j.pnpbp.2009.07.025
• Kasparek, T; Prikryl, R; Schwarz, D; Tronerova, S; Ceskova, E; Mikl, M; Vanicek, J Movement sequencing abilities and basal ganglia morphology in first-episode schizophrenia WORLD JOURNAL OF BIOLOGICAL PSYCHIATRY 2009 https://doi.org/10.1080/15622970701882433
• Schwarz, D; Kasparek, T; Provaznik, I; Jarkovsky, J A deformable registration method for automated morphometry of MRI brain images in neuropsychiatric research IEEE TRANSACTIONS ON MEDICAL IMAGING 2007 https://doi.org/10.1109/TMI.2007.892512