JUSSI TOHKA

Professor

Lääketieteellinen kuva-analyysi

Contact info

Organization

Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences

Email

jussi.tohka@uef.fi

Phone

+358 50 575 7318

Keywords

image analysis machine learning neuroinformatics signal processing

RESEARCH GROUPS - UEF

PROJECTS - UEF

Enhancing the innovation potential by advancing the know-how on biomedical image analysis - Kuopio Biomedical Image Analysis Center (KUBIAC)

Links

Publications

Abdollahzadeh, Ali; Belevich, Ilya; Jokitalo, Eija; Sierra, Alejandra; Tohka, Jussi. 2021. DeepACSON automated segmentation of white matter in 3D electron microscopy Communications biology 4 1: 179. 2021
De Feo, Riccardo; Shatillo, Artem; Sierra, Alejandra; Valverde, Juan Miguel; Gröhn, Olli; Giove, Federico; Tohka, Jussi. 2021. Automated joint skull-stripping and segmentation with Multi-Task U-Net in large mouse brain MRI databases Neuroimage 229: 117734. 2021
Kotila, Aija; Tohka, Jussi; Kauppi, Jukka-Pekka; Gabbatore, Ilaria; Mäkinen, Leena; Hurtig, Tuula M; Ebeling, Hanna E; Korhonen, Vesa; Kiviniemi, Vesa J; Loukusa, Soile. 2021. Neural-level associations of non-verbal pragmatic comprehension in young Finnish autistic adults International journal of circumpolar health 80 1: 1909333. 2021
Manninen, Eppu; Chary, Karthik; Lapinlampi, Niina; Andrade, Pedro; Paananen, Tomi; Sierra, Alejandra; Tohka, Jussi; Gröhn, Olli; Pitkänen, Asla. 2021. Acute thalamic damage as a prognostic biomarker for post-traumatic epileptogenesis Epilepsia 62 8: 1852-1864. 2021
Miocchi, Paolo; Sierra, Alejandra; Maugeri, Laura; Stefanutti, Eleonora; Abdollahzadeh, Ali; Mangini, Fabio; Moraschi, Marta; Bukreeva, Inna; Massimi, Lorenzo; Brun, Francesco; Tohka, Jussi; Gröhn, Olli; Mittone, Alberto; Bravin, Alberto; Nicaise, Charles; Giove, Federico; Cedola, Alessia; Fratini, Michela. 2021. Steerable3D: An ImageJ plugin for neurovascular enhancement in 3-D segmentation Physica medica 81: 197-209. 2021
Prakash, Mithilesh; Abdelaziz, Mahmoud; Zhang, Linda; Strange, Bryan A; Tohka, Jussi; for the Alzheimer's Disease Neuroimaging Initiative. 2021. Quantitative Longitudinal Predictions of Alzheimer's Disease by Multi-Modal Predictive Learning Journal of Alzheimer's disease 79 4: 1533-1546. 2021
Tohka, Jussi; van Gils, Mark. 2021. Evaluation of machine learning algorithms for health and wellness applications: A tutorial Computers in biology and medicine 132: 104324. 2021
Valverde, Juan Miguel; Imani, Vandad; Abdollahzadeh, Ali; De Feo, Riccardo; Prakash, Mithilesh; Ciszek, Robert; Tohka, Jussi. 2021. Transfer Learning in Magnetic Resonance Brain Imaging: A Systematic Review Journal of imaging 7 4: 66. 2021
Abdollahzadeh, Ali; Sierra, Alejandra; Tohka, Jussi. 2021. Cylindrical Shape Decomposition for 3D Segmentation of Tubular Objects IEEE access 9: 23979-23995. 2021
San Martín Molina, Isabel; Salo, Raimo A; Abdollahzadeh, Ali; Tohka, Jussi; Gröhn, Olli; Sierra, Alejandra. 2020. In vivo diffusion tensor imaging in acute and subacute phases of mild traumatic brain injury in rats eNeuro 7 3: ENEURO.0476-19.2020. 2020
Yakubova, Aliya; Davidyuk, Yuriy; Tohka, Jussi; Khayrutdinova, Olga; Kudryavtsev, Igor; Nurkhametova, Dilyara; Kamshilin, Alexei; Giniatullin, Rashid; Rizvanov, Albert. 2020. Searching for Predictors of Migraine Chronification: a Pilot Study of 1911A>G Polymorphism of TRPV1 Gene in Episodic Versus Chronic Migraine Journal of molecular neuroscience 2021; 71 3: 618-624. 2020
Valverde, Juan Miguel; Shatillo, Artem; De Feo, Riccardo; Gröhn, Olli; Sierra, Alejandra; Tohka, Jussi. 2020. RatLesNetv2: A Fully Convolutional Network for Rodent Brain Lesion Segmentation Frontiers in neuroscience 14: 610239. 2020
Tei, S; Kauppi, JP; Jankowski, KF; Fujino, J; Monti, RP; Tohka, J; Abe, N; Murai, T; Takahashi, H; Hari, R. 2020. Brain and behavioral alterations in subjects with social anxiety dominated by empathic embarrassment Proceedings of the National Academy of Sciences of the United States of America 117 8: 4385-4391. 2020
Sevilla-Salcedo, Carlos; Gómez-Verdejo, Vanessa; Tohka, Jussi; Alzheimer's Disease Neuroimaging Initiative. 2020. Regularized Bagged Canonical Component Analysis for Multiclass Learning in Brain Imaging Neuroinformatics 18: 641-659. 2020
Vuokila, Niina; Gupta, Shalini Das; Huusko, Riina; Tohka, Jussi; Puhakka, Noora; Pitkänen, Asla. 2020. Elevated acute plasma miR-124-3p level relates to evolution of larger cortical lesion area after traumatic brain injury Neuroscience 433: 21-35. 2020
Salmi, J; Metwaly, M; Tohka, J; Alho, K; Leppämäki, S; Tani, P; Koski, A; Vanderwal, T; Laine, M. 2020. ADHD desynchronizes brain activity during watching a distracted multi-talker conversation Neuroimage 216: 116352. 2020
Saarinen, A I L; Huhtaniska, S; Pudas, J; Björnholm, L; Jukuri, T; Tohka, J; Granö, N; Barnett, JH; Kiviniemi, V; Veijola, J; Hintsanen, M; Lieslehto, J. 2020. Structural and functional alterations in the brain gray matter among first-degree relatives of schizophrenia patients: A multimodal meta-analysis of fMRI and VBM studies Schizophrenia research 216: 14-23. 2020
Rostalski, Hannah; Hietanen, Tomi; Leskelä, Stina; Behánová, Andrea; Abdollahzadeh, Ali; Wittrahm, Rebekka; Mäkinen, Petra; Huber, Nadine; Hoffmann, Dorit; Solje, Eino; Remes, Anne M; Natunen, Teemu; Takalo, Mari; Tohka, Jussi; Hiltunen, Mikko; Haapasalo, Annakaisa. 2020. BV-2 Microglial Cells Overexpressing C9orf72 Hexanucleotide Repeat Expansion Produce DPR Proteins and Show Normal Functionality but No RNA Foci Frontiers in neurology 11: 550140. 2020
Manninen, Eppu Matias; Chary, Karthik; Lapinlampi, Niina; Andrade, Pedro; Paananen, Tomi; Sierra Lopez, Alejandra; Tohka, Jussi; Gröhn, Olli; Pitkanen, Asla. 2020. Early increase in cortical T2 relaxation is a prognostic biomarker for the evolution of severe cortical damage, but not for epileptogenesis, after experimental traumatic brain injury Journal of neurotrauma 37 23: 2580-2594. 2020
Kärkkäinen, Mikko; Prakash, Mithilesh; Zare, Marzieh; Tohka, Jussi. 2020. Structural Brain Imaging Phenotypes of Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD) Found by Hierarchical Clustering International journal of alzheimers disease 2020: 2142854. 2020
Fratini, Michela; Abdollahzadeh, Ali; DiNuzzo, Mauro; Salo, Raimo; Maugeri, Laura; Cedola, Alessia; Giove, Federico; Gröhn, Olli; Tohka, Jussi; Sierra, Alejandra. 2020. Multiscale Imaging Approach for Studying the Central Nervous System: Methodology and Perspective Frontiers in neuroscience 14: 72. 2020
Tiihonen, J; Koskuvi, M; Storvik, M; Hyötyläinen, I; Gao, Y; Puttonen, KA; Giniatullina, R; Poguzhelskaya, E; Ojansuu, I; Vaurio, O; Cannon, TD; Lönnqvist, J; Therman, S; Suvisaari, J; Kaprio, J; Cheng, L; Hill, AF; Lähteenvuo, M; Tohka, J; Giniatullin, R; et al.. 2019. Sex-specific transcriptional and proteomic signatures in schizophrenia Nature communications 10 1: 3933. 2019
Predicting Intelligence Based on Cortical WM/GM Contrast, Cortical Thickness and Volumetry. Valverde, JM; Imani, V; Lewis, JD; Tohka, J / Adolescent Brain Cognitive Development Neurocognitive Prediction. ABCD-NP 2019. 2019. 2019
Lipponen, A; Natunen, T; Hujo, M; Ciszek, R; Hämäläinen, E; Tohka, J; Hiltunen, M; Paananen, J; Poulsen, D; Kansanen, E; Ekolle Ndode-Ekane, X; Levonen, AL; Pitkänen, A. 2019. In Vitro and In Vivo Pipeline for Validation of Disease-Modifying Effects of Systems Biology-Derived Network Treatments for Traumatic Brain Injury - Lessons Learned International journal of molecular sciences 20 21: 5395. 2019
Lewis, JD; Fonov, VS; Collins, DL; Evans, AC; Tohka, J. 2019. Cortical and subcortical T1 white/gray contrast, chronological age, and cognitive performance Neuroimage 196: 276-288. 2019
Hassan, Syeda Sakira; Huttunen, Heikki; Niemi, Jari; Tohka, Jussi. 2019. Bayesian receiver operating characteristic metric for linear classifiers Pattern recognition letters 128: 52-59. 2019
Gómez-Verdejo, V; Parrado-Hernández, E; Tohka, J. 2019. Sign-Consistency Based Variable Importance for Machine Learning in Brain Imaging Neuroinformatics 17: 593-609. 2019
Casillas-Espinosa, PM; Andrade, P; Santana-Gomez, C; Paananen, T; Smith, G; Ali, I; Ciszek, R; Ndode-Ekane, XE; Brady, RD; Tohka, J; Hudson, MR; Perucca, P; Braine, EL; Immonen, R; Puhakka, N; Shultz, SR; Jones, NC; Staba, RJ; Pitkänen, A; O'Brien, TJ. 2019. Harmonization of the pipeline for seizure detection to phenotype post-traumatic epilepsy in a preclinical multicenter study on post-traumatic epileptogenesis Epilepsy research 156: 106131. 2019
Automatic Rodent Brain MRI Lesion Segmentation with Fully Convolutional Networks. Valverde, JM; Shatillo, A; De Feo, R; Gröhn, O; Sierra, A; Tohka, J / Machine Learning in Medical Imaging. MLMI 2019. 2019. 2019
Abdollahzadeh, A; Belevich, I; Jokitalo, E; Tohka, J; Sierra, A. 2019. Automated 3D Axonal Morphometry of White Matter Scientific reports 9 1: 6084. 2019
Ciszek, R; Ndode-Ekane, XE; Gomez, CS; Casillas-Espinosa, PM; Ali, I; Smith, G; Puhakka, N; Lapinlampi, N; Andrade, P; Kamnaksh, A; Immonen, R; Paananen, T; Hudson, MR; Brady, RD; Shultz, SR; O'Brien, TJ; Staba, RJ; Tohka, J; Pitkänen, A. 2018. Informatics tools to assess the success of procedural harmonization in preclinical multicenter biomarker discovery study on post-traumatic epileptogenesis EPILEPSY RESEARCH 2019; 150: 17-26. 2018
Gómez-Sancho, Marta; Tohka, Jussi; Gómez-Verdejo, Vanessa. 2018. Comparison of feature representations in MRI-based MCI-to-AD conversion prediction Magnetic resonance imaging 50: 84-95. 2018
Huhtaniska, S; Korkala, I; Heikka, T; Björnholm, L; Lehtiniemi, H; Hulkko, AP; Moilanen, J; Tohka, J; Manjón, J; Coupé, P; Kiviniemi, V; Isohanni, M; Koponen, H; Murray, GK; Miettunen, J; Jääskeläinen, E. 2018. Antipsychotic and benzodiazepine use and brain morphology in schizophrenia and affective psychoses - Systematic reviews and birth cohort study PSYCHIATRY RESEARCH: NEUROIMAGING 281: 43-52. 2018
Lewis, John D; Evans, Alan C; Tohka, Jussi. 2018. T1 white/gray contrast as a predictor of chronological age, and an index of cognitive performance Neuroimage 173: 341-350. 2018
Huhtaniska S, Jääskeläinen E, Heikka T. Moilanen JS, Lehtiniemi H, Tohka J, Manjón JV, Coupé P, Björnholm L, Koponen H, Veijola J, Isohanni M, Kiviniemi V, Murray GK, Miettunen J. 2017. Long-term antipsychotic and benzodiazepine use and brain volume changes in schizophrenia: The Northern Finland Birth Cohort 1966 study. PSYCHIATRY RESEARCH: NEUROIMAGING 266: 73-82. 2017
Kauppi JP, Pajula J, Niemi J, Hari R, Tohka J. 2017. Functional brain segmentation using inter-subject correlation in fMRI. HUMAN BRAIN MAPPING 38 5: 2643-2665. 2017
Moradi, Elaheh; Khundrakpam, Budhachandra; Lewis, John D; Evans, Alan C; Tohka, Jussi. 2017. Predicting symptom severity in autism spectrum disorder based on cortical thickness measures in agglomerative data Neuroimage 144 Part A: 128-141. 2017
Moradi E, Hallikainen I, Hänninen T, Tohka J. 2016. Rey's Auditory Verbal Learning Test scores can be predicted from whole brain MRI in Alzheimer's disease. NEUROIMAGE: CLINICAL 2017; 13: 415-427. 2016