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Jussi Tohka

Jussi Tohka

Professor

Biomedical image analysis

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

[email protected] | +358 50 575 7318

Information Publications

Research groups

Biomedical MRI 01.01.1995 -
Biomedical Image Analysis 01.11.2016 -
Heart surgery imaging 01.01.2022 -

Projects

Enhancing the innovation potential by advancing the know-how on biomedical image analysis - Kuopio Biomedical Image Analysis Center (KUBIAC) Finished 01.10.2019 - 30.06.2022
Neuro-Innovation 01.05.2021 - 30.04.2026
UEF Brain Research Unit 2.0 Finished 01.03.2023 - 28.02.2025

Keywords

image analysis machine learning neuroinformatics signal processing

Publications

74/74 items

Damage in thalamic projection to perilesional cortex as a prognostic biomarker for experimental post‐traumatic epilepsy
Manninen, Eppu; Cabeen, Ryan; Immonen, Riikka; Ndode‐Ekane, Xavier Ekolle; Andrade, Pedro; Harris, Neil G.; Wright, David K.; Tohka, Jussi; Gröhn, Olli; Pitkänen, Asla. 2025. Epilepsia. [First published: 20 May 2025]: 1-12 A1 Journal article (refereed), original research
Editorial: Computational intelligence for signal and image processing, volume II
Koundal, Deepika; Tohka, Jussi. 2025. Frontiers in computational neuroscience. 19: B1 Non-refereed journal articles
Predicting Knee Osteoarthritis Severity from Radiographic Predictors: Data from the Osteoarthritis Initiative
Nurmirinta, Teemu AT.; Turunen, Mikael J; Tohka, Jussi; Mononen, Mika E; Liukkonen, Mimmi K. 2025. Annals of biomedical engineering. [Published: 09 May 2025]: 1-10 A1 Journal article (refereed), original research
Segment Anything for Dendrites from Electron Microscopy
Zhuo, Zewen; Belevich, Ilya; Leinonen, Ville; Jokitalo, Eija; Malm, Tarja; Sierra, Alejandra; Tohka, Jussi. Teoksessa: (toim.) , 2025. The Sixth IEEE International Image Processing, Applications and Systems Conference (IPAS'6) - Conference Proceedings. s. 1-6. IEEE A4 Conference proceedings
ComBating inter‐site differences in field strength: harmonizing preclinical traumatic brain injury MRI data
Quach, Mara; Ali, Idrish; Shultz, Sandy R; Casillas‐Espinosa, Pablo M; Hudson, Matthew R; Jones, Nigel C; Silva, Juliana C; Yamakawa, Glenn R; Braine, Emma L; Immonen, Riikka; Staba, Richard J; Tohka, Jussi; Harris, Neil G; Gröhn, Olli; O'Brien, Terence J; Wright, David K. 2024. Nmr in biomedicine. 37: A1 Journal article (refereed), original research
Estimating Dementia Onset: AT(N) Profiles and Predictive Modeling in Mild Cognitive Impairment Patients
Platero, Carlos; Tohka, Jussi; Strange, Bryan. 2024. Current alzheimer research. 2023; 20: 778-790 A1 Journal article (refereed), original research
Intelligence and cortical morphometry: caveats in brain-behavior associations
Lewis, John D; Imani, Vandad; Tohka, Jussi. 2024. Brain structure and function. 229: 1417-1432 A1 Journal article (refereed), original research
Machine learning prediction of future amyloid beta positivity in amyloid-negative individuals
Moradi, Elaheh; Prakash, Mithilesh; Hall, Anette; Solomon, Alina; Strange, Bryan; Tohka, Jussi; Alzheimer’s Disease Neuroimaging Initiative. 2024. Alzheimer's research and therapy. 16: . 46 A1 Journal article (refereed), original research
Multi-objective genetic algorithm for multi-view feature selection
Imani, Vandad; Sevilla-Salcedo, Carlos; Moradi, Elaheh; Fortino, Vittorio; Tohka, Jussi; for the Alzheimer’s Disease Neuroimaging Initiative. 2024. Applied soft computing. 167: . 112332 A1 Journal article (refereed), original research
No-Clean-Reference Image Super-Resolution: Application to Electron Microscopy
Khateri, Mohammad; Ghahremani, Morteza; Sierra, Alejandra; Tohka, Jussi. 2024. IEEE Transactions on computational imaging. 10: 1094-1110 A1 Journal article (refereed), original research
Optimizing Feature Selection for Binary Classification with Noisy Labels: A Genetic Algorithm Approach
Imani, Vandad; Moradi, Elaheh; Sevilla-Salcedo, Carlos; Fortino, Vittorio; Tohka, Jussi. Teoksessa: Daimi, Kevin; Al Sadoon, Abeer(toim.) , 2024. Proceedings of the Second International Conference on Advances in Computing Research (ACR’24). s. 392-403. Springer A4 Conference proceedings
Sauron U-Net: Simple automated redundancy elimination in medical image segmentation via filter pruning
Valverde, Juan Miguel; Shatillo, Artem; Tohka, Jussi. 2024. Neurocomputing. 594: . 127817 A1 Journal article (refereed), original research
Two-Stage Classification of Future Knee Osteoarthritis Severity After 8 Years Using MRI: Data from the Osteoarthritis Initiative
Nurmirinta, Teemu AT; Turunen, Mikael J; Korhonen, Rami K; Tohka, Jussi; Liukkonen, Mimmi K; Mononen, Mika E. 2024. Annals of biomedical engineering. 52: 3172-3183 A1 Journal article (refereed), original research
Volume electron microscopy in injured rat brain validates white matter microstructure metrics from diffusion MRI
Coronado-Leija, Ricardo; Abdollahzadeh, Ali; Lee, Hong-Hsi; Coelho, Santiago; Ades-Aron, Benjamin; Liao, Ying; Salo, Raimo A.; Tohka, Jussi; Sierra, Alejandra; Novikov, Dmitry S.; Fieremans, Els. 2024. Imaging neuroscience. 2: 1-20 A1 Journal article (refereed), original research
Brain structure and phenotypic profile of superagers compared with age-matched older adults: a longitudinal analysis from the Vallecas Project
Garo-Pascual, Marta; Gaser, Christian; Zhang, Linda; Tohka, Jussi; Medina, Miguel; Strange, Bryan A. 2023. The Lancet healthy longevity. 4: e374-e385 A1 Journal article (refereed), original research
Image data harmonization tools for the analysis of post-traumatic epilepsy development in preclinical multisite MRI studies
Bhagavatula, Sweta; Cabeen, Ryan; Harris, Neil G.; Gröhn, Olli; Wright, David K.; Garner, Rachael; Bennett, Alexis; Alba, Celina; Martinez, Aubrey; Ndode-Ekane, Xavier Ekolle; Andrade, Pedro; Paananen, Tomi; Ciszek, Robert; Immonen, Riikka; Manninen, Eppu; Puhakka, Noora; Tohka, Jussi; Heiskanen, Mette; Ali, Idrish; Shultz, Sandy R.; Casillas-Espinosa, Pablo M.; Yamakawa, Glenn R.; Jones, Nigel C.; Hudson, Matthew R.; Silva, Juliana C.; Braine, Emma L.; Brady, Rhys D.; Santana-Gomez, Cesar E.; S. 2023. Epilepsy research. 195: A1 Journal article (refereed), original research
Node of Ranvier remodeling in chronic psychosocial stress and anxiety
Koskinen, Maija-Kreetta; Laine, Mikaela; Abdollahzadeh, Ali; Gigliotta, Adrien; Mazzini, Giulia; Journée, Sarah; Alenius, Varpu; Trontti, Kalevi; Tohka, Jussi; Hyytiä, Petri; Sierra, Alejandra; Hovatta, Iiris. 2023. Neuropsychopharmacology. 48: 1532-1540 A1 Journal article (refereed), original research
Region-wise loss for biomedical image segmentation
Valverde, Juan Miguel; Tohka, Jussi. 2023. Pattern recognition. 136: A1 Journal article (refereed), original research
Self-Supervised Super-Resolution Approach for Isotropic Reconstruction of 3D Electron Microscopy Images from Anisotropic Acquisition
Khateri, Mohammad; Ghahremani, Morteza; Sierra, Alejandra; Tohka, Jussi. Teoksessa: Sole, Aditya; Le Moan, Steven; Qureshi, Muhammad Ali(toim.) , 2023. Proceedings: 2023 11th European Workshop on Visual Information Processing (EUVIP). s. 1-6. IEEE A4 Conference proceedings
SproutAngio: an open-source bioimage informatics tool for quantitative analysis of sprouting angiogenesis and lumen space
Beter, M; Abdollahzadeh, A; Pulkkinen, HH; Huang, H; Orsenigo, F; Magnusson, PU; Ylä-Herttuala, S; Tohka, J; Laakkonen, JP. 2023. Scientific reports. 13: . 7279 A1 Journal article (refereed), original research
A multiscale tissue assessment in a rat model of mild traumatic brain injury
San Martín Molina, Isabel; Fratini, Michela; Campi, Gaetano; Burghammer, Manfred; Grünewald, Tilman A; Salo, Raimo A; Narvaez, Omar; Aggarwal, Manisha; Tohka, Jussi; Sierra, Alejandra. 2022. Journal of neuropathology and experimental neurology. 82: 71-83 A1 Journal article (refereed), original research
Acute Hippocampal Damage as a Prognostic Biomarker for Cognitive Decline but Not for Epileptogenesis after Experimental Traumatic Brain Injury
Manninen, Eppu; Chary, Karthik; De Feo, Riccardo; Hämäläinen, Elina; Andrade, Pedro; Paananen, Tomi; Sierra, Alejandra; Tohka, Jussi; Gröhn, Olli; Pitkänen, Asla. 2022. Biomedicines. 10: A1 Journal article (refereed), original research
Automatic Cerebral Hemisphere Segmentation in Rat MRI with Ischemic Lesions via Attention-based Convolutional Neural Networks
Valverde, Juan Miguel; Shatillo, Artem; De Feo, Riccardo; Tohka, Jussi. 2022. Neuroinformatics. 2023; 21: 57-70 A1 Journal article (refereed), original research
Convolutional Neural Networks Enable Robust Automatic Segmentation of the Rat Hippocampus in MRI After Traumatic Brain Injury
De Feo, Riccardo; Hämäläinen, Elina; Manninen, Eppu; Immonen, Riikka; Valverde, Juan Miguel; Ndode-Ekane, Xavier Ekolle; Gröhn, Olli; Pitkänen, Asla; Tohka, Jussi. 2022. Frontiers in neurology. 13: . 820267 A1 Journal article (refereed), original research
Hippocampal position and orientation as prognostic biomarkers for posttraumatic epileptogenesis: An experimental study in a rat lateral fluid percussion model
De Feo, Riccardo; Manninen, Eppu; Chary, Karthik; Hämäläinen, Elina; Immonen, Riikka; Andrade, Pedro; Ndode‐Ekane, Xavier Ekolle; Gröhn, Olli; Pitkänen, Asla; Tohka, Jussi. 2022. Epilepsia. 63: 1849-1861 A1 Journal article (refereed), original research
Histopathological modeling of status epilepticus-induced brain damage based on in vivo diffusion tensor imaging in rats
San Martín Molina, Isabel; Salo, Raimo A.; Gröhn, Olli; Tohka, Jussi; Sierra, Alejandra. 2022. Frontiers in neuroscience. 16: . 944432 A1 Journal article (refereed), original research
Individualized prediction of future cognition based on developmental changes in cortical anatomy
Khundrakpam, Budhachandra; Booij, Linda; Jeon, Seun; Karama, Sherif; Tohka, Jussi; Evans, Alan C.. 2022. Neuroimage : reports. 2: A1 Journal article (refereed), original research
Multi-task longitudinal forecasting with missing values on Alzheimer’s disease
Sevilla-Salcedo, Carlos; Imani, Vandad; M Olmos, Pablo; Gómez-Verdejo, Vanessa; Tohka, Jussi. 2022. Computer methods and programs in biomedicine. 226: A1 Journal article (refereed), original research
The role of the meningeal lymphatic system in local meningeal inflammation and trigeminal nociception
Mikhailov, Nikita; Virenque, Anaïs; Koroleva, Kseniia; Eme-Scolan, Elisa; Teleman, Matei; Abdollahzadeh, Ali; Giniatullina, Raisa; Gafurov, Oleg; Krivoshein, Georgii; Malm, Tarja; Hämäläinen, Riikka H; Sierra, Alejandra; Tohka, Jussi; Rua, Rejane; Noe, Francesco M; Giniatullin, Rashid. 2022. Scientific reports. 12: . 8804 A1 Journal article (refereed), original research
What does FEXI measure?
Khateri, Mohammad; Reisert, Marco; Sierra, Alejandra; Tohka, Jussi; Kiselev, Valerij G.. 2022. Nmr in biomedicine. 35: A1 Journal article (refereed), original research
gACSON software for automated segmentation and morphology analyses of myelinated axons in 3D electron microscopy
Behanova, Andrea; Abdollahzadeh, Ali; Belevich, Ilya; Jokitalo, Eija; Sierra, Alejandra; Tohka, Jussi. 2022. Computer methods and programs in biomedicine. 220: A1 Journal article (refereed), original research
Acute thalamic damage as a prognostic biomarker for post-traumatic epileptogenesis
Manninen, Eppu; Chary, Karthik; Lapinlampi, Niina; Andrade, Pedro; Paananen, Tomi; Sierra, Alejandra; Tohka, Jussi; Gröhn, Olli; Pitkänen, Asla. 2021. Epilepsia. 62: 1852-1864 A1 Journal article (refereed), original research
Automated joint skull-stripping and segmentation with Multi-Task U-Net in large mouse brain MRI databases
De Feo, Riccardo; Shatillo, Artem; Sierra, Alejandra; Valverde, Juan Miguel; Gröhn, Olli; Giove, Federico; Tohka, Jussi. 2021. Neuroimage. 229: 117734 A1 Journal article (refereed), original research
Comparing methods of detecting and segmenting unruptured intracranial aneurysms on TOF-MRAS: The ADAM Challenge
Timmins, Kimberley M; van der Schaaf, Irene C; Bennink, Edwin; Ruigrok, Ynte M; An, Xingle; Baumgartner, Michael; Bourdon, Pascal; De Feo, Riccardo; Noto, Tommaso Di; Dubost, Florian; Fava-Sanches, Augusto; Feng, Xue; Giroud, Corentin; Inteneural Group; Hu, Minghui; Jaeger, Paul F; Kaiponen, Juhana; Klimont, Michal; Li, Yuexiang; Li, Hongwei; et al. [incl. Tohka, Jussi]. 2021. Neuroimage. 238: 118216 A1 Journal article (refereed), original research
Comparison of Single and Multitask Learning for Predicting Cognitive Decline Based on MRI Data
Imani, Vandad; Prakash, Mithilesh; Zare, Marzieh; Tohka, Jussi. 2021. IEEE access. 9: 154275-154291 A1 Journal article (refereed), original research
Contribution of astrocytes to familial risk and clinical manifestation of schizophrenia
Koskuvi, Marja; Lehtonen, ¦árka; Trontti, Kalevi; Keuters, Meike; Wu, Ying-Chieh; Koivisto, Hennariikka; Ludwig, Anastasia; Plotnikova, Lidiia; Virtanen, Pekka LJ; Räsänen, Noora; Kaipainen, Satu; Hyötyläinen, Ida; Dhungana, Hiramani; Giniatullina, Raisa; Ojansuu, Ilkka; Vaurio, Olli; Cannon, Tyrone D; Lönnqvist, Jouko; Therman, Sebastian; Suvisaari, Jaana; Kaprio, Jaakko; Lähteenvuo, Markku; Tohka, Jussi; Giniatullin, Rashid; Rivera, Claudio; Hovatta, Iiris; Tanila, Heikki; Tiihonen, Jari; Koi. 2021. Glia. 2022; 70: 650-660 A1 Journal article (refereed), original research
Cylindrical Shape Decomposition for 3D Segmentation of Tubular Objects
Abdollahzadeh, Ali; Sierra, Alejandra; Tohka, Jussi. 2021. IEEE access. 9: 23979-23995 A1 Journal article (refereed), original research
DeepACSON automated segmentation of white matter in 3D electron microscopy
Abdollahzadeh, Ali; Belevich, Ilya; Jokitalo, Eija; Sierra, Alejandra; Tohka, Jussi. 2021. Communications biology. 4: 179 A1 Journal article (refereed), original research
Evaluation of machine learning algorithms for health and wellness applications: A tutorial
Tohka, Jussi; van Gils, Mark. 2021. Computers in biology and medicine. 132: 104324 A1 Journal article (refereed), original research
Microstructural Tissue Changes in a Rat Model of Mild Traumatic Brain Injury
Chary Karthik, Narvaez Omar, Salo Raimo A, San Martín Molina Isabel, Tohka Jussi, Aggarwal Manisha, Gröhn Olli, Sierra Alejandra. 2021. Frontiers in neuroscience. 15: 746214 A1 Journal article (refereed), original research
Neural-level associations of non-verbal pragmatic comprehension in young Finnish autistic adults
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. International journal of circumpolar health. 80: 1909333 A1 Journal article (refereed), original research
Quantitative Longitudinal Predictions of Alzheimer's Disease by Multi-Modal Predictive Learning
Prakash, Mithilesh; Abdelaziz, Mahmoud; Zhang, Linda; Strange, Bryan A; Tohka, Jussi; for the Alzheimer's Disease Neuroimaging Initiative. 2021. Journal of Alzheimer's disease. 79: 1533-1546 A1 Journal article (refereed), original research
Steerable3D: An ImageJ plugin for neurovascular enhancement in 3-D segmentation
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. Physica medica. 81: 197-209 A1 Journal article (refereed), original research
The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up
Marinescu, Razvan V.; Oxtoby, Neil P.; Young, Alexandra L.; Bron, Esther E.; Toga, Arthur W.; Weiner, Michael W.; Barkhof, Frederik; Fox, Nick C.; Eshaghi, Arman; Toni, Tina; Salaterski, Marcin; Lunina, Veronika; Ansart, Manon; Durrleman, Stanley; Lu, Pascal; Iddi, Samuel; Li, Dan; Thompson, Wesley K.; Donohue, Michael C.; Nahon, Aviv et al [incl. Tohka, Jussi; Ciszek, Robert]. 2021. The journal of machine learning for biomedical imaging. Published online: 31 December 2021: 1 - 60 A1 Journal article (refereed), original research
Transfer Learning in Magnetic Resonance Brain Imaging: A Systematic Review
Valverde, Juan Miguel; Imani, Vandad; Abdollahzadeh, Ali; De Feo, Riccardo; Prakash, Mithilesh; Ciszek, Robert; Tohka, Jussi. 2021. Journal of imaging. 7: 66 A2 Review article, Literature review, Systematic review
ADHD desynchronizes brain activity during watching a distracted multi-talker conversation
Salmi, J; Metwaly, M; Tohka, J; Alho, K; Leppämäki, S; Tani, P; Koski, A; Vanderwal, T; Laine, M. 2020. Neuroimage. 216: 116352 A1 Journal article (refereed), original research
BV-2 Microglial Cells Overexpressing C9orf72 Hexanucleotide Repeat Expansion Produce DPR Proteins and Show Normal Functionality but No RNA Foci
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. Frontiers in neurology. 11: 550140 A1 Journal article (refereed), original research
Brain and behavioral alterations in subjects with social anxiety dominated by empathic embarrassment
Tei, S; Kauppi, JP; Jankowski, KF; Fujino, J; Monti, RP; Tohka, J; Abe, N; Murai, T; Takahashi, H; Hari, R. 2020. Proceedings of the National Academy of Sciences of the United States of America. 117: 4385-4391 A1 Journal article (refereed), original research
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
Manninen, Eppu Matias; Chary, Karthik; Lapinlampi, Niina; Andrade, Pedro; Paananen, Tomi; Sierra Lopez, Alejandra; Tohka, Jussi; Gröhn, Olli; Pitkanen, Asla. 2020. Journal of neurotrauma. 37: 2580-2594 A1 Journal article (refereed), original research
Elevated acute plasma miR-124-3p level relates to evolution of larger cortical lesion area after traumatic brain injury
Vuokila, Niina; Gupta, Shalini Das; Huusko, Riina; Tohka, Jussi; Puhakka, Noora; Pitkänen, Asla. 2020. Neuroscience. 433: 21-35 A1 Journal article (refereed), original research
In vivo diffusion tensor imaging in acute and subacute phases of mild traumatic brain injury in rats
San Martín Molina, Isabel; Salo, Raimo A; Abdollahzadeh, Ali; Tohka, Jussi; Gröhn, Olli; Sierra, Alejandra. 2020. eNeuro. 7: ENEURO.0476-19.2020 A1 Journal article (refereed), original research
Multiscale Imaging Approach for Studying the Central Nervous System: Methodology and Perspective
Fratini, Michela; Abdollahzadeh, Ali; DiNuzzo, Mauro; Salo, Raimo; Maugeri, Laura; Cedola, Alessia; Giove, Federico; Gröhn, Olli; Tohka, Jussi; Sierra, Alejandra. 2020. Frontiers in neuroscience. 14: 72 A2 Review article, Literature review, Systematic review
RatLesNetv2: A Fully Convolutional Network for Rodent Brain Lesion Segmentation
Valverde, Juan Miguel; Shatillo, Artem; De Feo, Riccardo; Gröhn, Olli; Sierra, Alejandra; Tohka, Jussi. 2020. Frontiers in neuroscience. 14: 610239 A1 Journal article (refereed), original research
Regularized Bagged Canonical Component Analysis for Multiclass Learning in Brain Imaging
Sevilla-Salcedo, Carlos; Gómez-Verdejo, Vanessa; Tohka, Jussi; Alzheimer's Disease Neuroimaging Initiative. 2020. Neuroinformatics. 18: 641-659 A1 Journal article (refereed), original research
Searching for Predictors of Migraine Chronification: a Pilot Study of 1911A>G Polymorphism of TRPV1 Gene in Episodic Versus Chronic Migraine
Yakubova, Aliya; Davidyuk, Yuriy; Tohka, Jussi; Khayrutdinova, Olga; Kudryavtsev, Igor; Nurkhametova, Dilyara; Kamshilin, Alexei; Giniatullin, Rashid; Rizvanov, Albert. 2020. Journal of molecular neuroscience. 2021; 71: 618-624 A1 Journal article (refereed), original research
Structural Brain Imaging Phenotypes of Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD) Found by Hierarchical Clustering
Kärkkäinen, Mikko; Prakash, Mithilesh; Zare, Marzieh; Tohka, Jussi. 2020. International journal of alzheimers disease. 2020: 2142854 A1 Journal article (refereed), original research
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
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. Schizophrenia research. 216: 14-23 A1 Journal article (refereed), original research
Automated 3D Axonal Morphometry of White Matter
Abdollahzadeh, A; Belevich, I; Jokitalo, E; Tohka, J; Sierra, A. 2019. Scientific reports. 9: 6084 A1 Journal article (refereed), original research
Automatic Rodent Brain MRI Lesion Segmentation with Fully Convolutional Networks
Valverde, JM; Shatillo, A; De Feo, R; Gröhn, O; Sierra, A; Tohka, J. Teoksessa: Suk, HI; Liu, M; Yan, P; Lian, C(toim.) , 2019. Machine Learning in Medical Imaging. MLMI 2019. s. 195-202. Springer A3 Book section, Chapters in research books
Bayesian receiver operating characteristic metric for linear classifiers
Hassan, Syeda Sakira; Huttunen, Heikki; Niemi, Jari; Tohka, Jussi. 2019. Pattern recognition letters. 128: 52-59 A1 Journal article (refereed), original research
Cortical and subcortical T1 white/gray contrast, chronological age, and cognitive performance
Lewis, JD; Fonov, VS; Collins, DL; Evans, AC; Tohka, J. 2019. Neuroimage. 196: 276-288 A1 Journal article (refereed), original research
Harmonization of the pipeline for seizure detection to phenotype post-traumatic epilepsy in a preclinical multicenter study on post-traumatic epileptogenesis
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. Epilepsy research. 156: 106131 A1 Journal article (refereed), original research
In Vitro and In Vivo Pipeline for Validation of Disease-Modifying Effects of Systems Biology-Derived Network Treatments for Traumatic Brain Injury - Lessons Learned
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. International journal of molecular sciences. 20: 5395 A1 Journal article (refereed), original research
Predicting Intelligence Based on Cortical WM/GM Contrast, Cortical Thickness and Volumetry
Valverde, JM; Imani, V; Lewis, JD; Tohka, J. Teoksessa: Pohl, K; Thompson, W; Adeli, E; Linguraru, M(toim.) , 2019. Adolescent Brain Cognitive Development Neurocognitive Prediction. ABCD-NP 2019. s. 57-65. Springer A3 Book section, Chapters in research books
Sex-specific transcriptional and proteomic signatures in schizophrenia
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. Nature communications. 10: 3933 A1 Journal article (refereed), original research
Sign-Consistency Based Variable Importance for Machine Learning in Brain Imaging
Gómez-Verdejo, V; Parrado-Hernández, E; Tohka, J. 2019. Neuroinformatics. 17: 593-609 A1 Journal article (refereed), original research
Antipsychotic and benzodiazepine use and brain morphology in schizophrenia and affective psychoses - Systematic reviews and birth cohort study
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. Psychiatry research: neuroimaging. 281: 43-52 A2 Review article, Literature review, Systematic review
Comparison of feature representations in MRI-based MCI-to-AD conversion prediction
Gómez-Sancho, Marta; Tohka, Jussi; Gómez-Verdejo, Vanessa. 2018. Magnetic resonance imaging. 50: 84-95 A1 Journal article (refereed), original research
Informatics tools to assess the success of procedural harmonization in preclinical multicenter biomarker discovery study on post-traumatic epileptogenesis
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. Epilepsy research. 2019; 150: 17-26 A1 Journal article (refereed), original research
T1 white/gray contrast as a predictor of chronological age, and an index of cognitive performance
Lewis, John D; Evans, Alan C; Tohka, Jussi. 2018. Neuroimage. 173: 341-350 A1 Journal article (refereed), original research
Functional brain segmentation using inter-subject correlation in fMRI
Kauppi JP, Pajula J, Niemi J, Hari R, Tohka J. 2017. Human brain mapping. 38: 2643-2665 A1 Journal article (refereed), original research
Long-term antipsychotic and benzodiazepine use and brain volume changes in schizophrenia: The Northern Finland Birth Cohort 1966 study
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. Psychiatry research: neuroimaging. 266: 73-82 A1 Journal article (refereed), original research
Predicting symptom severity in autism spectrum disorder based on cortical thickness measures in agglomerative data
Moradi, Elaheh; Khundrakpam, Budhachandra; Lewis, John D; Evans, Alan C; Tohka, Jussi. 2017. Neuroimage. 144: 128-141 A1 Journal article (refereed), original research
Rey's Auditory Verbal Learning Test scores can be predicted from whole brain MRI in Alzheimer's disease
Moradi E, Hallikainen I, Hänninen T, Tohka J. 2016. Neuroimage : clinical. 2017; 13: 415-427 A1 Journal article (refereed), original research

University of Eastern Finland Joensuu, Kuopio © University of Eastern Finland

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Jussi Tohka

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Damage in thalamic projection to perilesional cortex as a prognostic biomarker for experimental post‐traumatic epilepsy

Editorial: Computational intelligence for signal and image processing, volume II

Predicting Knee Osteoarthritis Severity from Radiographic Predictors: Data from the Osteoarthritis Initiative

Segment Anything for Dendrites from Electron Microscopy

ComBating inter‐site differences in field strength: harmonizing preclinical traumatic brain injury MRI data

Estimating Dementia Onset: AT(N) Profiles and Predictive Modeling in Mild Cognitive Impairment Patients

Intelligence and cortical morphometry: caveats in brain-behavior associations

Machine learning prediction of future amyloid beta positivity in amyloid-negative individuals

Multi-objective genetic algorithm for multi-view feature selection

No-Clean-Reference Image Super-Resolution: Application to Electron Microscopy

Optimizing Feature Selection for Binary Classification with Noisy Labels: A Genetic Algorithm Approach

Sauron U-Net: Simple automated redundancy elimination in medical image segmentation via filter pruning

Two-Stage Classification of Future Knee Osteoarthritis Severity After 8 Years Using MRI: Data from the Osteoarthritis Initiative

Volume electron microscopy in injured rat brain validates white matter microstructure metrics from diffusion MRI

Brain structure and phenotypic profile of superagers compared with age-matched older adults: a longitudinal analysis from the Vallecas Project

Image data harmonization tools for the analysis of post-traumatic epilepsy development in preclinical multisite MRI studies

Node of Ranvier remodeling in chronic psychosocial stress and anxiety

Region-wise loss for biomedical image segmentation

Self-Supervised Super-Resolution Approach for Isotropic Reconstruction of 3D Electron Microscopy Images from Anisotropic Acquisition

SproutAngio: an open-source bioimage informatics tool for quantitative analysis of sprouting angiogenesis and lumen space

A multiscale tissue assessment in a rat model of mild traumatic brain injury

Acute Hippocampal Damage as a Prognostic Biomarker for Cognitive Decline but Not for Epileptogenesis after Experimental Traumatic Brain Injury

Automatic Cerebral Hemisphere Segmentation in Rat MRI with Ischemic Lesions via Attention-based Convolutional Neural Networks

Convolutional Neural Networks Enable Robust Automatic Segmentation of the Rat Hippocampus in MRI After Traumatic Brain Injury

Hippocampal position and orientation as prognostic biomarkers for posttraumatic epileptogenesis: An experimental study in a rat lateral fluid percussion model

Histopathological modeling of status epilepticus-induced brain damage based on in vivo diffusion tensor imaging in rats

Individualized prediction of future cognition based on developmental changes in cortical anatomy

Multi-task longitudinal forecasting with missing values on Alzheimer’s disease

The role of the meningeal lymphatic system in local meningeal inflammation and trigeminal nociception

What does FEXI measure?

gACSON software for automated segmentation and morphology analyses of myelinated axons in 3D electron microscopy

Acute thalamic damage as a prognostic biomarker for post-traumatic epileptogenesis

Automated joint skull-stripping and segmentation with Multi-Task U-Net in large mouse brain MRI databases

Comparing methods of detecting and segmenting unruptured intracranial aneurysms on TOF-MRAS: The ADAM Challenge

Comparison of Single and Multitask Learning for Predicting Cognitive Decline Based on MRI Data

Contribution of astrocytes to familial risk and clinical manifestation of schizophrenia

Cylindrical Shape Decomposition for 3D Segmentation of Tubular Objects

DeepACSON automated segmentation of white matter in 3D electron microscopy

Evaluation of machine learning algorithms for health and wellness applications: A tutorial

Microstructural Tissue Changes in a Rat Model of Mild Traumatic Brain Injury

Neural-level associations of non-verbal pragmatic comprehension in young Finnish autistic adults

Quantitative Longitudinal Predictions of Alzheimer's Disease by Multi-Modal Predictive Learning

Steerable3D: An ImageJ plugin for neurovascular enhancement in 3-D segmentation

The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up

Transfer Learning in Magnetic Resonance Brain Imaging: A Systematic Review

ADHD desynchronizes brain activity during watching a distracted multi-talker conversation

BV-2 Microglial Cells Overexpressing C9orf72 Hexanucleotide Repeat Expansion Produce DPR Proteins and Show Normal Functionality but No RNA Foci

Brain and behavioral alterations in subjects with social anxiety dominated by empathic embarrassment

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

Elevated acute plasma miR-124-3p level relates to evolution of larger cortical lesion area after traumatic brain injury

In vivo diffusion tensor imaging in acute and subacute phases of mild traumatic brain injury in rats

Multiscale Imaging Approach for Studying the Central Nervous System: Methodology and Perspective

RatLesNetv2: A Fully Convolutional Network for Rodent Brain Lesion Segmentation

Regularized Bagged Canonical Component Analysis for Multiclass Learning in Brain Imaging

Searching for Predictors of Migraine Chronification: a Pilot Study of 1911A>G Polymorphism of TRPV1 Gene in Episodic Versus Chronic Migraine

Structural Brain Imaging Phenotypes of Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD) Found by Hierarchical Clustering

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

Automated 3D Axonal Morphometry of White Matter

Automatic Rodent Brain MRI Lesion Segmentation with Fully Convolutional Networks

Bayesian receiver operating characteristic metric for linear classifiers

Cortical and subcortical T1 white/gray contrast, chronological age, and cognitive performance

Harmonization of the pipeline for seizure detection to phenotype post-traumatic epilepsy in a preclinical multicenter study on post-traumatic epileptogenesis

In Vitro and In Vivo Pipeline for Validation of Disease-Modifying Effects of Systems Biology-Derived Network Treatments for Traumatic Brain Injury - Lessons Learned

Predicting Intelligence Based on Cortical WM/GM Contrast, Cortical Thickness and Volumetry

Sex-specific transcriptional and proteomic signatures in schizophrenia

Sign-Consistency Based Variable Importance for Machine Learning in Brain Imaging

Antipsychotic and benzodiazepine use and brain morphology in schizophrenia and affective psychoses - Systematic reviews and birth cohort study

Comparison of feature representations in MRI-based MCI-to-AD conversion prediction

Informatics tools to assess the success of procedural harmonization in preclinical multicenter biomarker discovery study on post-traumatic epileptogenesis

T1 white/gray contrast as a predictor of chronological age, and an index of cognitive performance

Functional brain segmentation using inter-subject correlation in fMRI

Long-term antipsychotic and benzodiazepine use and brain volume changes in schizophrenia: The Northern Finland Birth Cohort 1966 study

Predicting symptom severity in autism spectrum disorder based on cortical thickness measures in agglomerative data

Rey's Auditory Verbal Learning Test scores can be predicted from whole brain MRI in Alzheimer's disease