Machine learning in brain imaging

Principal investigator: Jussi Tohka [Google Scholar profile] [ORCID]

Associate professor of biomedical image analysis

Head of biomedical image analysis group

A. I. Virtanen Institute for Molecular Sciences

University of Eastern Finland

P.O.Box 1627 (Neulaniementie 2), FI-70211 Kuopio, Finland

Adjunct professor (docent)

Department of Signal Processing, Tampere University of Technology, Finland

email: jussi dot tohka at uef dot fi


Mithilesh Prakash, Post-doc, 2019 -

Linda Zhang, Visiting post-doc 2019

Ali Abdollahzadeh, PhD student, 2016 -, (jointly supervised with Alejandra Sierra Lopez and Olli Gröhn)

Robert Ciszek, PhD student, 2017 -, (jointly supervised with Asla Pitkänen)

Juan Miguel Valverde Martinez, PhD student, 2018 -

Vandad Imani, PhD student, 2019 -

Abu Kiani, MSc student, 2018 -,

Andrea Beháňová, MSc student, 2019 -

Mikko Kärkkäinen, PhD, MD student


19th September 2018: Two positions open: an early stage researcher (3,5 years) and a post-doc (3 years) in Brain Image Analysis/Machine Learning . Further information to apply:

18th June 2018: The Academy of Finland granted 438 875 EUR for the project "Predictive brain image analysis".

19th January 2018: 4-year PhD student position in brain image analysis at University of Eastern Finland, Kuopio, Finland

A 4-year PhD student position available in brain image analysis in Genommed doctoral programme of University of Eastern Finland, Kuopio, Finland . Research topics include automated segmentation of small animal brain MRI and multi-view learning in brain imaging, details in . The position is in Jussi Tohka’s group . The applicant must hold an MSc degree and must not have carried out his/hers main activity in Finland for more than 12 months in the 3 years immediately prior to their recruitment under the project.

The deadline for applications is 31st of January 2018, but prospective candidates are asked to contact Jussi Tohka before the application deadline.

The salary is determined in accordance with the salary system of Finnish universities and is based on levels 2-4 of the job requirement level chart for teaching and research staff. The typical starting salary is at the level 2.4 (currently 2305 EUR/month). Benefits include access to free health care, social security insurance, pension contributions, unemployment insurance contributions, annual paid leave, and parental benefits.

More information, application requirements, and a link to online application system:

12th January 2018: Pre-prints available:

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

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

- 3D Axonal Morphometry of White Matter

12th June 2017: We will present three posters at the OHBM 2017 meeting in Vancouver Canada:

1691: Comparing fMRI inter-subject correlations between groups using ISC-toolbox

3892: Machine learning and domain adaptation for cortical thickness in autism

3893: Voxel importance in classifier ensembles based on sign consistency patterns

26th May 2017: Elaheh Moradi successfully defended her PhD. Congratulations!

5th April 2017: Elaheh Moradi will defend her PhD-thesis, "Machine Learning Methods for Structural Brain MRI" at Tampere University of Technology, Finland on 26th May 2017

5th April 2017: Sign-Consistency Based Variable Importance For Machine Learning In Brain Imaging - preprint available at bioRxiv

20th March 2017: We are editing a research topic (special issue) "Machine Learning in Imaging Neurodevelopment and Neurodegeneration" in Frontiers:

24th February 2017: Advanced methods on biomedical image analysis summer school will be organized in Brno, Czech Republic, on 3 - 9 September 2017 (I will teach there). See for more info.

23rd February 2017: A paper on functional brain segmentation using inter-subject correlation accepted for human brain mapping. See . The introduced FuSeISC

tool will be integrated to the ISC Toolbox, but the developer version is already available:

24th January 2017: A paper on prediction of the RAVLT scores based on MRI is online here (open access)

2nd January 2017: Marta Gomez started her Msc thesis work

1st November 2016: Ali Abdollahzadeh started his PhD studies at University of Eastern Finland

23th Sep 2016: From 1st Nov 2016, I will be with AI Virtanen Institute for Molecular Sciences, University of Eastern Finland.

23th Sep 2016: A paper on how to correct between-site variability of MRI based cortical thickness accepted to NeuroImage: E. Moradi, B Khundrakpam, J. Lewis, A Evans, J. Tohka: Predicting symptom severity in autism spectrum disorder based on cortical thickness measures in agglomerative data, see or

22nd Apr 2016: Juha Pajula defended successfully his PhD thesis "Inter-Subject Correlation Analysis for Functional Magnetic Imaging: Properties and Validation"

26th Jan 2016: Sorry for the long silence; Few papers published recently, one on feature selection stability in structural brain imaging in Neuroinfomatics, [Preprint here], one on effect of the sample size in inter-subject correlation analysis in fMRI in Computational Intelligence and Neuroscience( see here) and one on model selection with Bayesian Error Estimator [Preprint here] .

16th Feb 2015: As of 16 Feb 2015 I am with Universidad Carlos III de Madrid as CONEX professor/distinguished researcher.

1st Feb 2015: We are editing a special issue on Validation and Simulation in Brain Image Analysis. It is to be published in Computational Intelligence and Neuroscience during the fall 2015. The deadline for papers is July 10. More info can be found here .

1st Dec 2014: We (Juha Pajula, Jukka-Pekka Kauppi and myself) won the first prize in the real-life cognition contest

1st Dec 2014: A paper published: Difference of Gaussians Revolved Along Elliptical Paths for Ultrasound Fetal Head Segmentation. Computerized Medical Imaging and Graphics , 38(8): 774 - 784, 2014 .

1st Dec 2014: A paper published: Machine learning framework for early MRI-based Alzheimer's conversion prediction in MCI subjects. NeuroImage , 104: 398 - 412, 2015.

24th July 2014 : Paper about effects of spatial smoothing on Inter subject correlation based fMRI analysis out, see Preprint

13th July 2014: Paper Published: An Automatic Framework for Quantitative Validation of Voxel Based Morphometry Measures of Anatomical Brain Asymmetry. NeuroImage , 100: 444 - 459, 2014 . See also the brainmorph webpage !

25th April 2014: Antonietta Pepe successfully defended her PhD thesis "Statistical shape analysis in neuroimaging: Methods, challenges, validation"

14th April 2014: Paper "Semi-supervised learning in MCI-to-AD conversion prediction - When is unlabeled data useful?" accepted to Pattern recognition in Neuroimaging 2014, see the paper here

31st March 2014: Paper "Evaluation and Comparison of Current Fetal Ultrasound Image Segmentation Methods for Biometric Measurements: A Grand Challenge" appeared in IEEE Transactions on Medical Imaging 33(4):797 - 813, 2014

27th January 2014: A new version (2.0) of ISC Toolbox released, check it out here, or see the related paper .