Publications of Jussi Tohka

Scientific monographs:

J. Tohka. Deformable Surface Models in Medical Image Analysis: Automatic surface extraction using deformable meshes. VDM Verlag Dr. Muller, Saarbrucken, Germany, 2009, 200 pages. [Amazon.com] [Amazon.co.uk]

J. Tohka. Global optimization-based deformable meshes for surface extraction from medical images, PhD dissertation, Tampere University of Technology, Finland, 2003 (Publications of Tampere University of Technology 432). [Abstract] , [ps], [pdf]

Refereed articles in international journals:

  1. J.-P. Kauppi, I.P. Jääskeläinen, M. Sams and J. Tohka . Inter-subject correlation of brain hemodynamic responses during watching a movie: localization in space and frequency, Frontiers in Neuroinformatics , in press, 2010
  2. L. Zhao, U. Ruotsalainen, J. Hirvonen, J. Hietala and J. Tohka . Automatic cerebral and cerebellar hemisphere segmentation in 3D MRI: adaptive disconnection algorithm. Medical Image Analysis , in press, 2010.
  3. J. Tohka , I.D. Dinov, D.W. Shattuck, and A.W. Toga. Brain MRI Tissue Classification Based on Local Markov Random Fields, Magnetic Resonance Imaging , in press , 2009.
  4. R.J. Farinha, U. Ruotsalainen, J. Hirvonen, L. Tuominen, J. Hietala, J.M. Fonseca, and J. Tohka . Segmentation of Striatal Brain Structures from High Resolution PET Images, International Journal of Biomedical Imaging vol. 2009, Article ID 156234, 12 pages, doi:10.1155/2009/156234, 2009.
  5. E. Krestyannikov, J. Tohka and U. Ruotsalainen. Joint penalized-likelihood reconstruction of time activity curves and regions-of-interest from projection data in brain PET. Physics in Medicine and Biology, 53:2877-2896, 2008.
  6. J. Tohka and A. Reilhac. Deconvolution-Based Partial Volume Correction in Raclopride-PET and Monte Carlo Comparison to MR Based Method. NeuroImage, 39(4):1570-1584, 2008.
  7. J.V. Manjón, J. Tohka , G. García-Martí, J. Carbonell-Caballero, J.J. Lull, L. Martí-Bonmatí and M. Robles. Robust MRI Brain Tissue Parameter Estimation by Multistage Outlier Rejection. Magnetic Resonance in Medicine, 59:866 - 873, 2008.
  8. J. Tohka , K. Foerde, A.R. Aron, S. M. Tom, A.W. Toga, and R.A. Poldrack. Automatic Independent Component Labeling for Artifact Removal in fMRI. NeuroImage, 39(3):1227-45, 2008. [Software] [Pubmed]
  9. E. Wallius, J. Tohka , J. Hirvonen, J. Hietala, and U. Ruotsalainen. Evaluation of the automatic three-dimensional delineation of caudate and putamen for PET receptor occupancy studies. Nuclear Medicine Communications , 29(1):53-65, 2008.
  10. J. Tohka , E. Krestyannikov, I.D. Dinov , A. MacKenzie-Graham, D.W. Shattuck , U. Ruotsalainen, and A.W. Toga. Genetic algorithms for finite mixture model based voxel classification in neuroimaging. IEEE Transactions on Medical Imaging , 26(5):696 - 711, 2007. [Software (Matlab)] [Software (C/C++)]
  11. D. Glotsos, J. Tohka , J. Soukka, J. Soini, and U. Ruotsalainen. Robust estimation of bioaffinity assay fluorescence signals. IEEE Transactions on Information Technology in Biomedicine , 10(4):733- 739 Oct. 2006
  12. J. Tohka , E. Wallius, J. Hirvonen, J. Hietala, and U. Ruotsalainen. Automatic extraction of caudate and putamen in [11C]raclopride PET using deformable surface models and normalized cuts. IEEE Transactions on Nuclear Science , 53(1):220-227 , 2006.
  13. A. Reilhac, G. Batan, C. Michel, C. Grova, J. Tohka , D.L. Collins, N. Costes, and A.C. Evans. PET-SORTEO: Validation and development of database of simulated PET volumes. IEEE Transactions on Nuclear Science , 52(5): 1321-1328 , 2005. [Database]
  14. J. Mykkänen, J. Tohka, J. Luoma, and U. Ruotsalainen. Automatic extraction of brain surface and mid-sagittal plane from PET images applying deformable models. Computer Methods and Programs in BioMedicine,17(1):1 - 17 , 2005. [See the related technical report]
  15. D. Glotsos, J. Tohka , P. Ravazoula, D. Cavouras, and G. Nikiforidis. Automated Diagnosis of Brain Tumours Astrocytomas Using Probabilistic Neural Network Clustering and Support Vector Machines, International Journal of Neural Systems , 15(1 -2):1 - 12, 2005 [Full text via EBSCO database]
  16. J. Tohka. Global deformable surface optimization using adaptive constraints and penalties. Image Analysis and Stereology, 24:9 - 19, 2005.
  17. J. Tohka, A. Kivimäki, A. Reilhac, J. Mykkänen, and U. Ruotsalainen.  Assessment of brain surface extraction from PET images using Monte Carlo simulations.IEEE Transactions in Nuclear Science,51(5):2641 - 2648, 2004.
  18. J. Tohka, A. Zijdenbos, and A.C. Evans. Fast and robust parameter estimation for statistical partial volume models in brain MRI. NeuroImage, 23(1):84 - 97, 2004.
  19. J. Tohka, J. Mykkänen. Deformable mesh for automated surface extraction from noisy images. International Journal of Image and Graphics, Special Issue on Deformable Models for Image Analysis and Pattern Recognition 4(3):405-432, July 2004 . [preprint]. [Software]
  20. J. Mykkänen, J. Tohka, and U. Ruotsalainen. Automated delineation of brain structures with snakes in PET. in Molecular and Pharmacological Brain Imaging with Positron Emission Tomography,  pages 39-43. Academic Press, 2001.

Refereed articles in international conferences:

  1. L. Zhao, J. Hietala and J. Tohka . Shape analysis of human brain interhemispheric fissure bending in MRI. Medical Image Computing and Computer-Assisted Intervention, MICCAI 2009 Lecture Notes in Computer Science vol. 5762, pp. 216 - 223, London, UK, 2009.
  2. H. Pölönen, J. Tohka and U. Ruotsalainen. Automatic Intensity Quantification of Fluorescence Targets from Microscope Images with Maximum Likelihood Estimation. In Proc. of European Signal Processing Conference (EUSIPCO-2009), pp. 1072 - 1076, Glasgow, UK, 2009.
  3. H. Pölönen, J. Tohka and U. Ruotsalainen. Automatic Quantification of Fluorescence from Clustered Targets in Microscope Images. Lecture Notes in Computer Science vol. 5575 (Proc. of Scandinavian Conference on Image Analysis (SCIA09)), pp. 667 - 675, Oslo, Norway, 2009.
  4. F. Momey, N. Boussion, D. Visvikis,J. Nuyts, N. Costes, J. Tohka and A. Reilhac. Evaluation of Deconvolution-Based Methods for the Correction of Partial Volume Effect in PET. In Proc. of IEEE Medical Imaging Conference, Dresden, Germany, in press, 2008.
  5. L. Zhao, J. Tohka .Automatic compartmental decomposition for 3D MR images of human brain. In Proc. of 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society ,pp. 3888-3891 ,Vancouver, Canada, 2008.
  6. L. Zhao, J. Tohka , U. Ruotsalainen. Accurate 3D left-right brain hemisphere segmentation in MR images based on shape bottlenecks and partial volume estimation. In Scandinavian Conference on Image Analysis, Aalborg, Denmark, June 10-14,Lecture Notes in Computer Science 4522 , pages 581 - 590 , Springer Verlag, 2007.
  7. H. Pölönen, M. Jansen, J. Tohka , E. Ikonen, U. Ruotsalainen: Automatic method for caveolar structure detection and intensity distribution analysis from microscopy images, In Proc. of European Signal Processing Conference (EUSIPCO 2007) , Poznan, Poland, September 3 - 7, pp. 1107 - 1111, 2007.
  8. E. Krestyannikov, J. Tohka , U. Ruotsalainen. Statistical modeling of attenuation corrected data in PET with application to reconstruction of regional time activity curves. In IEEE International Symposium on Biomedical Imaging (IEEE-ISBI), Washington D.C., US, 12-15 April, 2007, pages 444 - 447 .
  9. E. Wallius, J. Tohka , J. Hirvonen, J. Hietala, U. Ruotsalainen U. A method for automatic extraction of striatal structures for dose-finding studies in PET. In Proc of IEEE Medical Imaging Conference (MIC2006) , pp. 3189 - 3194, October 29-November 4, San Diego, California, USA, 2006.
  10. A. Juslin, J. Tohka , J. Lötjönen, U. Ruotsalainen. Comparison of image segmentation and registration based methods for analysis of misaligned dynamic H2-O-15 cardiac PET images. In Proc . of IEEE Medical Imaging Conference (MIC2006) , pp. 3200 - 3204, October 29-November 4 2006, San Diego, California, USA, 2006.
  11. J. Tohka , A. Reilhac. A Monte Carlo study of deconvolution algorithms for partial volume correction in quantitative PET. In Proc. of IEEE Medical Imaging Conference (MIC2006) , pp. 3339 - 3345, October 29-November 4, San Diego, California, USA, 2006.[Erratum]
  12. E. Krestyannikov, J. Tohka, U. Ruotsalainen. Segmentation of dynamic emission tomography data in projection space. In Computer Vision Approaches to Medical Image Analysis (CVAMIA) Workshop, Graz Austria, Lecture Notes in Computer Science vol. 4241 , pp. 108 - 119, 2006.
  13. A. Juslin, J. Tohka . Unsupervised segmentation of cardiac PET transmission images for automatic heart volume extraction. In Proc. of IEEE 2006 International Conference of the Engineering in Medicine and Biology Society (EMBC06) , pp. 1077 - 1080 , August 30-September 3 2006, New York, USA. [Software]
  14. J. Tohka, E. Krestyannikov, I. Dinov, D. Shattuck, U. Ruotsalainen, A.W. Toga. Genetic algorithms for finite mixture model based tissue classification in brain MRI. In Proc. of European Medical and Biological Engineering Conference, IFMBE Proceedings vol. 11, pp. 4077 - 4082, Prague, Czech Republic, 2005. [Paper] [Software]
  15. J. Mykkänen, J. Itäranta, J. Tohka. Object oriented implementation for the dual surface minimisation algorithm. In Connecting Medical Informatics and Bio-Informatics, Proceedings of MIE2005, volume 116 of Studies in Health Technology and Informatics, , pp. 477 - 482. IOS-Press. Geneva, Switzerland, 2005. [Software]
  16. A. Juslin, A. Reilhac, M. Magadan-Mendez, E. Alban, J. Tohka, and U. Ruotsalainen. Assessment of separation of functional components with ICA from cardiac perfusion PET phantom images for volume extraction with deformable surface model. In Proc of 3rd Int. Conf. on Functional Imaging and Modeling of the Heart (FIMH'05), Lecture Notes in Computer Science 3504, pp. 338 - 347, Barcelona, Spain, June 2005.
  17. E. Alban, J. Tohka, and U. Ruotsalainen. Adaptive Edge Detection Based on 3D Kernel Functions for Biomedical Image Analysis. In SPIE Electronic Imaging, Image Processing: Algorithms and Systems IV, Proc.SPIE 5672 , pp.224 - 235, San Jose, CA, USA, January 2005.
  18. G. Batan, A. Reilhac, C. Grova, D.L. Collins, J. Tohka, N. Costes, and A. Evans. A database of simulated PET volumes with anatomical variability. In Proc. of IEEE Medical Imaging Conference (MIC2004) , pp. 3699 - 3702, Rome, Italy, October 2004.
  19. J. Tohka, E. Wallius, J. Hirvonen, J. Hietala, and U. Ruotsalainen. Improved Reproducibility in Dopamine D2-Receptor Studies with Automatic Segmentation of Striatum from PET Images, In Proc of IEEE Medical Imaging Conference (MIC2004), pp. 2690 - 2694, Rome, Italy, October 2004.[Paper]
  20. D. Glotsos, J. Tohka, J.Soukka, J. Soini, and U. Ruotsalainen.A New Robust Clustering Method for the Automatic Identification of Different Types of Analytes in Multi-Parametric Bioaffinity Assays, In Proc. of the 4th European Symposium on Biomedical Engineering, 25-27 June 2004, Patras, Greece, paper S4.03 (4 pages).
  21. D. Glotsos, J. Tohka, J. Soukka, J. Soini, and U. Ruotsalainen. A New Method for Concentration Estimation in Multiparametric Bioaffinity Immunoassays, In Proc. of the 4th European Symposium on Biomedical Engineering, 25-27 June 2004, Patras, Greece, paper S4.02 (4 pages).
  22. J. Tohka. Surface Smoothing Based on a Sphere Shape Model. In Proc. of 6th Nordic Signal Processing Symposium, NORSIG2004, pp. 17 - 20, Espoo, Finland, June, 2004.  [Link to proceedings]
  23. H. Koivistoinen, J.Tohka, and U. Ruotsalainen. Comparison of Pattern Classification Methods in Segmentation of Dynamic PET Brain Images. In Proc. of 6th Nordic Signal Processing Symposium, NORSIG2004, pp. 73 - 76, Espoo, Finland, June, 2004. [Link to proceedings]
  24. D.Glotsos, J. Tohka, J. Soukka, and U. Ruotsalainen. A new approach to robust clustering by density estimation in an autocorrelation derived feature space. In Proc. of 6th Nordic Signal Processing Symposium, NORSIG2004, pp. 296 - 299, Espoo, Finland,June, 2004.[Link to proceedings]
  25. J. Mykkänen, J. Tohka, and U. Ruotsalainen. Delineation of brain structures from positron emission tomography images with deformable models.In the new navigators: from professionals to patients, Studies in Health Technology and Informatics volume 95, Proc. of Medical Informatics Europe,  pp. 33 - 38, IOS-Press, St. Malo, France, June,  2003. [Paper]
  26. J. Tohka, A. Kivimäki, A. Reilhac, J. Mykkänen, U. Ruotsalainen. Brain surface extraction from PET images using deformable models: Assessment using Monte-Carlo simulator, In Proc. of IEEE Medical Imaging Conference (MIC2003), pp. 3115 - 3119, Portland, Oregon, USA, October, 2003. [Errata]
  27. J. Tohka. Surface extraction from volumetric images using deformable meshes: A comparative study. in Proc. of 7th European Conference on Computer Vision, Lecture Notes in Computer Science 2352 , pp. 350 - 364,  Springer-Verlag,Copenhagen, Denmark, May 2002. [Paper] [Abstract]
  28. U. Ruotsalainen, J. Mykkänen, J. Luoma, J. Tohka and S. Alenius. Methods to improve repeatability in quantification of brain PET images, In World Congress on Neuroinformatics, AGRESIM Reprort no. 20, pp. 659 - 664, Agresim-Verlag, Vienna, Austria, September 2001. [Abstract]
  29. J. Tohka. Global optimization of deformable surface meshes based on genetic algorithms. in Proc. of 11th International Conference of Image Analysis and Processing, pp. 459 - 464, IEEE CS Press, Palermo, Italy, September 2001. [Paper]  [Abstract]

Articles in national conferences:

  1. L. Zhao, J. Tohka, J. Hirvonen, J. Hietala, and U. Ruotsalainen. Evaluation for a novel brain hemisphere segmentation method using MR images of schizophrenics and healthy controls. In proc. of Finnish Signal Processing Symposium (FINSIG'07), Oulu, Finland, ISBN 978-951-42-8546-2, 2007.
  2. J. Tohka. Note on connections between active contours and Rayleigh quotients.In Proceedings of 2001 Finnish Signal Processing Symposium, pp. 59 - 62, Espoo, Finland, June 2001.  [Paper]

Refereed international conference abstracts:

  1. J. P. Kauppi, I. Jaaskelainen, M. Sams and J. Tohka . A new software tool for analyzing BOLD fMRI during movie watching. Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics. doi: 10.3389/conf.neuro.11.2009.08.032
  2. A. Pepe, L. Zhao, J. Tohka ,J. Koikkalainen, J. Hietala and U. Ruotsalainen. Automatic statistical shape analysis of human cerebral asymmetry in 3D MRI. 15th Annual Meeting of the Organisation of Human Brain Mapping, San Francisco, June 18 - 23, 2009.
  3. J.-P. Kauppi, I.P. Jääskeläinen, M. Sams and J. Tohka . Low-Frequency Specific Inter-subject Hemodynamic Synchronization in Frontal Cortex During Natural Vision. 15th Annual Meeting of the Organisation of Human Brain Mapping, San Francisco, June 18-23, 2009.
  4. I.P. Jääskeläinen, J.-P. Kauppi, K. Koskentalo, J. Saramäki, J. Tohka and M. Sams. Use of naturalistic stimuli in disclosing brain dynamics. Frontiers in Human Neuroscience. Conference Abstract: Tuning the Brain for Music. doi: 10.3389/conf.neuro.09.2009.02.013
  5. L. Zhao, U. Ruotsalainen, J. Hirvonen, J. Hietala and J. Tohka . Study of cerebral asymmetry in schizophrenia based on an novel automatic cerebral hemisphere segmentation method for MRI. Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008.
  6. A. Pepe, L. Zhao,J. Koikkalainen, J. Tohka , J. Hietala and U. Ruotsalainen. Automatic analysis of cerebral shape asymmetry in 3D MRI. Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008.
  7. J. Tohka , A. Reilhac. Deconvolution as an alternative to MR-based partial volume correction in Raclopride PET. Abstracts of the Turku PET Symposium, p. 48, 2008
  8. J. Tohka , I.D. Dinov, D.W. Shattuck, and A.W. Toga. Brain MRI Segmentation Based on Local Markov Random Fields and Sub Volume Probabilistic Atlases. 14th Annual Meeting of the Organisation of Human Brain Mapping, Melbourne, Australia, 2008.
  9. J. Tohka , I.D. Dinov, D.W. Shattuck, and A.W. Toga. GAMIXTURE+MRFSEG: A flexible tool for voxel classification. In proc. of Nordic Neuroinformatics Workshop, pp. 10, 2007.
  10. L. Zhao, J. Tohka and U. Ruotsalainen. Automatic human brain hemisphere segmentation in MRI including brain compartmental decomposition. In proc. of Nordic Neuroinformatics workshop, pp. 36, 2007.
  11. E. Wallius, J. Tohka , J. Hirvonen, J. Hietala, U. Ruotsalainen. Reduced standard deviation of binding potential values with automatic segmentation of striatum in PET - implications to statistical power. BrainPET'07 Conference, Osaka Japan, May 20-24, 2007.
  12. L. Zhao, J. Tohka , U. Ruotsalainen. Accurate brain hemisphere segmentation in 3D MRI based on shape bottlenecks and partial volume estimation. 13th Annual meeting of Human Brain Mapping, Chicago, IL, USA, June 10-14, 2007.
  13. J. Kunnari, J. Tohka . Comparison of three modified EM-algorithms in segmentation of dynamic PET images. 13th Annual meeting of Human Brain Mapping, Chicago, IL, USA, June 10-14, 2007.
  14. J. Tohka , E. Wallius, J. Hirvonen, J. Hietala, U. Ruotsalainen. Partial volume effect, segmentation inaccuracy, and reproducibility in striatal D2 dopamine receptor availability with raclopride PET. Organization for Human Brain Mapping 2006, Florence, Italy, June 11-15, 2006.
  15. J. Tohka , K. Foerde, A.W. Toga, R.A. Poldrack. Automatic independent component labeling for artifact reduction in fMRI. Organization for Human Brain Mapping, 2006, Florence, Italy, June 11-15, 2006.
  16. K. Sederholm, J. Tohka , V. Oikonen, U. Ruotsalainen, S. Peltonen. Robust estimation of regional parameter values as a simple method for partial volume correction in PET imaging. Annales Universitatis Turkuensis D 660, X Turku PET Symposium: p. 82, 2005.
  17. E. Wallius, J. Tohka , J. Hietala, U. Ruotsalainen. Automatic extraction of caudate and putamen from images during medication in [C-11]-raclopride PET. Annales Universitatis Turkuensis D 660, X Turku PET Symposium: p. 85, 2005.
  18. A. Kivimäki, J. Tohka, M. Anttila, U. Ruotsalainen. Automatic extraction of the heart volumes from dynamic FDG PET emission images for movement corrections. In EANM'04 - Annual Congress of the European Assocation of Nuclear Medicine, European Journal of Nuclear Medicine and Molecular Imaging 31(Suppl. 2):S406, September 4 - 8, 2004 in Helsinki, Finland
  19. A. Kivimäki, J. Tohka, U. Ruotsalainen. Monte Carlo Study of Automated MRI-PET Image Registration with Brain Images having pathological defects. In 2nd Nordic Neuroinformatics Workshop, Drobak, Norway, September, 2004.
  20. J. Tohka, A. Zijdenbos, U. Ruotsalainen, A. Evans. Overview on partial volume estimation in brain MRI: Models and methods. 1st Nordic Workshop on Brain Imaging and Neuroinformatics, Tampere, Finland, 2003. [Abstract]
  21. H. Koivistoinen, J. Tohka, U. Ruotsalainen.  Unsupervised learning methods in delineation of brain regions from PET images based on dynamic tracer distribution. 1st Nordic Workshop on Brain Imaging and Neuroinformatics, Tampere, Finland, 2003
  22. J. Tohka. Target extraction from emission tomography images with deformable models. In  Workshop on Deformable Models, Gullmarstrand, Sweden, August 2000.
  23. J. Mykkänen, J. Tohka, and U. Ruotsalainen. Automated delineation of brain structures with snakes in PET.XIX International Symposium on Cerebral Blood Flow, Metabolism and Function, IV International Conference on Quantification of Brain Function with PET, Cerebral Blood Flow and Metabolism 19(Suppl. 1):778, Copenhagen, Denmark, June 1999.

Lecture notes

  1. J. Tohka. Introduction to Pattern Recognition, 74 pages, 2006 - 2008 [pdf] .
  2. J. Tohka. Johdatus hahmontunnistukseen, 72 pages, 2006 - 2008 [pdf] .

Other:

  1. J. Tohka.  Deformable surface meshes based on global optimization. Digest of TISE Seminar 2002, June 10, 2002, Ylöjärvi, Finland, pp. 7 -8, 2002.
  2. J. Tohka. Automated surface extraction with deformable meshes. Online tutorial in CVonline. 2002.
  3. J. Mykkänen, J. Tohka, J. Luoma, and U. Ruotsalainen. Automatic extraction of brain surface and mid-sagittal plane from PET images applying deformable models. Technical Report  A-2003-1, Department of  Computer and Information Sciences, University of Tampere, 2003. [Paper]