Journal Papers


  1. Fernandes CM, Fachada N, Merelo J, Rosa AC. 2019. Steady state particle swarm. PeerJ Computer Science 5:e202
  2. Ruthven M., Freitas AC, Boubertakh R , Miquel ME (2019)  Application of radial GRAPPA techniques to single-and multislice dynamics speech MRI using a 16-channel neurovascular coilMagnetic resonance in medicine 82 (3), 948-958
  3. Abreu R, Leal A, Figueiredo P (2019) Identification of epileptic brain states by dynamic functional connectivity analysis of simultaneous EEG-fMRI. Scientific Reports 24;9(1):638. doi: 10.1038/s41598-018-36976-y.
  4. Gaspar AS, Nunes RG, Ferrazzi G , Hughes EJ, Hutter J, Malik SJ , McCabe L, Baruteau KP, Rutherford MA, Hajnal JV, Price AN (2019) Optimizing maternal fat suppression with constrained image‐based shimming in fetal MR. Magnetic resonance in medicine 81 (1), 477-485.


  1. Favrod O, Roinishvili M, da Cruz JR, Brand A, Okruashvili M, Gamkrelidze T, Figueiredo P, Herzog MH, Chkonia E, Shaquiri A (2018) Electrophysiological correlates of visual backward masking in patients with first episode psychosis. Psychiatry Research: Neuroimaging 282, 64-72. doi: 10.1016/j.pscychresns.2018.10.008.
  2. da Cruz JR, Rodrigues J, Thoresen JC, Chicherov V, Figueiredo P, Herzog MH, Sandi C (2018) Dominant people are faster to respond and exhibit a distinct neural signal for promptness. Cerebral Cortex 28(10), 3740–3751. doi: 10.1093/cercor/bhy195.
  3. Marques JS, Barata C, Sanches J, Figueiredo P, Miranda Lemos J (2018) Artificial Intelligence in Radiology: From Image Processing to Diagnosis, Acta Radiológica Portuguesa 30(2), 5-8.
  4. Gastao Cruz, Torben Schneider, Tom Bruijnen, Andreia Gaspar, Botnar, RM., Prieto C. (2018) Accelerated magnetic resonance fingerprinting using soft-weighted key-hole (MRF-SOHO), PLOS ONE Vol 13, No 8.
  5. J. Figueiredo, Isabel Rodrigues, Joao Ribeiro, M. Fernandes, S. Melo, B. Sousa, J. Paredes, R. Seruca, João Sanches (2018) Geometric compensation applied to image analysis of cell populations with morphological variability: a new role for a classical concept, Scientific Reports, 8(1):10266.
  6. M Tavares, S Reimão, I Chendo, M Carvalho, P Levy, RG Nunes, Neuromelanin magnetic resonance imaging of the substantia nigra in first episode psychosis patients consumers of illicit substances. Schizophrenia Research, in Press, doi: 10.1016/j.schres.2018.02.033.
  7. J Leote, RG Nunes, L Cerqueira, R Loução, HA Ferreira. Reconstruction of white matter fibre tracts using diffusion kurtosis tensor imaging at 1.5 T: Pre-surgical planning in patients with gliomas. European Journal of Radiology Open 5, 20-23, 2018.
  8. da Cruz JE, Chicherov V, Herzog MH, Figueiredo P (2018) An automatic pre-processing pipeline for EEG analysis (App) based on robust statistics. Clinical Neurophysiology 129(7), 1427-1437. doi:10.1016/j.clinph.2018.04.600.
  9. Rita Gouveia Nunes, G. Ferrazzi, A. N. Price, J. Hutter, Andreia Gaspar, M. Rutherford, J. V. Hajnal (2018) Inner Volume Echo Volumar Imaging (IVEVI) for Robust Fetal Brain Imaging, Magnetic Resonance in Medicine 80 (1), 279-285.
  10. Jorge J, Figueiredo P, Gruetter R, van der Zwaag W (2018) Mapping and characterization of positive and negative BOLD responses to visual stimulation in multiple regions brain regions at 7T. Human Brain Mapping 39(6), 2426-2441. doi:10.1002/hbm.24012.
  11. Abreu R, Leal A, Figueiredo P (2018) EEG-informed fMRI: a review of data analysis methods. Front. Hum. Neurosci. 12:29. doi:10.3389/fnhum.2018.00029.
  12. R.G. Nunes and J.V Hajnal, Distortion correction of echo planar images applying the concept of finite rate of innovation to point spread function mapping (FRIP). MAGMA. 2018 Jan 3. doi: 10.1007/s10334-017-0669-1.
  13. Abreu R, Lopes da Silva F, Leal A, Figueiredo P (2018)  EEG synchronization measures predict epilepsy-related BOLD-fMRI fluctuations better than commonly used univariate metrics. Clinical Neurophysiology 129(3), 618-635. doi:10.1016/j.clinph.2017.12.038.
  14. Marques D R, Gomes A A, Caetano G, Castelo-Branco M (2018) Insomnia Disorder and Brain’s Default-Mode Network, Current Neurology and Neuroscience Reports 18:45 doi:10.1007/s11910-018-0861-3.
  15. Fachada N, Rosa A (2018) micompm: A MATLAB/Octave toolbox for multivariate independent comparison of observations. Journal of Open Source Software, 3(23), 430,


  1. S. Melo, J. Figueiredo, M. Gonçalves, E. Morais-de-Sá, João Sanches, R. Seruca, Predicting the Functional Impact of CDH1 Missense Mutations in Hereditary Diffuse Gastric Cancer, International Journal of Molecular Sciences, 18, 2687, December, 2017.
  2. M. Kuklisova-Murgasova, G. Lockwood Estrin, Rita Gouveia Nunes, S. J. Malik, M. Rutherford, D. Rueckert, J. V. Hajnal, Distortion correction in fetal EPI using non-rigid registration with a Laplacian constraint, IEEE Transactions on Medical Imaging (in press), 2017.
  3. L. Correia Guedes, S. Reimao, P. Paulino, Rita Gouveia Nunes, P. Bouça, D. Abreu, N. Gonçalves, A. Di Fonzo, L. Zhang, M. L. Quadri, M. Fabbri, C. Godinho, P. Pita Lobo, D. Neutel, M. Coelho, M. M. Rosa, J. Campos, G. Miltenberger-Miltenyi, T. Outeiro, C. Sampaio, V. Bonifati, J. J. Fereira, Neuromelanin Magnetic Resonance Imaging of the Substantia Nigra in LRRK2 and GBA-related Parkinson’s disease, Movement Disorders, Vol. 32, Issue 9, pp. 1331-1333, September, 2017.
  4. N. Adubeiro, M. L. Nogueira, Rita Gouveia Nunes, E. Ribeiro, H. A. Ferreira, S. Alves, J. M. F. LA Fuente, Apparent diffusion coefficient in the analysis of prostate cancer: determination of optimal b-value pair to differentiate normal from malignant tissue, Clinical Imaging [Epub ahead of print], 2017.
  5. Nuno Fachada, V. V. Lopes, R. C. Martins, Agostinho Rosa, cf4ocl: A C framework for OpenCL, Science of Computer Programming, Vol. 143, pp. 9-19, September, 2017.
  6. M. Fabbri, S. Reimao, M. Carvalho, Rita Gouveia Nunes, D. Abreu, L. Correia Guedes, P. P. Lobo, C. Godinho, M. Coelho, N. C. Gonçalves, M. M. Rosa, A. Antonini, J. J. Fereira, Substantia nigra neuromelanin as an imaging biomarker of disease progression in Parkinson’s disease, Journal of Parkinson’s Disease, vol. 7, no. 3, pp. 491-501, 2017.
  7. Nelson Perdigão, Agostinho Rosa, S. O Donoghue, The Dark Proteome Database, BioData Mining, pp. 10-24. Springer Nature. July, 2017.
  8. Rodolfo Abreu, Sandro Nunes, A. Leal, Patrícia Figueiredo, Physiological noise correction using ECG-derived respiratory signals for enhanced mapping of spontaneous neuronal activity with simultaneous EEG-fMRI, Neuroimage, Vol. 154, pp. 115-127, July, 2017.
  9. R Gil-Gouveia, Joana Pinto, Patrícia Figueiredo, P. Vilela, I. Martins, An Arterial Spin Labeling MRI Perfusion Study of Migraine without Aura Attacks, Frontiers in Neurology, 8, 280, 2017.
  10.  W. Nan, F. Wan, L. Chang, S. H. Pun, M. I Vai, Agostinho Rosa, An exploratory study of intensive neurofeedback training for schizophrenia, Behavioural Neurology, vol. 2017, Article ID 6914216, 2017.
  11.  Joana Pinto, Sandro Nunes, M. Bianciardi, A. Dias, L. M. Silveira, L. L. Wald, Patrícia Figueiredo, Improved 7 Tesla resting-state fMRI connectivity measurements by cluster-based modeling of respiratory volume and heart rate effects, NeuroImage, Vol. 153, pp. 262-272, June, 2017.
  12.  Nuno Fachada, V. V. Lopes, R. C. Martins, Agostinho Rosa, Parallelization strategies for spatial agent-based models, International Journal of Parallel Programming, vol. 45, issue 3, pp. 449-481, June, 2017.
  13.  S. Brandão, M. Parente, E. Silva, T. da Roza, T. Mascarenhas, J. Leitão, J. Cunha, R. Natal Jorge, Rita Gouveia Nunes, Pubovisceralis muscle fiber architecture determination: comparison between biomechanical modeling and diffusion tensor imaging, Annals of Biomedical Engineering, Vol. 45, Issue 5, pp. 1255-1265, May, 2017.
  14.  A. Ferro, T. Mestre, P. Carneiro, I. Sahumbaiev, R. Seruca, João Sanches, Blue intensity matters for cell cycle profiling in fluorescence DAPI-stained images, Laboratory Investigation (Nature), 97(5):615-625, May, 2017.
  15.  D. Marques, A. Gomes, V. Clemente, J. M. Santos, I. Duarte, Gina Caetano, M. Castelo-Branco, Unbalanced resting-state networks activity in psychophysiological insomnia, Sleep and Biological Rhythms, Vol. 15, Issue 2, pp. 167–177, April, 2017.
  16. Teresa Murta, U. J. Chaudhary, T. Tierney, A. Dias, Marco Leite, D. W. Carmichael, Patrícia Figueiredo, L. Lemieux, Phase-amplitude coupling and the BOLD signal: A simultaneous intracranial EEG (icEEG) – fMRI study in humans performing a finger-tapping task, Neuroimage, Vol. 146, 438–451, February, 2017.
  17. Nuno Fachada, Vitor Lopes, R. C. Martins, Agostinho Rosa, Model-independent comparison of simulation output, Simulation Modelling Practice and Theory, Vol. 72, pp. 131–149, March, 2017.


  1. C. Gomes, P. Figueiredo, A. Mayes (2016) Priming for novel object associations: neural differences from object item priming and equivalent forms of recognition. Hippocampus 26(4): 472-91.
  2. R. Abreu, M. Leite, A. Leal, P. Figueiredo (2016) Objective selection of epilepsy-related independent components from EEG dataJournal of Neuroscience Methods 258: 67-78.
  3. J. Pinto, J. Jorge, I. Sousa, P. Vilela, P. Figueiredo (2016) Fourier modeling of the BOLD response to a breath-hold task: Optimization and reproducibility. NeuroImage 135: 223-31.
  4. T. Murta, U. J. Chaudhary, T. Tierney, A. Dias, M. Leite, D. W. Carmichael, P. Figueiredo, L. Lemieux (2016) Phase-amplitude coupling and the BOLD signal: A simultaneous intracranial EEG (icEEG)-fMRI study in humans performing a finger-tapping task. NeuroImage 146: 438-451.
  5. T. Murta, L. Hu, T. Tierney, U. J. Chaudhary, M. C. Walker, D. W. Carmichael, P. Figueiredo, L. Lemieux (2016) A study of the electro-haemodynamic coupling using simultaneously acquired intracranial EEG and fMRI data in humans. NeuroImage 142: 371-380.
  6. R. Abreu, M. Leite, J. Jorge, F. Grouiller, W. van der Zwaag, A. Leal, P. Figueiredo (2016) Ballistocardiogram artifact correction taking into account physiological signal preservation in simultaneous EEG-fMRI. NeuroImage 135: 45-63.
  7. R. Abreu, S. Nunes, A. Leal, P. Figueiredo (2016) Physiological noise correction using ECG-derived respiratory signals for enhanced mapping of spontaneous neuronal activity with simultaneous EEG-fMRI. NeuroImage [Epub ahead of print].
  8. A. Leal, J. P. Vieira, R. Lopes, R. G. Nunes, S. I. Gonçalves, F. Lopes da Silva, P. Figueiredo (2016) Dynamics of epileptic activity in a peculiar case of childhood absence epilepsy and correlation with thalamic levels of GABA. Epilepsy & Behavior Case Reports 5: 57-65.
  9. L. Saba, N. Dey, A. S. Ashour, S. Samanta, S. S. Nath, S. Chakraborty, J. Sanches, D. Kumar, R. T. Marinho, J. S. Suri (2016) Automated stratification of liver disease in ultrasound: An online accurate feature classification paradigm. Computer Methods and Programs in Biomedicine 130: 118-134.
  10. T. Mestre, J. Figueiredo, A. S. Ribeiro, J. Paredes, R. Seruca, J. Sanches (2016) Quantification of topological features in cell meshes to explore E-cadherin dysfunction. Scientific reports 6: 25101.
  11. S. A. Sousa, J. H. Leitão, R. C. Martins, J. Sanches, J. S. Suri, A. Giorgetti (2016) Bioinformatics Applications in Life Sciences and Technologies. BioMed Research International 2016: 3603827.
  12. A. S. Ribeiro, F. A. Carvalho, J. Figueiredo, R. Carvalho, T. Mestre, J. Monteiro, A. F. Guedes, M. Fonseca, J. Sanches, R. Seruca, N. C. Santos, J. Paredes (2016) Atomic force microscopy and graph analysis to study the P-cadherin/SFK mechanotransduction signalling in breast cancer cellsNanoscale 8(46): 19390-19401.
  13. N. Fachada, V. Lopes, R. C. Martins, A. C. Rosa (2016) Parallelization Strategies for Spatial Agent-Based ModelsInternational Journal of Parallel Programming 1-33.
  14. P.G. Sanchez, G. Romero, J. González, A. M. Mora, M. G. Arenas, P. A. Castillo, C. Fernandes, J. J. Merelo (2016) Studying the effect of population size in distributed evolutionary algorithms on heterogeneous clustersApplied Soft Computing 38: 530–547.
  15. F. Wan, J. N. da Cruz, W. Nan, C. M. Wong, M. I. Vai, A. C. Rosa (2016) Alpha neurofeedback training improves SSVEP-based BCI performanceJournal of Neural Engineering 13: 036019.
  16. N. Fachada, V. Lopes, R. C. Martins, A. C. Rosa (2016) PerfAndPubTools – Tools for software performance analysis and publishing of resultsJournal of Open Research Software 4(1): e18.
  17. C. Fernandes, J. L. J. Laredo, J. J. Merelo, C. Cotta, A. C. Rosa (2016) Dynamic Topologies for Particle Swarm. Transaction on Computational Collective Intelligence XXIV 9770: 1-18.
  18. N. Fachada V. Lopes, R. C. Martins, A. C. Rosa (2016) SimOutUtils – Utilities for analyzing simulation outputJournal of Open Research Software 4(1): e38.
  19. N. Fachada, J. Rodrigues, V. Lopes, R. C. Martins, A. C. Rosa (2016) micompr: An R Package for Multivariate Independent Comparison of ObservationsThe R Journal, Vol. 8/2.

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