PUBLICATIONS

 

Book chapters

• H. A. Ferreira, “Computer-assisted diagnosis of neuropsychiatric disorders using machine learning” in Handbook of Research on Ubiquitous Machine Learning and its Applications, N. F. M. Nunes and T. S. R. Araújo (Eds), IGI Global (in preparation).

 

Theses

 

2015

• Filipe Miguel Sobreira Rodrigues, "Establishing a Framework for the development of Multimodal Virtual Reality Interfaces with Applicability in Education and Clinical Practice", Master thesis in Biomedical Engineering, Faculty of Sciences and Technology, New University of Lisbon, 2015.

• Ricardo Sérgio Gomes Almeida Loução, "Structural connectivity based on diffusion Kurtosis imaging", Master thesis in Biomedical Engineering, Faculty of Sciences and Technology, New University of Lisbon, 2015.

• José Tiago Quenino Soeiro, "Visualização de dados médicos em realidade aumentada", Master thesis in Informatics, Faculty of Sciences, University of Lisbon, 2015

• André João de Jesus Sousa Ticló, "Análise da evolução da conectividade estrutural em doentes de Parkinson",  Master thesis in Biomedical Engineering, Faculty of Sciences and Technology, New University of Lisbon, 2015.

 

2014

• Joana Paula Fontinha de Brito, "Dynamic functional connectivity of BOLD fMRI signal during both rest and task execution states", Master thesis in Biomedical Engineering and Biophysics, Faculty of Sciences, University of Lisbon, 2014.

• Vânia Sofia Santos Tavares, "Epileptogenic focus localization and complexity analysis of its BOLD signal", Master thesis in Biomedical Engineering and Biophysics, Faculty of Sciences, University of Lisbon, 2014.

• Ricardo Filipe Henriques Ribeiro, "Desenvolvimento de uma interface de visualização de conectividade cerebral usando realidade virtual e controlo por gestos", Master thesis in Biomedical Engineering, Faculty of Sciences and Technology, New University of Lisbon, 2014.

• Vanessa Sofia Gomes Leitão, "Imagem por curtose de difusão em doenças neurodegenerativas", Master thesis in Biomedical Engineering, Faculty of Sciences and Technology, New University of Lisbon, 2014.

 

2013

• João Marcos Silva Sousa, "Análise da conectividade estrutural na doença de Parkinson", Master thesis in Biomedical Engineering, Faculty of Sciences and Technology, New University of Lisbon, 2013

• G. Ribeiro, “Desenvolvimento e melhoramento de software de visualização de imagem médica”, Relatório de Estágio de Licenciatura em Engenharia Biomédica e Biofísica, Departamento de Física da Faculdade de Ciências da Universidade de Lisboa, September 2013, Lisboa.

• A.C. Mendes, “Characterization of gray matter in the limbic system”, Relatório de Estágio de Licenciatura em Engenharia Biomédica e Biofísica, Departamento de Física da Faculdade de Ciências da Universidade de Lisboa, September 2013, Lisboa.

• D. Sousa, “Estudo dos valores de curtose de difusão na substância cinzenta com base em modelos multi-compartimentais”, Relatório de Projecto de Licenciatura em Física, Departamento de Física da Faculdade de Ciências da Universidade de Lisboa, 14 June 2013, Lisboa.

 

2012

• Ana Catarina Costeira Borralho, "Avaliação de dados funcionais em repouso do cérebro normal: causalidade de Granger", Mestrado em Radiações Aplicadas às Tecnologias da Saúde, Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, 2012.

• Sandra Cristina Jorge da Silva, "Caracterização de regiões encefálicas no cérebro normal por tensor de difusão e aplicação à epilepsia pós-traumática", Mestrado em Radiações Aplicadas às Tecnologias da Saúde, Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, 2012.

• Carmen Sofia dos Santos Ferra, "Conectividade estrutural do cérebro", Mestrado em Radiações Aplicadas às Tecnologias da Saúde, Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, 2012.

 

 

Patents

 

2014

• R. N. Henriques, M. M. Correia, R. G. Nunes, H. A. Ferreira, SISTEMA E MÉTODO PARA DETERMINAÇÃO DE MÉTRICAS E FIBRAS COM BASE EM IMAGEM POR CURTOSE DE DIFUSÃO, INPI 20141000078147 PPP, 6 October 2014. (slide)

 

 

International peer-reviewed scientific journals

 

Submitted/In submission

• In submission: A. C. Mendes, A. Santos Ribeiro, A.-M. Oros-Peusquens, K.-J. Langen, C. W. Lucas, N. J. Shah, H. A. Ferreira, “Brain connectivity study of brain tumor patients using MR-PET data: a pilot study”

• In resubmission: J. Brito, A. Andrade, H. Ferreira, K. Koschutnig, D. Fink, G. Pfurtscheller, "Dynamics of slow BOLD oscillations measured with the phase component of wavelet coherence".

• Submitted: J. Leote, R. G. Nunes, L. Cerqueira, H. A. Ferreira, “Corticospinal MRI tractography in patients with space-occupying brain lesions: a comparison between probabilistic, diffusion tensor and kurtosis streamline methods”

• Submitted: F. Lucena, T. F. Vaz, A. Santos Ribeiro, Luís M. Lacerda, N. A. da Silva, D. Nutt, J. McGonigle, H. A. Ferreira, "Assessment of the quality of brain regions and neuroimaging / connectivity metrics as biomarkers of Alzheimer’s Disease".

 

Accepted

• J. P. Santos, M. Martins, H. A. Ferreira, J. Ramalho, D. Seixas, “Neural Imprints of National Brands versus Own-label Brands”, Journal of Product and Brand Management (accepted for publication)

 

2015

• A. Santos-Ribeiro, L. M. Lacerda, H. A. Ferreira (2015), “Multimodal Imaging Brain Connectivity Analysis Toolbox (MIBCA)”, PeerJ 3: e1078 (July 2015)

• A. Santos-Ribeiro, L. M. Lacerda, N. A. da Silva, H. A. Ferreira, “Multimodal imaging of brain connectivity using the MIBCA toolbox: preliminary application to Alzheimer’s Disease”, IEEE Transactions on Nuclear Science 62(3): 604-611 (June 2015) 

• R. Neto-Henriques, M. M. Correia, R. G. Nunes, H. A. Ferreira (2015), “Exploring the 3D geometry of the diffusion kurtosis tensor – impact on the development of robust tractography procedures and novel biomarkers”, Neuroimage 111: 85-99 (May 2015).

 

National peer-reviewed scientific journals

 

2014

• C. Ferra, Hugo A. Ferreira, Pedro Gonçalves-Pereira, Rui Manaças, A. Andrade (2014), “Diferenças na conectividade estrutural entre um cérebro normal e um cérebro com patologia”, Revista Saúde & Tecnologia #T2: e29-e38.

 

 

Proceedings of international scientific meetings

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2015

• F. Lucena, T. Vaz, J. Pé-Leve, A. Santos-Ribeiro, L. Lacerda,  N. Silva, D. Nutt, J. McGonigle, H. A. Ferreira, “Evaluation of the quality of neuroimaging features as Alzheimer’s Disease biomarkers”, in European Journal of Nuclear Medicine and Molecular Medicine 42, pp. S828.

• J. Soeiro, A. P. Cláudio, M. B. Carmo, H. A. Ferreira, "Visualizing the brain on a mixed reality smartphone application", Proceedings of the 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 25-29 August 2015, Milan, Italy, pp. 5090-5093. (peer-reviewed)

• A. Ticlo, S. Reimão, H. Ferreira, J. M. Sousa, D. Abreu, J. Ferreira, J. Campos, R. G. Nunes, “Serial Measurements of Structural Connectivity and Diffusion-Tensor Metrics in Parkinson's Disease”, Proc. Intl. Soc. Magn. Reson. Med. 23: 4296 (2015).

• V. Tavares, A. Santos-Ribeiro, C. Capela, L. Cerqueira, H. A. Ferreira, “Method for epileptogenic focus localization using BOLD signal complexity analysis”, ISMRM 23rd Annual Meeting, Proc. Intl. Soc. Magn. Reson. Med. 23: 3922 (2015).

• R. Ribeiro, I. Neiva, H. A. Ferreira, “BrainVR: the virtual reality brain connectivity navigator”, Proc. Intl. Soc. Magn. Reson. Med. 23: 1340 (2015).

• R. Neto-Henriques, M. M. Correia, R. G. Nunes, H. A. Ferreira, “Resolving crossing fibers and generalizing biomarkers using the diffusion kurtosis tensor”, ISMRM 23rd Annual Meeting, Proc. Intl. Soc. Magn. Reson. Med. 23: 1028 (2015).

• J. Leote, R. G. Nunes, L. Cerqueira, H. A. Ferreira, "Corticospinal MRI tractography in space-occupying brain lesions by diffusion tensor and kurtosis imaging methods", EJNMMI Physics 2015, 2(Suppl 1): A82.

• V. Tavares, A. Santos-Ribeiro, C. Capela, L. Cerqueira, H. A. Ferreira, "Epileptogenic focus localisation: a new approach", EJNMMI Physics 2015, 2(Suppl 1): A81.

• A. C. Mendes, A. Santos-Ribeiro, A.-M. Oros-Peusquens, K.-J. Langen, N. J. Shah, H.A. Ferreira, "Brain connectivity study of brain tumor patients using MR-PET data: preliminary results", EJNMMI Physics 2015, 2(Suppl 1): A75.

• T. F. Vaz, F. Lucena, J. Pé-Leve, A. Santos-Ribeiro, L. Lacerda, N. Silva, D. Nutt, J. McGonigle, H. A. Ferreira, "Assessment of brain regions and multimodal neuroimaging metrics as biomarkers of Alzheimer’s Disease", EJNMMI Physics 2015, 2(Suppl 1): A46.

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2014

• A. Santos-Ribeiro, L. M. Lacerda, N. A. da Silva, H. A. Ferreira (2014), "Multimodal Imaging Brain Connectivity Analysis (MIBCA) Toolbox: preliminary application to Alzheimer's Disease", EJNMMI 1(S1): A61

• J. M. Sousa, R. G. Nunes, S. Reimão, J. Ferreira, H. A. Ferreira (2014), “Analysis of structural connectivity in Parkinson’s Disease using graph theory analysis”, Proc. Intl. Soc. Magn. Reson. Med. 22: 1921.

• L. M. Lacerda, A. Santos-Ribeiro, N. A. da Silva, R. Neto-Henriques, H. A. Ferreira (2014), “Multimodality imaging brain connectivity toolbox”, Proc. Intl. Soc. Magn. Reson. Med. 22: 3003. ISMRM 2014 Magna Cum Laude

• R. Neto-Henriques, L. Lacerda, R. Nunes, M. M. Correia, H. A. Ferreira (2014), “Diffusion kurtosis imaging based tractography”, Proc. Intl. Soc. Magn. Reson. Med. 22: 4525.

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2013

• H. A. Ferreira, F. Rodrigues, M. I. Meyer, A. Santos-Ribeiro, P. M. Gonçalves-Pereira, R. Manaças, A. Andrade (2013), “Complexity analysis of resting-state networks”, MAGMA 26 (S1): 225.

• A. Santos-Ribeiro, L. Lacerda, J. Rodrigues, J. M. Sousa, H. A. Ferreira (2013), “Multimodal imaging brain connectivity analysis”, MAGMA 26 (S1): 232.

• L. Lacerda, F. dell’Acqua, R. Manaças, P. Gonçalves-Pereira, R. Neto-Henriques, A. Andrade, R. Nunes, H. A. Ferreira (2013), “Automatic dissection and structural connectivity of the limbic system”, Epilepsia 54(S3): 308-309.

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2012

• H.A. Ferreira, A.R. Rocha, P.M. Gonçalves-Pereira, R.M. Manaças, A. Andrade (2012), “Multiscale entropy analysis of blood-oxygen level dependent brain signals”, MAGMA 25 (S1): 82-83

• H. A. Ferreira, A. C. Borralho, P.M. Gonçalves-Pereira, R. Manaças, A. Andrade (2012), “Granger causality analysis of resting-state networks in post-traumatic epilepsy patients”,  Epilepsia 53(S5): 64.

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Proceedings of national scientific meetings

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2015

• R. Loucao, R. G. Nunes, R. Neto-Henriques, M. Correia, H. Ferreira (2015), "Human brain tractography: A DTI vs DKI comparison analysis", In: 2015 IEEE 4th Portuguese Meeting on Bioengineering (ENBENG), 26-28 February 2015, Porto, Portugal (pp. 1-2). DOI: 10.1109/ENBENG.2015.7088820

• D. N. Sousa, H. A. Ferreira (2015), "Diffusion kurtosis imaging: Monte Carlo simulation of diffusion processes using crowd process", In: 2015 IEEE 4th Portuguese Meeting on Bioengineering (ENBENG), 26-28 February 2015, Porto, Portugal, pp. 1-4. DOI: 10.1109/ENBENG.2015.7088857

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Other publications in international scientific platforms

​

2014

• Publications in international open-access platforms A. Santos-Ribeiro, L. M. Lacerda, H. A. Ferreira (2014), “Multimodal Imaging Brain Connectivity Analysis Toolbox (MIBCA)”, PeerJ PrePrints 2:e699v1

• V. Tavares, J. Brito, H. Ferreira, A. Andrade, K. Koschutnig, G. Pfurtscheller (2014), “Temporal clustering analysis to evaluate slow oscillations around 0.1 Hz”, F1000Posters 2014, 5: 818. 

• H.A. Ferreira, C. Ferra, P. Gonçalves-Pereira, R. Manaças, A. Andrade (2014), “Pipeline methodology for structural connectivity analysis: application to the normal brain”, F1000Posters 2014, 5: 13.

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2013

• L. Lacerda, R. Neto-Henriques, F. dell’Acqua, R. Nunes, A. Andrade, R. Manaças, P. Gonçalves-Pereira, and H. Ferreira, “Functional and structural connectivity of the limbic system using automatic parcellation”, F1000Posters 2013, 4: 639.

 

 

Reports

 

2014

• A. C. Mendes, “Brain connectivity with PET/MR in tumours”, Internship report, Mestrado Integrado em Engenharia Biomédica e Biofísica, Departamento de Física da Faculdade de Ciências da Universidade de Lisboa, December 2014, Lisboa. (presentation of preliminary results)

• N. Pereira, “Memory functional connectivity study in patients with temporal lobe epilepsy”, Internship report, Mestrado Integrado em Engenharia Biomédica e Biofísica, Departamento de Física da Faculdade de Ciências da Universidade de Lisboa, December 2014, Lisboa.

• R. Ribeiro, “Ferramenta de Visualização de Conectividade”, Technical Report 3, IBEB-FCUL, FCT-PTDC/SAU-ENB/120718/2010, Lisboa, September 2014.

• F. Fernandes, “Ferramenta de Conectividade Cerebral a partir de Imagem Multimodal”, Technical Report 2, IBEB-FCUL, FCT-PTDC/SAU-ENB/120718/2010, Lisboa, September 2014.

 

2013    

• F. Borlinhas, “Correlação entre métricas de difusão por ressonância magnética e parâmetros de conectividade estrutural do cérebro humano”, Relatório de Neurociências, Mestrado Integrado em Engenharia Biomédica e Biofísica, Departamento de Física da Faculdade de Ciências da Universidade de Lisboa, December 2013, Lisboa.

• F. Guerreiro, F. Melo, M. Carmo, N. Vilhena, “Construção de um holograma tridimensional da representação esquemática de grafos de conectividade cerebral”, Relatório de Neurociências, Mestrado Integrado em Engenharia Biomédica e Biofísica, Departamento de Física da Faculdade de Ciências da Universidade de Lisboa, December 2013, Lisboa.

 

2012

• H.A. Ferreira, P.M. Gonçalves-Pereira, R. Manaças, A. Andrade, “Automated detection of brain networks derived from Independent Component Analysis of fMRI signals”, Technical Report 1, IBEB-FCUL, FCT-PTDC/SAU-ENB/120718/2010, Lisboa, 2012

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Software Applications (see also the Gallery)

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• ACBC tool: Automatic Classification of Brain Connectivity matrices add-on for the MIBCA toolbox (Maximiano et al., 2015)

• Brain AR/VR: smartphone/tablet application for visualizing the brain in Augmented Reality (Soeiro et al., 2015)

• Brain Connectivity Leap v1.0 and 2.0: enhanced brain connectivity navigator with gesture control and haptic feedback (Rodrigues et al., 2015)

• Brain Connectivity Touch, adapted and implemented for the Museum of Universal Values, Mafra, (Rodrigues et al., 2016)

• DKIu – United DKI: software for DKI data analysis (Neto-Henriques et al., 2015)

• MIBCA – Multimodal Imaging Brain Connectivity Toolbox (Santos Ribeiro et al., 2015)

• Diffusion kurtosis imaging: Monte-Carlo simulation of water diffusion  (Sousa and Ferreira, 2015)

• BrainVR: brain connectivity navigator (Ribeiro, 2014)

• Implementation of the multi-compartment models for water diffusion (Sousa, 2013)

 

 

Other outputs (see also the Gallery)

 

Models

• DKI-based tractography (Neto-Henriques et al., 2014, 2015).

• DKI multi-compartment models for studying white-matter (Neto-Henriques et al., 2013) and grey-matter (Sousa, 2013).

 

Protocols/Methods

• Paradigm for studying memory functional connectivity of temporal epilepsy patients using Psychopy software for stimuli presentation and an in-house developed Button-Box (Pereira, 2014; collaboration with Hospital de São José)

• Protocol for distributed processing of Monte-Carlo DKI simulations (Sousa and Ferreira, 2015; work in collaboration with the company Crowdprocess)

• Protocol for brain connectivity data analysis (within the scope of communications done and the MIBCA toolbox software)

• Method developed in MATLAB for SWI data analysis (A.C. Mendes, 2014)

• Method developed in MATLAB for 2d temporal clustering analysis (TCA) of BOLD signals (Tavares, 2014)

• Method developed in MATLAB for complexity analysis of BOLD signals using detrended fluctuation analysis (DFA) and multiscale entropy analysis (MSE) (Tavares, 2014, Thesis)

• Method developed in MATLAB for improved epileptogenic tissue identification from BOLD signals using 2dTCA with DFA and MSE analysis of BOLD signals (Tavares, 2014, Thesis)

• Method developed in MATLAB for functional dynamic analysis of BOLD signals using wavelet transforms, magnitude and phase coherence and delay calculation (Brito, 2014, Thesis)

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