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Dr Henriques completed his master's degree in biomedical engineering and Biophysics in 2012 at the Faculty of Science, University of Lisbon, PT (2007-2012). During the last year of his master, he implemented the main diffusion magnetic resonance imaging (dMRI) algorithms of the large collaborative project Cambridge Centre for Ageing and Neuroscience (cam-can.org). After a brief period as a research assistant at the Institute of Biophysics and Biomedical Engineering, University of Lisbon, PT (2012-2013), Dr Henriques was awarded a fellowship from the Portuguese Foundation for Science and Technology (FCT) to pursue his PhD at the Cognition and Brain Sciences Unit (CBSU), University of Cambridge, UK (2013-2018). His PhD project was focused on exploring the potentials and limitations of advanced dMRI analysis and their application to study microstructural age-related changes (Henriques, University of Cambridge PhD thesis, 2018; Henriques et al., NIMG 2015; Henriques et al., ReScience 2017; Price et al., Nat Commun 2017; Huber et al., Dev Cogn Neurosci 2019; Bergmann et al., NMR Biomed. 2019). After his PhD, Dr Henriques was invited to join the Shamesh Lab at the Champalimaud Foundation, PT (2017-2021) as a postdoctoral fellow. There he exploited the capabilities of the pre-clinical high field scanners to validate different state-of-the-art dMRI models (Henriques et al., MRM 2019) and developed novel methods to extract unique tissue microstructural information from advanced dMRI sequences (Henriques et al., Neurosci Methods 2021). Specifically, he established the Correlation tensor MRI (CTI) - an innovative dMRI methodology that avoids the use of simplified models by characterizing microstructural tissue using different sources of non-Gaussian diffusion (Henriques et al., NIMG 2020; Henriques et al., MRM 2021). Recently, Dr Henriques was awarded a six-year postdoctoral fellowship to continue working at the Champalimaud Foundation to explore the potential of CTI to address the current needs of stroke imaging (Alves et al., NIMG 2022) and the translate it to the clinics (Novello, Henriques et al., NIMG 2022) . Dr Henriques is also an active contributor of the large-scale open-source project diffusion in python (dipy.org) which aim is to promote the reproducibility of research based on dMRI techniques (top 5 collaborator over more than 100 collaborators). During his career, Dr Henriques author in 24 main authorship in peer-reviewed publications (including 10 first-author, 2 last-author, and 6 second-author papers) and in 44 consortium papers. His work was also presented on more than 15 international conferences with a total of 64 abstracts accepted (10 of the 28 first-author abstracts were selected for oral presentations). He was also a supervisor of the Mathematical Biology lectures at the University of Cambridge (having supervised 10 undergraduate students), he supervised 2 master projects, 6 Google Summer of Code projects and he was a jury element of 2 master and 1 doctoral thesis.
Identification

Personal identification

Full name
Rafael Neto Henriques

Citation names

  • Henriques, Rafael

Author identifiers

Ciência ID
731E-D1D9-090B
ORCID iD
0000-0002-3891-8189

Email addresses

  • rafael.henriques@neuro.fchampalimaud.org (Professional)

Knowledge fields

  • Engineering and Technology - Medical Engineering

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Italian Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2018/10/03
Concluded
Doctor of Philosophy in Biological Sciences (Doutoramento)
Major in Medical Science
University of Cambridge, United Kingdom
"Advanced Methods for Diffusion MRI Data Analysis and their Application to the Healthy Ageing Brain" (THESIS/DISSERTATION)
n/a
2012
Concluded
Mestrado Integrado em Engenharia Biomédica e Biofísica (Mestrado)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Diffusion Kurtosis Imaging of the Healthy Human Brain" (THESIS/DISSERTATION)
17
Affiliation

Science

Category
Host institution
Employer
2018/10/03 - Current Postdoc (Research) Centro Champalimaud, Portugal
Centro Champalimaud, Portugal
2017/10/01 - 2018/10/02 Research Assistant (Research) Centro Champalimaud, Portugal
Centro Champalimaud, Portugal
2013/10/01 - 2017/09/30 Research Trainee (Research) University of Cambridge - Cognition and Brain Sciences Unit, United Kingdom
University of Cambridge - Cognition and Brain Sciences Unit, United Kingdom
2012/11/17 - 2013/09/30 Researcher (Research) Universidade de Lisboa Instituto de Biofísica e Engenharia Biomédica, Portugal
Universidade de Lisboa Instituto de Biofísica e Engenharia Biomédica, Portugal
2010/06/15 - 2010/09/15 Research Trainee (Research) University of Toronto Oral Dynamics Laboratory, Canada
University of Toronto Oral Dynamics Laboratory, Canada
Projects

Grant

Designation Funders
2013/01/01 - 2017/09/30 Advanced Methods for Diffusion MRI Data Analysis and their application to the Healthy Ageing Brain
SFRH/BD/89114/2012
PhD Student Fellow
University of Cambridge - Cognition and Brain Sciences Unit, United Kingdom
Fundação para a Ciência e a Tecnologia
Concluded
2010/10/01 - 2016/03/31 Systems Cognitive Neuroscience of Healthy Ageing: Population-Representative Studies of Functional Plasticity and Neural Change
Invited Scientist Fellow
University of Cambridge, United Kingdom
Biotechnology and Biological Sciences Research Council
Concluded
2012/01/01 - 2013/09/30 Comprehensive multi-parametric analysis of the limbic system connectivity in post-traumatic epilepsy patients Fundação para a Ciência e a Tecnologia
Concluded

Contract

Designation Funders
2022/06/01 - 2028/06/01 Correlation Tensor MRI: a paradigm shift for stroke management
Post-doc
Fundação Champalimaud, Portugal
FCT - Fundação para a Ciência e a Tecnologia
Ongoing
2017/10/01 - 2021/02/28 Sensing activity-induced cell swellings and ensuing neurotransmitter releases for in-vivo functional imaging sans hemodynamics
Post-doc
Centro Champalimaud, Portugal
European Research Council
Concluded
2009/10/01 - 2010/07/31 Neuroimaging with MATLAB: MRI Brain Segmentation
Integration into Research Grant Fellow
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
Concluded
Outputs

Publications

Conference abstract
  1. Henriques, Rafael; Alves, R.; Ianus, A.; Jespersen, S.N.; Shemesh N.. "Correlation Tensor MRI Directional Metrics in Stroke Improve Lesion Characterization". Paper presented in 19th European Molecular Imaging Meeting, Porto, 2024.
  2. Villalón-Reina, J.E.; Nir, T.M.; Nourollahimoghadam, E.; Jahanshad, N.; Thompson, P.M.; Henriques, Rafael. "Computing Fiber Orientation Dispersion from Single shell Diffusion MRI". Paper presented in 29th Annual Meeting of the OHBM, Montreal, 2023.
    Published
  3. Henriques, Rafael; Simoes, R.V.; Monteiro, S.; Ianus, A.; Carvalho, T.; Jespersen, S.N.; Shemesh N.. "Correlation Tensor Imaging Enhances Histological Differences Between Mouse Glioblastoma Subtypes". Paper presented in 2023 ISMRM & ISMRT Annual Meeting, Toronto, 2023.
    Published
  4. Simões, R.V.; Henriques, Rafael; Olesen, J.V.; Cardoso, B.M.; Fernandes, F.F.; Carvalho, T.; Jespersen, S.N.; Shemesh N.. "Probing Tumor Heterogeneity in Mouse Glioblastoma with Dynamic Glucose-Enhanced Deuterium Metabolic Imaging". Paper presented in 2023 ISMRM & ISMRT Annual Meeting, Toronto, 2023.
    Published
  5. Ianus, A., ; Palombo, M.; Simões, R.V.; Henriques, Rafael; Carvalho, T.; Shemesh N.. "Soma and Neurite Density Imaging (SANDI) characterizes microscopic differences between two glioma mouse model subtypes.". Paper presented in 2023 ISMRM & ISMRT Annual Meeting, Toronto, 2023.
    Published
  6. Jespersen, S.N.; Alves, R.; Olesen, J.V.; Henriques, R.N.; Shemesh N.. "Exchange-driven Microscopic Kurtosis in Correlation Tensor MRI". Paper presented in 2023 ISMRM & ISMRT Annual Meeting, Toronto, 2023.
    Published
  7. Alves, R.; Henriques, Rafael; Olesen, J.V.; Jespersen, S.N.; Shemesh N.. "Mapping biophysical changes in stroked tissue via the Standard Model with Exchange (SMEX) diffusion model". Paper presented in 2023 ISMRM & ISMRT Annual Meeting, Toronto, 2023.
    Published
  8. Slator, P.J.; Simões, R.V.; Henriques, Rafael; Carvalho, T.; Alexander, D.C.; Shemesh, N.; Ianus, A.. "Characterising glioma heterogeneity with diffusion-relaxation MRI and InSpect". Paper presented in 2023 ISMRM & ISMRT Annual Meeting, Toronto, 2023.
    Published
  9. Bilreiro, C.; Andrade, L.; Henriques, Rafael; Loução, N.; Shemesh, N.; Matos C.. "Diffusion tensor imaging and diffusion kurtosis imaging of the pancreas at 3 Tesla MRI - reproducibility and normal findings". Paper presented in 108th Scientific Assembly and Annual meeting Radiological Society of North America 2022, Chicago, 2022.
    Published
  10. Henriques, Rafael; Simões, R.V.; Monteiro, S.; Carvalho, T.; Jespersen, S.N.; Shemesh, N.. "Correlation Tensor Imaging Reveals Histologic Differences Between Mouse Glioblastoma Subtypes". Paper presented in ISMRM Workshop on Diffusion MRI: From Research to Clinic, Amsterdam, 2022.
    Published
  11. Alves, R.; Henriques, Rafael; Jespersen, S.N.; Shemesh, N.. "Correlation Tensor MRI Unravels Dynamic Alterations in Underlying Kurtosis Sources Along Stroke Progression". Paper presented in ISMRM Workshop on Diffusion MRI: From Research to Clinic, Amsterdam, 2022.
    Published
  12. Henriques, Rafael; Alves, R.,; Jespersen, S.N.; Shemesh, N.. "Three-dimensional characterization of diffusion kurtosis sources". Paper presented in 2nd Annual Meeting of the ISMRM Iberian Chapter, Lisbon, 2022.
    Published
  13. Alves, R.; Henriques, Rafael; Jespersen, S.N.; Shemesh, N.. "Correlation Tensor imaging Disentangles Kurtosis Sources along stroke progression". Paper presented in 2nd Annual Meeting of the ISMRM Iberian Chapter, Lisbon, 2022.
    Published
  14. Henriques, Rafael; Jespersen, Sune N; Shemesh, Noam. "Hybrid PCA denoising - improving PCA denoising in the presence of spatial correlations". Paper presented in Joint Annual Meeting of the ISMRM-ESMRMB, London, 2022.
    Published
  15. Novello, L.; Henriques, Rafael; Andrada Ianus; Feiweier, T.; Shemesh, Noam; Jovicich, J.. "First templates of human brain kurtosis sources: relevance of microscopic kurtosis from Correlation Tensor MRI at 3 Tesla". Paper presented in Joint Annual Meeting of the ISMRM-ESMRMB, London, 2022.
    Published
  16. Alves, Rita; Henriques, Rafael; Jespersen, S.N.; Shemesh, Noam. "Correlation Tensor MRI reveals dynamic changes in diffusion kurtosis sources along stroke progression". Paper presented in Joint Annual Meeting of the ISMRM-ESMRMB, 2022.
    Published
  17. Simões, R.V.; Henriques, Rafael; Cardoso, B.M.; Fernandes, F.; Carvalho, T.; Shemesh, N.. "Modulation of glucose metabolic fluxes according to tumor cell proliferation in mouse glioblastoma subtypes.". Paper presented in Joint Annual Meeting of the ISMRM-ESMRMB, London, 2022.
    Published
  18. Alves, R.; Henriques, Rafael; Kerkelä, L.; Chavarrías C.; Jespersen, S.N.; Shemesh, N.. "Dynamics of Diffusion Kurtosis Sources Along Stroke Progression Revealed by Correlation Tensor Imaging Diffusion". Paper presented in ISMRM Diffusion Study Group Trainee Day: 24 Hours of Diffusion Around the World (virtual meeting), 2021.
    Published
  19. Henriques, Rafael; Jespersen, S.N.; Shemesh N., 2021. "Evidence for microscopic kurtosis in neural tissue revealed by Correlation Tensor MRI". Paper presented in 1st Annual Meeting of the ISMRM Iberian Chapter (virtual meeting), 2021.
    Published
  20. Alves, R.; Henriques, Rafael; Jespersen, S.N.; Shemesh, N.. "Deciphering the underlying sources of diffusion kurtosis in focal ischemia by Correlation Tensor MRI". Paper presented in 1st Annual Meeting of the ISMRM Iberian Chapter (virtual meeting), 2021.
    Published
  21. Simões, R.V.; Henriques, Rafael; Cardoso, B. M.; Olesen, J.L.; Jespersen, S.N.; Shemesh, Noam. "Non-invasive assessment of glycolytic and oxidative metabolism in mouse glioma using DGE 2H-MRS. 2021". Paper presented in 29th Annual Meeting of the ISMRM (Virtual), Virtual, 2021.
    Published
  22. Henriques, Rafael; Correia, M.M.; Marrale, M.; Huber, Elizabeth; Kruper, J.; Koudoro, S.; Yeatman, Jason D.; Garyfallidis, E; Rokem, A.. "Diffusional Kurtosis Imaging in the Diffusion Imaging in Python Project". Paper presented in 29th Annual Meeting of the ISMRM (Virtual), 2021.
    Published
  23. Henriques, Rafael; Jespersen, S.N.; Jones, D.K.; Veraart, J.. "Towards more robust and reproducible Diffusion Kurtosis Imaging". Paper presented in 29th Annual Meeting of the ISMRM (Virtual), Virtual, 2021.
    Published
  24. Henriques, Rafael; Jespersen, S.N.; Shemesh, Noam. "Intra-compartmental kurtosis biases tensor-valued multidimensional diffusion". Paper presented in 29th Annual Meeting of the ISMRM, Virtual, 2021.
    Accepted
  25. Alves, R.; Henriques, Rafael; Jespersen, S.N.; Shemesh, Noam. "Resolving the underlying sources of diffusion kurtosis in focal ischemia by Correlation Tensor MRI.". Paper presented in 29th Annual Meeting of the ISMRM (Virtual), 2021.
    Published
  26. Novello, L.; Henriques, Rafael; Ianus, A.; Feiweier, T.; Shemesh, Noam; Jovicich, J.. "Human brain in vivo correlation tensor MRI on clinical 3T system". Paper presented in 29th Annual Meeting of the ISMRM (Virtual), 2021.
    Published
  27. Simoes, R.V.; Henriques, Rafael; Cardoso, B.M.; Carvalho, T.; Shemesh, Noam. "Glucose oxidation rate as a potential marker for GBM staging: correlation with histopathology and cell proliferation in a mouse model". Paper presented in 29th Annual Meeting of the ISMRM (Virtual), 2021.
    Published
  28. Alves, Rita; Henriques, Rafael; Shemesh, Noam. "Improving Stroke Detection with Correlation Tensor MRI". Paper presented in The Brain Conference “Brain Stroke: Why, how, and hope”, Federation of European Neuroscience Societies, Rungstedgaard, 2021.
  29. Alves, Rita; Henriques, Rafael; Shemesh, Noam. "Mapping Microstructural Dynamics in a Mouse Stroke Model Using Diffusion MRI". Paper presented in iMed 12.0 Conference, Lisbon, 2020.
    Published
  30. Henriques, Rafael; Golub, M.; Nunes, Rita. "Lesion detection using Free-Water elimination DTI - is this technique really specific to free water?". Paper presented in 28th Annual Meeting of the ISMRM (virtual), 2020.
    Published
  31. Henriques, Rafael; Jespersen, S.N.; Shemesh, Noam. "Correlation Tensor Imaging - resolving non-Gaussian diffusion sources of in vivo tissues". Paper presented in 28th Annual Meeting of the ISMRM (virtual), 2020.
    Published
  32. Henriques, Rafael; Olesen, J.L.; Jespersen, S.N.; Shemesh, Noam. "Measuring the full diffusional intra- and inter-compartmental kurtosis tensors using double diffusion encoding". Paper presented in 28th Annual Meeting of the ISMRM (virtual), 2020.
    Published
  33. Grilo, J.M.; Golub, M.; Reimão, S.; Henriques, Rafael; Fouto, A.; Lobo, P.P.; Fabbri, M.; Ferreira, J.J.; Nunes, R.G. "Substantia nigra changes in Parkinson’s Disease: correlation between Neuromelanin contrast and Free Water fraction". Paper presented in 28th Annual Meeting of the ISMRM (virtual), 2020.
    Published
  34. Henriques, Rafael; Veraart, J.. "Promoting the clinical applicability of Diffusion Kurtosis Imaging.". Paper presented in 25th Annual Meeting of the OHBM, Rome, 2019.
    Published
  35. Golub, M.; Henriques, Rafael; Pasternak, O.; Nunes, R.G.. "Open-source algorithm for single-shell free water DTI: potentials and limitations". Paper presented in 25th Annual Meeting of the OHBM, Rome, 2019.
    Published
  36. Kerkelä, Leevi; Henriques, Rafael; Hall, Matt G.; Clark, Chris A.; Shemesh, Noam. "Experimental validation and SNR analysis of a clinical double diffusion encoding sequence.". Paper presented in 27th Annual Meeting of the ISMRM, Montréal, 2019.
    Published
  37. Kerkelä, Leevi; Henriques, Rafael; Hall, Matt G.; Shemesh, Noam; Clark, Chris A.. "Precision of microscopic fractional anisotropy estimation using double diffusion encoding.". Paper presented in 27th Annual Meeting of the ISMRM, Montréal, 2019.
    Published
  38. Simões, R.V.; Caja-Galán, S.; Henriques, Rafael; Costa-Silva, B.; Shemesh, Noam. "Detection of pre-metastatic niches in perfused mouse livers by diffusion-weighted imaging at ultra-high field". Paper presented in 27th Annual Meeting of the ISMRM, Montréal, 2019.
    Published
  39. Yon, M.; Bao, Q.; Henriques, Rafael; Shemesh, Noam; Frydman, L.. "Spatiotemporal Encoding (SPEN) at ultra-high fields: Applications to high resolution (<100 um isotropic) in vivo mouse brain DTI". Paper presented in 27th Annual Meeting of the ISMRM, Montréal, 2019.
    Published
  40. Henriques, Rafael; Tax, C.M.W.; Shemesh, Noam; Veraart, J.. "Biophysical modeling of the white matter: from theory towards clinical practice". Paper presented in 27th Annual Meeting of the ISMRM, Montréal, 2019.
    Published
  41. Henriques, Rafael; Jespersen, S.N.; Shemesh, Noam. "The two-compartment diffusion "standard model" misestimates microscopic anisotropy in-vivo.". Paper presented in 27th Annual Meeting of the ISMRM, Montréal, 2019.
    Published
  42. Duarte, T.; Henriques, Rafael; Nunes, D.; Zeiler, S.R.; Krakauer, J.W.; Shemesh, Noam. "Learning-induced microstructural changes in specific layers of primary motor cortex revealed by diffusion kurtosis tensor imaging.". Paper presented in 27th Annual Meeting of the ISMRM, Montréal, 2019.
    Published
  43. Henriques, Rafael; Sune Jespersen; Noam Shemesh. "Correlation-tensor imaging: resolving different sources of non-Gaussian diffusion". Paper presented in 27th Annual Meeting of the ISMRM, Montréal., 2019.
    Published
  44. Henriques, Rafael; Correia, M.M.; Nunes, R.G.; Ferreira, H.A.. "PCA denoising using random matrix theory provides an optimal compromise between noise suppression and preservation of non-Gaussian diffusion". Paper presented in Joint Annual Meeting of the ISMRM-ESMRMB, Paris, 2018.
    Published
  45. Henriques, Rafael; Shemesh, Noam. "Validity Regimes of the Spherical Mean Technique". Paper presented in Joint Annual Meeting of the ISMRM-ESMRMB, Paris, 2018.
    Published
  46. Henriques, Rafael; Bergmann, Ø.; Rokem, A.; Pasternak, O.; Correia, M.M.. "Exploring the potentials and limitations of improved free-water elimination DTI techniques.". Paper presented in 25th Annual Meeting of the ISMRM, Honolulu, 2017.
    Published
  47. Henriques, Rafael; Correia, Marta. "Interpreting age-related changes based on the mean signal diffusion kurtosis". Paper presented in 25th Annual Meeting of the ISMRM, Honolulu, 2017.
    Published
  48. Rokem, A.; Huber, Elizabeth; Mehta, P.; Henriques, Rafael; Balazinska, M.; Yeatman, J.. "Diffusion Kurtosis Imaging for the Human Connectome Project". Paper presented in Annual Meeting of the Society for Neuroscience, San Diego, 2016.
    Published
  49. Henriques, Rafael; Correia, M.M.; Dell’Acqua, F.. "Tract specific measures from the fODF - a way to characterize simultaneously fiber crossing and dispersion.". Paper presented in ISMRM's Workshop on Breaking the Barriers of Diffusion MRI, Lisbon, 2016.
    Published
  50. Henriques, Rafael; CamCAN; Correia, M.M.. "Reducing inter and intravolume instabilities on diffusion-weighted data for ageing studies". Paper presented in 22nd Annual Meeting of the OHBM, Geneva, 2016.
    Published
  51. Prince, D.; Tyler, L.; Henriques, Rafael; Campbell, K.; Williams, N.; Treder, M.; Taylor, J.; CamCAN; Henson, R.. "Age-Related Delay in Visual and Auditory Evoked Responses is Mediated by White- and Gray-matter Differences.". Paper presented in 22nd Annual Meeting of the OHBM., Geneva, 2016.
    Published
  52. Henriques, Rafael; Correia, M.M.; Dell'Acqua, F.. "Mapping fibre dispersion and tract specific metrics in multiple fibre orientations using multi Bingham distributions". Paper presented in 24th Annual Meeting of the ISMRM, Singapore, 2016.
    Published
  53. Loução, R.; Elsner, K.; Nunes, R.G.; Henriques, Rafael; Correia, M.M.; Ribeiro, A.; Ferreira, H.A.. "Effects of the Number of Diffusion Directions in Diffusion Kurtosis Imaging: a Structural Connectivity Study using in vivo data.". Paper presented in 24th Annual Meeting of the ISMRM, Singapore, 2016.
    Published
  54. Henriques, Rafael; Lacerda, L.; Dell'Acqua, F.; Correia, M.M.. "Fiber direction estimates on diffusion MRI multi-shell protocols - comparison of the performances of DTI, DKI and Richardson-Lucy SD based tractography.". Paper presented in 32nd Annual Meeting of the ESMRMB, Edinburgh, 2015.
    Published
  55. Henriques, Rafael; Ferreira, H.A.; Correia, M.M.. "United Diffusion Kurtosis Imaging Toolbox". Paper presented in 32nd Annual Meeting of the ESMRMB, Edinburgh, 2015.
    Published
  56. Loução, R.; Nunes, R.G.; Henriques, Rafael; Correia, M.M.; Santos Ribeiro, A.; Ferreira, H.A.. "Structural Connectivity based on Diffusion Kurtosis Imaging". Paper presented in 32nd Annual Meeting of the ESMRMB, Edinburgh, 2015.
    Published
  57. Henriques, Rafael; Correia, M.M.; Nunes, R.G.; Ferreira, H.A.. "Resolving crossing fibers and generalizing biomarkers using the diffusion kurtosis tensor.". Paper presented in 23rd Annual Meeting of the ISMRM, Toronto, 2015.
    Published
  58. Henriques, Rafael; Correia, M.M.; Nunes, R.G.; Ferreira, H.A.. "Diffusion Kurtosis Imaging based Tractography". Paper presented in Joint Annual Meeting of the ISMRM-ESMRMB, Milan, 2014.
    Published
  59. Lacerda, L.M.; Ribeiro, A.S.; da Silva, N.A.; Henriques, Rafael; Ferreira, H.A.. "Multimodal Imaging Brain Connectivity Analysis Toolbox.". Paper presented in Joint Annual Meeting of the ISMRM-ESMRMB, Milan, 2014.
    Published
  60. Henriques, Rafael; Correia, M.M.; Nunes, R.G.; Ramalho, J.; Ferreira, H.A.. "Advances on Multi-Compartment Model Simulations to Interpret the 3D Geometry of Diffusion Kurtosis". Paper presented in 19th Annual Meeting of the OHBM, Seattle, 2013.
    Published
  61. Henriques, Rafael; Correia, M.M.; CamCAN. "Towards optimization of diffusion kurtosis imaging to study brain changes with age". Paper presented in 29th Anual Meeting of the ESMRMB, Lisbon, 2012.
    Published
  62. Terband, H.; Van Brenk, F.; Henriques, Rafael; van Lieshout, P.; Maassen, B.; Lowit, A.. "Speech rate strategies in younger and older adults". Paper presented in Motor Speech Conference 2012, Edegem, 2012.
    Published
  63. Henriques, Rafael; van Lieshout, P.. "A Comparison of Methods for Decoupling Tongues and Lips from Jaw Movements in 3D Articulography". Paper presented in International Conference on Speech Motor Control, Groningen, 2011.
    Published
  64. Ribeiro, A.; Fernandes, C.; Salvado, D.; Lacerda, L.; Costa, M.; Henriques, Rafael; Evans, G.; Almeida, P.; Ferreira, H.. "Combined use of Electrocardiography and Accelerometry to evaluate the physical condition of a subject". Paper presented in Conference on Electronics Telecommunications and Computers, Lisbon, 2011.
    Published
Conference paper
  1. Villalón-Reina, J.E.; Nir, T.M.; Nourollahimoghadam, E.; Dhinagar, N.; Jahanshad, N.; Thompson, P.M.; Henriques, Rafael. "Evaluating Fiber Orientation Dispersion Measures Computed From Single-Shell Diffusion MRI". Paper presented in 2023 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Sydney, 2023.
    Published • 10.1109/EMBC40787.2023.10340067
Journal article
  1. Fouto, A.R.; Henriques, Rafael; Golub, M.; Freitas, A.C.; Ruiz-Tagle, A.; Esteves, I.; Gil-Gouveia, R.; et al. "Impact of Truncating Diffusion MRI Scans on Diffusional Kurtosis Imaging". Magnetic Resonance Materials in Physics, Biology and Medicine (2024): https://doi.org/10.1007/s10334-024-01153-y.
    Published
  2. Henriques, Rafael; Ianus, Andrada; Novello, Lisa; Jovicich, Jorge; Jespersen, Sune N; Shemesh, Noam. "Efficient PCA denoising of spatially correlated redundant MRI data". Imaging Neuroscience 1 (2023): 1-26. http://dx.doi.org/10.1162/imag_a_00049.
    10.1162/imag_a_00049
  3. Henriques, Rafael; Henson, Richard; Cam-CAN; Correia, Marta Morgado. "Unique information from common diffusion MRI models about white-matter differences across the human adult lifespan". Imaging Neuroscience 1 (2023): 1-25. http://dx.doi.org/10.1162/imag_a_00051.
    10.1162/imag_a_00051
  4. Sandgaard, Anders Dyhr; Kiselev, Valerij G.; Henriques, Rafael Neto; Shemesh, Noam; Jespersen, Sune Nørhøj. "Incorporating the effect of white matter microstructure in the estimation of magnetic susceptibility in ex vivo mouse brain". Magnetic Resonance in Medicine 91 2 (2023): 699-715. http://dx.doi.org/10.1002/mrm.29867.
    10.1002/mrm.29867
  5. Novello, Lisa; Henriques, Rafael Neto; Ianus, Andrada; Feiweier, Thorsten; Shemesh, Noam; Jovicich, Jorge. "In vivo Correlation Tensor MRI reveals microscopic kurtosis in the human brain on a clinical 3T scanner". NeuroImage 254 (2022): 119137. http://dx.doi.org/10.1016/j.neuroimage.2022.119137.
    10.1016/j.neuroimage.2022.119137
  6. Alves, Rita; Henriques, Rafael Neto; Kerkelä, Leevi; Chavarrías, Cristina; Jespersen, Sune N; Shemesh, Noam. "Correlation Tensor MRI deciphers underlying kurtosis sources in stroke". NeuroImage 247 (2022): 118833. http://dx.doi.org/10.1016/j.neuroimage.2021.118833.
    Published • 10.1016/j.neuroimage.2021.118833
  7. Simões, Rui V.; Henriques, Rafael N.; Cardoso, Beatriz M.; Fernandes, Francisca F.; Carvalho, Tânia; Shemesh, Noam. "Glucose fluxes in glycolytic and oxidative pathways detected in vivo by deuterium magnetic resonance spectroscopy reflect proliferation in mouse glioblastoma". NeuroImage: Clinical 33 (2022): 102932. http://dx.doi.org/10.1016/j.nicl.2021.102932.
    10.1016/j.nicl.2021.102932
  8. Henriques, Rafael Neto; Jespersen, Sune N.; Shemesh, Noam. "Evidence for microscopic kurtosis in neural tissue revealed by correlation tensor MRI". Magnetic Resonance in Medicine 86 6 (2021): 3111-3130. http://dx.doi.org/10.1002/mrm.28938.
    10.1002/mrm.28938
  9. Henriques, Rafael Neto; Correia, Marta M.; Marrale, Maurizio; Huber, Elizabeth; Kruper, John; Koudoro, Serge; Yeatman, Jason D.; Garyfallidis, Eleftherios; Rokem, Ariel. "Diffusional Kurtosis Imaging in the Diffusion Imaging in Python Project". Frontiers in Human Neuroscience 15 (2021): http://dx.doi.org/10.3389/fnhum.2021.675433.
    10.3389/fnhum.2021.675433
  10. Marc Golub; Rafael Neto Henriques; Rita Gouveia Nunes. "Free-water DTI estimates from single b-value data might seem plausible but must be interpreted with care". Magnetic Resonance in Medicine 85 5 (2021): 2537-2551. https://doi.org/10.1002/mrm.28599.
    10.1002/mrm.28599
  11. Henriques, Rafael; Jespersen, Sune N.; Jones, Derek K.; Veraart, Jelle. "Towards more robust and reproducible Diffusion Kurtosis Imaging". Magnetic Resonance in Medicine 86 3 (2021): 1600-1613. https://doi.org/10.1002/mrm.28730.
    Published
  12. Henriques, Rafael N.; Palombo, Marco; Jespersen, Sune N.; Shemesh, Noam; Lundell, Henrik; Ianus, Andrada. "Double diffusion encoding and applications for biomedical imaging". Journal of Neuroscience Methods 348 (2021): 108989. http://dx.doi.org/10.1016/j.jneumeth.2020.108989.
    10.1016/j.jneumeth.2020.108989
  13. Yon, Maxime; Bao, Qingjia; Chitrit, Odélia Jacqueline; Henriques, Rafael Neto; Shemesh, Noam; Frydman, Lucio. "High-Resolution 3D in vivo Brain Diffusion Tensor Imaging at Ultrahigh Fields: Following Maturation on Juvenile and Adult Mice". Frontiers in Neuroscience 14 (2020): http://dx.doi.org/10.3389/fnins.2020.590900.
    10.3389/fnins.2020.590900
  14. Henriques, Rafael. "Correlation tensor magnetic resonance imaging". NeuroImage 211 (2020): 116605. http://dx.doi.org/10.1016/j.neuroimage.2020.116605.
    Open access • 10.1016/j.neuroimage.2020.116605
  15. Bergmann, Ørjan; Henriques, Rafael; Westin, Carl-Fredrik; Pasternak, Ofer. "Fast and accurate initialization of the free-water imaging model parameters from multi-shell diffusion MRI". NMR in Biomedicine 33 3 (2019): http://dx.doi.org/10.1002/nbm.4219.
    10.1002/nbm.4219
  16. Kerkelä, Leevi; Henriques, Rafael Neto; Hall, Matt G.; Clark, Chris A.; Shemesh, Noam. "Validation and noise robustness assessment of microscopic anisotropy estimation with clinically feasible double diffusion encoding MRI". Magnetic Resonance in Medicine (2019): http://dx.doi.org/10.1002/mrm.28048.
    10.1002/mrm.28048
  17. Henriques, Rafael. "Microscopic anisotropy misestimation in spherical-mean single diffusion encoding MRI". Magnetic Resonance in Medicine (2019): http://dx.doi.org/10.1002/mrm.27606.
    10.1002/mrm.27606
  18. Huber, Elizabeth; Henriques, Rafael Neto; Owen, Julia P.; Rokem, Ariel; Yeatman, Jason D.. "Applying microstructural models to understand the role of white matter in cognitive development". Developmental Cognitive Neuroscience 36 (2019): 100624. http://dx.doi.org/10.1016/j.dcn.2019.100624.
    10.1016/j.dcn.2019.100624
  19. Henriques, Rafael. "Sustainable computational science: the ReScience initiative". PeerJ Computer Science (2017): http://dx.doi.org/10.7717/peerj-cs.142.
    10.7717/peerj-cs.142
  20. Henriques, Rafael. "Age-Related Delay in Visual and Auditory Evoked Responses is Mediated by White- and Gray-matter Differences". Nature Communications (2017):
    10.1038/ncomms15671
  21. Henriques, Rafael. "[Re] Optimization of a free water elimination two-compartment model for diffusion tensor imaging". ReScience (2017):
    10.5281/zenodo.495237
  22. Henriques, Rafael. "Exploring the 3D geometry of the diffusion kurtosis tensor--impact on the development of robust tractography procedures and novel biomarkers.". Neuroimage (2015):
    10.1016/j.neuroimage.2015.02.004
  23. Garyfallidis, Eleftherios; Brett, Matthew; Amirbekian, Bagrat; Rokem, Ariel; van der Walt, Stefan; Descoteaux, Maxime; Nimmo-Smith, Ian. "Dipy, a library for the analysis of diffusion MRI data". Frontiers in Neuroinformatics 8 (2014): http://dx.doi.org/10.3389/fninf.2014.00008.
    10.3389/fninf.2014.00008
  24. Henriques, Rafael. "A comparison of methods for decoupling tongue and lower lip from jaw movements in 3D articulography.". J Speech Lang Hear Res (2013):
    10.1044/1092-4388(2013/12-0016)
Thesis / Dissertation
  1. Henriques, Rafael. "Advanced Methods for Diffusion MRI Data Analysis and their Application to the Healthy Ageing Brain". PhD, University of Cambridge - Cognition and Brain Sciences Unit, 2018. https://www.repository.cam.ac.uk/handle/1810/281993.
  2. Henriques, Rafael. "Diffusion Kurtosis Imaging of the Healthy Human Brain". Master, Universidade de Lisboa Faculdade de Ciências, 2012. https://core.ac.uk/download/pdf/12428129.pdf.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2023/11/07 Diffusion Imaging in Python (DIPY) and its contributions to open and reproducible research MRI together workshop
European Society for Magnetic Resonance in Medicine and Biology
2022/06/07 Diffusion Artefacts and pre-processing Joint Annual Meeting of the ISMRM-ESMRMB
International Society for Magnetic Resonance in Medicine (London, United Kingdom)
2022/01/30 Correlation Tensor MRI - resolving kurtosis sources in health and disease. Microstructural imageries series
New York University (NYU) school of medicine (New York, United States)
2021/12/16 Ressonância magnética por contraste de difusão. Biomedical Engineering and Biophysics Seminars
Faculty of Science University of Lisbon (Lisboa, Portugal)
2021/06/10 Diffusion MRI - free water imaging and beyond. CES Weekly talk series.
Clinical & Experimental Sciences (CES) Division. Southampton General Hospital ( Southampton, United Kingdom)
2021/04/04 Correlation Tensor Imaging. UCL Quantitative MRI interest group
University College London (London, United Kingdom)
2021/03/15 Diffusion Kurtosis Imaging & Microstructural Models Annual Dipy workshop (Virtual edition).
Indiana University, Bloomington, USA
2020/11/24 Diffusion MRI with Python Pybrain workshop
Cognition and Brain Sciences Unit, University of Cambridge, UK (Virtual)
2020/08/08 Correlation Tensor Imaging - resolving non-Gaussian diffusion sources of in vivo tissues 28th Annual Meeting of the ISMRM
ISMRM (Paris, France)
2020/08/08 Measuring the full diffusional intra- and inter-compartmental kurtosis tensors using double diffusion encoding 28th Annual Meeting of the ISMRM
ISMRM (Paris, France)
2019/10/15 Correlation Tensor Imaging Clinical Imaging Sciences Centre (CISC) Seminar section
Clinical Imaging Sciences Centre (CISC) (Brighton, United Kingdom)
2019/05/13 Biophysical modeling of the white matter: from theory towards clinical practice ISMRM 27th Annual Meeting & Exhibition
ISMRM (Montreal)
2019/05/11 The two-compartment diffusion "standard model" misestimates microscopic anisotropy in-vivo ISMRM 27th Annual Meeting & Exhibition
ISMRM (Montreal, Canada)
2019/03/16 Diffusion Representation Techniques and Microstructural Models Dipy workshop
Indiana University, Bloomington, USA (Bloomington, United States)
2018/04/24 Validity Regimes of the Spherical Mean Technique Joint Annual Meeting ISMRM-ESMRMB 2018
ISMRM-ESMRMB (Paris, France)
2017/04/27 Interpreting age-related changes based on the mean signal diffusion kurtosis ISMRM 25th Annual Meeting & Exhibition
ISMRM (Honolulu, United States)
2015/10/03 Fiber direction estimates on diffusion MRI multi-shell protocols -comparison of the performances of DTI, DKI and Richardson-Lucy SD based tractography ESMRMB 2015, 32nd Annual Scientific Meeting
ESMRMB (Edinburgh, United Kingdom)
2015/06/05 Resolving crossing fibers and generalizing biomarkers using the diffusion kurtosis tensor ISMRM 23rd Annual Meeting & Exhibition
ISMRM (Toronto, Canada)

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2020/01/26 - 2021/02/23 Diffusion Microscopic Anisotropy Estimation in the Brain
Supervisor
Biomedical Engineering (Master)
NOVA School of Science and Technology, Portugal
2018/02/01 - 2018/11/27 Implementation of an algorithm for estimating free-water fraction in Diffusion-Weighted Magnetic Resonance Imaging
Co-supervisor
Instituto Superior Técnico Departamento de Física, Portugal

Jury of academic degree

Topic
Role
Candidate name (Type of degree)
Institution / Organization
2020/06/12 Combined brain language connectivity and intraoperativeneurophysiologic techniques in awake craniotomy for eloquent-area brain tumor resection
(Thesis) Arguer
João Carlos Leote Rebocho (PhD)
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2019/02/18 Integration of Multi-shell Diffusion Imaging derived Metrics in Tractography Reconstructions of Clinical Data
(Thesis) Main arguer
Joana Rita Simões Guido (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018/11/12 Identification of brain connectivity disruptions due to thalamic lesions in early development using Diffusion-Weighted MRI
(Thesis) Main arguer
Ana Rita Veiga de Oliveira (Master)
Instituto Superior Técnico Departamento de Física, Portugal

Committee member

Activity description
Role
Institution / Organization
2023/02/01 - 2024/12/31 Official Google Summer of Code (GSoC) administration. Admin of the "Diffusion in Python" sub-organization of the "Python" organization of the Google Summer of Code (GSoC) program which objective is to support new contributors (typically master or PhD students) into open-source software development by financing 3-months projects.
Member
Google Inc, United States
2020/08/15 - 2022/05/15 I was the elected trainee representative for the Diffusion Study Group (DSG) of the prestigious International Society for Magnetic Resonance in Medicine (ISMRM). The DSG has the mission to facilitate the technological development, evaluation, and clinical application of diffusion MRI.
Member
International Society for Magnetic Resonance in Medicine, United States

Interview (newspaper / magazine)

Activity description Newspaper / Forum
2021/07/31 Interviewed for the Portuguese National Newspaper Público Público

Mentoring / Tutoring

Topic Student name
2023/06/01 - 2023/09/30 DIPY: Correlation Tensor Magnetic Resonance Imaging Shilpi Prasad
2023/06/01 - 2023/09/30 Generative Synthetic MRI Data Vara Lakshmi
2022/06/01 - 2022/09/30 Improving GPU-accelerated Monte Carlo simulations in Disimpy Joel Hurtado Moreno
2022/06/01 - 2022/09/30 Implementation of White Matter Substrates in Disimpy Renata Cruz
2013/10/15 - 2015/06/15 Mathematical biology - Natural Sciences Tripos - University of Cambridge, UK 10 Students
Distinctions

Award

2022 Individual Call to Scientific Employment Stimulus (2021.01773.CEECIND)
FCT - Fundação para a Ciência e a Tecnologia, Portugal
2021 Best pre-clinical oral presentation award
1st annual meeting of the ISMRM-IBERIAN chapter , United States
2020 Magna Cum Laude Award for the oral presentation: Measuring the full diffusional intra- and inter-compartmental kurtosis tensors using double diffusion encoding.
International Society for Magnetic Resonance in Medicine, United States
2020 Summa Cum Laude Merit Award for the oral presentation: Correlation Tensor Imaging - resolving non-Gaussian diffusion sources of in vivo tissues.
International Society for Magnetic Resonance in Medicine, United States
2017 Travel grant for a two weeks project at the University of Washington eScience Institute
International Neuroinformatics Coordinating Facility, Sweden
2017 Magna Cum Laude Award for the oral presentation: Interpreting age-related changes based on the mean signal diffusion kurtosis.
International Society for Magnetic Resonance in Medicine, United States
2016 Travel Grant to present a poster at ISMRM Workshop on "Breaking the Barries of Diffusion MRI"
Guarantors Of Brain, United Kingdom
2015 Google Summer of Code 2015 participation award
Google Inc, United States
2013 PhD research grant (SFRH/BD/89114/2012)
FCT - Fundação para a Ciência e a Tecnologia, Portugal
2009 Integration into Research Grant
FCT - Fundação para a Ciência e a Tecnologia, Portugal

Other distinction

2022 Reproducibility Research Honourable mention
International Society for Magnetic Resonance in Medicine, United States
2022 NeuroImage Cover featuring the original article "In vivo Correlation Tensor MRI reveals microscopic kurtosis in the human brain on a clinical 3T scanner"
Elsevier BV, Netherlands
2022 Top 10% most downloaded paper during its first 12 months for the original article “Towards more robust and reproducible Diffusion Kurtosis Imaging” submitted at the Journal “Magnetic Resonance in Medicine"
J B Wiley Co, United States
2020 Top 10% most downloaded paper during its first 12 months for the original article “Microscopic anisotropy misestimation in spherical-mean Single Diffusion Encoding MRI.” submitted at the Journal “Magnetic Resonance in medicine”
J B Wiley Co, United States
2017 25th ISMRM annual meeting Trainee Stipend Award
International Society for Magnetic Resonance in Medicine, United States
2017 1st Place for Best Research Project Presentation at the diffusion study group. Poster presentation: Exploring the potentials and limitations of improved free-water elimination DTI techniques.
International Society for Magnetic Resonance in Medicine, United States
2017 Marie Sklodowska-Curie Actions Seal of Excellence for the Postdoctoral Fellowship proposal titled “NAPALM: Mapping specific aspects of neuroplasticity using advanced MRI sequences and ultra-field MRI”
European Commission Marie Sklodowska-Curie Actions, Belgium
2016 24th ISMRM annual meeting Trainee Stipend Award
International Society for Magnetic Resonance in Medicine, United States
2015 Certificate of Merit for presenting the poster "United Diffusion Kurtosis Imaging (UDKI) Toolbox"
European Society for Magnetic Resonance in Medicine and Biology, Belgium
2011 Erasmus student mobility for placements scholarship
European Commission, Belgium
2009 One of the best 40 first year student (2007/2008) of the Faculty of Science, University of Lisbon
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal