Welcome to my academic webpage. Here you can find all the information about my research career.

Short bio

 I finished my degree in Computer Science (2009) and the Msc in Automation, Computation and Systems (2010) at the University of Girona. A few years later, I finished my PhD student in the VICOROB Group at the University of Girona under the supervision of Dr. Xavier Lladó and Dr. Arnau Oliver.
After a productive post-doc oportunity at the Research Institute of the Hospital Vall d'Hebron (VHIR) under the supervision of Dr. Àlex Rovira, I went back to NIC-VICOROB to continue my research in brain image analysis. Currently, I'm continuing my medical imaging career at the Brain and Mind Centre of the University of Sydney.
Therefore, I am developing new tools and working with all my teammates to integrate all our previous research in new and exciting ways while continuing with our recent contributions.
My main goal is the analysis and implementation of techniques to automatically analyse and process brain MRI (including multiple sclerosis, Alzheimer's disease and tumor patients), although I am greatly interested on other computer vision topics.

Research interests: computer vision, image processing, magnetic resonance imaging, lesion detection and segmentation, deep learning.

Publications

Journals

  1. [NINF 2021] J. Bernal, S. Valverde, K. Kushibar, M. Cabezas, A. Oliver, X. Lladó & The Alzheimer’s Disease Neuroimaging Initiative "Generating Longitudinal Atrophy Evaluation Datasets on Brain Magnetic Resonance Images Using Convolutional Neural Networks and Segmentation Priors". Neuroinformatics, 2021. PDF
  2. [S 2021] S. Kentsch, M. Cabezas, L. Tomhave, J. Groß, B. Burkhard, M.L. Lopez Caceres, K. Waki and Y. Diez "Analysis of UAV-Acquired Wetland Orthomosaics Using GIS, Computer Vision, Computational Topology and Deep Learning". Sensors, Volume 21(2), 471, 2021. PDF
  3. [RS 2020] M. Cabezas, S. Kentsch, L. Tomhave, J. Gross, M.L. Lopez Caceres and Y. Diez "Detection of Invasive Species in Wetlands: Practical DL with Heavily Imbalanced Data". Remote Sensing, Volume 12(20), 3431, 2020. PDF
  4. [NI-CL 2020] M. Salem, S. Valverde, M. Cabezas, D. Pareto, A. Oliver, J. Salvi, À. Rovira, and X. Lladó. "A fully convolutional neural network for new T2-w lesion detection in multiple sclerosis". NeuroImage: Clinical, Volume 25, 102149, 2020. [JCR N IF 3.943, Q1(3/14)] PDF
  5. [NI-CL 2020] M. Rakic, M. Cabezas, K. Kushibar, A. Oliver, X. Lladó. "Improving the Detection of Autism Spectrum Disorder by Combining Structural and Functional MRI Information". NeuroImage: Clinical, 25, 102181, 2020. [JCR N IF 3.943, Q1(3/14)] PDF
  6. [SREP 2019] K. Kushibar, S. Valverde, S. González-Villà, J. Bernal, M. Cabezas, A. Oliver, and X. Lladó. "Supervised domain adaptation for automatic sub-cortical brain structure segmentation with minimal user interaction". Nature. Scientific Reports 9(6742), 2019. [JCR MS IF 4.011, Q1(15/69)] PDF
  7. [IEEE ACCESS 2019] M. Salem, S. Valverde, M. Cabezas, D. Pareto, A. Oliver, J. Salvi, À. Rovira, and X. Lladó. "Multiple Sclerosis Lesion Synthesis in MRI using an encoder-decoder U-NET". IEEE Access, 7, pp. 25171-25185, 2019. [JCR CSIS IF 3.557, Q1(24/148)] PDF
  8. [NI-CL 2019] S. Valverde, M. Salem, M. Cabezas, D. Pareto, J. C. Vilanova, Ll. Ramió-Torrentà, À. Rovira, and J. Salvi, A. Oliver, X. Lladó. "One-shot domain adaptation in multiple sclerosis lesion segmentation using convolutional neural networks". NeuroImage: Clinical, 21. 2019. [JCR N IF 3.869, Q1(3/14)] PDF
  9. [SREP 2018] O. Commowick, A. Istace, M. Kain, B. Laurent, F. Leray, M. Simon, S. C. Pop, P. Girard, R. Améli, J.-C. Ferré, A. Kerbrat, T. Tourdias, F. Cervenansky, T. Glatard, J. Beaumont, S. Doyle, F. Forbes, J. Knight, A. Khademi, A. Mahbod, C. Wang, R. McKinley, F. Wagner, J. Muschelli, E. Sweeney, E. Roura, X. Lladó, M. M. Santos, W. P. Santos, A. G. Silva-Filho, X. Tomas-Fernandez, H. Urien, I. Bloch, S. Valverde, M. Cabezas, F. J. Vera-Olmos, N. Malpica, C. Guttmann, S. Vukusic, G. Edan, M. Dojat, M. Styner, S. K. Warfield, F. Cotton & C. Barillot "Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure". Nature. Scientific Reports, 8. 2018. [JCR MS IF 4.122, Q1(12/64)] PDF
  10. [MIA 2018] K. Kushibar, S. Valverde, S. González-Villà, J. Bernal, M. Cabezas, A. Oliver, X. Lladó. "Automated sub-cortical brain structure segmentation combining spatial and deep convolutional features". Medical Image Analysis, 48, pp. 177-186, 2018. [JCR CSAI IF 5.356, Q1(6/105)] PDF PDF
  11. [NI-CL 2018] M. Salem, M. Cabezas, S. Valverde, D. Pareto, A. Oliver, J. Salvi, À. Rovira, and X. Lladó. "A supervised framework with intensity subtraction and deformation field features for the detection of new T2-w lesions in multiple sclerosis". NeuroImage: Clinical, 17C, pp. 607-615, 2018. [JCR N IF 3.869, Q1(3/14)] PDF
  12. [NI-Cl 2017] S. González-Villà, S. Valverde, M. Cabezas, D. Pareto, J.C. Vilanova, Ll. Ramió-Torrentà, À. Rovira, A. Oliver, X. LLadó. "Evaluating the effect of multiple sclerosis lesions on automatic brain structure segmentation". NeuroImage: Clinical, 15, pp. 228-238, 2017. [JCR N IF 3.857, Q1(3/14)] PDF
  13. [NI 2017] S. Valverde, M. Cabezas, E. Roura, S. González-Villà, D. Pareto, J.C. Vilanova, Ll. Ramió-Torrentà, À. Rovira, A. Oliver, and X. Lladó. "Improving automated multiple sclerosis lesion segmentation with a cascaded 3D convolutional neural network approach". NeuroImage, 155, pp. 159-168, 2017. [JCR NI IF 5.463, Q1(1/14)] PDF PDF
  14. [AJNR 2016] M. Cabezas, J.F. Corral, A. Oliver, Y. Diez, M. Tintoré, C. Auger, X. Montalban, X. Lladó, D. Pareto, and À. Rovira. "Improved automatic detection of new T2 lesions in multiple sclerosis using deformation fields". American Journal of Neuroradiology, 37(11), pp. 1816-1823, 2016. [JCR RNMMI IF 3.589, Q1(19/125)] PDF
  15. [AJNR 2015] S. Valverde, A. Oliver, Y. Díez, M. Cabezas, J.C. Vilanova, Ll. Ramió-Torrentà, À. Rovira, and X. Lladó. "Evaluating the effects of white matter multiple sclerosis lesions on the volume estimation of six brain tissue segmentation methods". American Journal of Neuroradiology, 36(6), pp. 1109-115, 2015. [JCR RNMMI IF 3.675, Q1(18/122)] PDF
  16. [NRAD 2015] E. Roura, A. Oliver, M. Cabezas, S. Valverde, D. Pareto, J.C. Vilanova, Ll. Ramió-Torrentà, À. Rovira, and X. Lladó. "A toolbox for multiple sclerosis lesion segmentation". Neuroradiology, 57(10), pp. 1031-1043, 2015. [JCR RNMMI IF 2.485, Q2(41/125)] (pdf KB) PDF
  17. [JMRI 2015] S. Valverde, A. Oliver, M. Cabezas, E. Roura, X. Lladó. "Comparison of ten brain tissue segmentation methods using revisited IBSR annotations". Journal of Magnetic Resonance Imaging, 41(1), pp. 93-101. 2015. [JCR RNMMI IF: 2.788 Q1(29/121)] PDF ResearhGate
  18. [JNM 2014] M. Cabezas, A. Oliver, S. Valverde, B. Beltran, J. Freixenet, J.C. Vilanova, Ll. Ramió-Torrentà, À. Rovira, and X. Lladó. "BOOST: a supervised approach for multiple sclerosis lesion segmentation". Journal of Neuroscience Methods, 237, pp. 108-117, 2014. [JCR N IF 1.959, Q3(182/251)] PDF ResearhGate
  19. [CMPB 2014] M. Cabezas, A. Oliver, E. Roura, J. Freixenet; J.C Vilanova, Ll. Ramió-Torrentà, A. Rovira, X. Lladó. "Automatic multiple sclerosis lesion detection in brain MRI by FLAIR thresholding". Computer Methods and Programs in Biomedicine, 115(3), pp. 147-161. 2014. [JCR CSTM IF 1.093, Q2(32/102)] PDF ResearhGate
  20. [NINF 2014] Y. Diez, A. Oliver, M. Cabezas, S. Valverde, R. Martí, J.C. Vilanova, Ll. Ramió-Torrentà, A. Rovira, and X. Lladó. "Intensity based methods for brain MRI longitudinal registration. A study on multiple sclerosis patients". Neuroinformatics, 12(3), pp. 365-379. 2014. [JCR CSTM IF 3.102, Q1(12/102)] PDF ResearhGate
  21. [CMPB 2014] E. Roura, A. Oliver, M. Cabezas, J.C. Vilanova, A. Rovira and Ll. Ramió-Torrentà, X. Lladó. "MARGA: Multispectral adapting region growing algorithm for brain extraction on axial MRI". Computer Methods and Programs in Biomedicine, 113(2), pp. 655-673. 2014. [JCR CSTM IF 1.093, Q2(32/102)] PDF ResearhGate
  22. [INFSCI 2012] X. Lladó, A. Oliver, M. Cabezas, J. Freixenet, J.C. Vilanova, A. Quiles, L. Valls, Ll. Ramió-Torrentà, A. Rovira. "Segmentation of multiple sclerosis lesions in brain MRI: a review of automated approaches". Information Sciences, 186(1), pp. 164-185. 2012. [JCR CSIS IF 3.643, Q1(6/132)] PDF ResearhGate
  23. [CMPB 2011] M. Cabezas, A. Oliver, X. Lladó, J. Freixenet, M. Bach-Cuadra. "A review of atlas-based segmentation for magnetic resonance brain images". Computer Methods and Programs in Biomedicine, 104(3), pp. e158-e177. 2011. [JCR CSTM IF 1.516, Q1(14/99),] PDF

Conferences

  1. [MICCAI-BRATS 2018] M. Cabezas, S. Valverde, S. González-Villà, A. Clèrigues, M. Salem, K. Kushibar, J. Bernal, A. Oliver, J. Salvi and X. Lladó. "Survival prediction using ensemble tumor segmentation and transfer learning ". Multimodal Brain Tumor Segmentation Challenge 2018 (BRATS) in Medical Imaging. MICCAI 2018. Granada, Spain. 16th September 2018. PDF PDF
  2. [MICCAI-MRBRAINS 2018] J. Bernal, M. Salem, K. Kushibar, A. Clérigues, S. Valverde, M. Cabezas, S. Gonzàlez-Villà, J. Salvi, A. Oliver, and X. Lladó. "MR Brain segmentation using an ensemble of multi-path u-shaped convolutional neural networks and tissue segmetnation priors". MR Brain tissue segmentation Challenge in Medical Imaging. MICCAI 2018. Granada, Spain. 16th September 2018. PDF
  3. [MICCAI-ISLES 2018] A. Clérigues, S. Valverde, J. Bernal, K. Kushibar, M. Cabezas, A. Oliver, and X. Lladó. "Ensemble of convolution neural networks for acute stroke anatomy differentiation". Ischiemic Stroke Lesion Segmentation (ISLES) in Medical Imaging. MICCAI 2018. Granada, Spain. 16th September 2018. PDF
  4. [MICCAI-iSeg 2017] J. Bernal, K. Kushibar, S. Valverde, M.Cabezas, S. González-Villà, M. Salem, J. Salvi, A. Oliver, Xavier Lladó. "Six-month infant brain tissue segmentation using three dimensional fully convolutional neural networks and pseudo-labelling". MICCAI Grand Challenge on 6-month infant brain MRI segmentation iSeg-2017. MICCAI 2017. Quebec, Canada. 14 September 2017. PDF
  5. [MICCAI-WMH 2017] S. Valverde, M.Cabezas, J. Bernal, K. Kushibar, S. González-Villà, M. Salem, J. Salvi, A. Oliver, Xavier Lladó. "White matter hyperintensities segmentation using a cascade of three convolutional neural networks". MICCAI Grand Challenge on White Matter Hyperintensties Segmentation. MICCAI 2017. Quebec, Canada. 14 September 2017. PDF
  6. [MS 2017] S. Valverde, M. Cabezas, E. Roura, S. González-Villà, D. Pareto, J.C. Vilanova, Ll. Ramió-Torrentà, A. Rovira, A. Oliver, X. Lladó. "A deep learning approach for multiple sclerosis lesion segmentation". Multiple Sclerosis, Paris. October 2017. PDF
  7. [MS 2017] S. González-Villà, S. Valverde, M. Cabezas, D. Pareto, J.C. Vilanova, Ll. Ramió-Torrentà, A. Rovira, A. Oliver, X. Lladó. "Do multiple sclerosis lesions affect automatic brain structure segmentation?". Multiple Sclerosis, Paris. October 2017. PDF
  8. [MS 2017] M. Salem, M. Cabezas, S. Valverde, D. Pareto, A. Rovira, A. Oliver, J. Salvi, A. Rovira, X. Lladó. "Supervised detection of newly appearing T2-w multiple sclerosis lesions with subtraction and deformation fields features". Multiple Sclerosis, Paris. October 2017. [JCR CN IF:4.840 Q1(27/194)] PDF
  9. [MS 2016] M. Cabezas, D. Pareto, A. Oliver, J.F. Corral, C. Auger, X. Aymerich, J. Sastre-Garriga, M. Tintoré, X. Montalban, X. Lladó, A. Rovira. "Detection of new multiple sclerosis lesions on longitudinal brain MRI". Multiple Sclerosis. 22(S3), pp 215-216. London. September 2016. PDF
  10. [MSSEG 2016] E. Roura, M. Cabezas, S. Valverde, S. González-Villà, J. Salvi, A. Oliver, and X. Lladó. "Unsupervised Multiple Sclerosis Lesion Detection and Segmentation using Rules and Level Sets". Multiple Sclerosis Lesions segmentation (MSSEG) Challenge. MICCAI 2016. Athens, Greece. 21 October 2016. PDF
  11. [MSSEG 2016] S. Valverde, M. Cabezas, E. Roura, S. González-Villà, J. Salvi, A. Oliver, and X. Lladó. "Multiple Sclerosis Lesion Detection and Segmentation using a Convolutional Neural Network of 3D Patches". Multiple Sclerosis Lesions segmentation (MSSEG) Challenge. MICCAI 2016. Athens, Greece. 21 October 2016. PDF
  12. [SPIE 2016] E. Roura, A. Oliver, M. Cabezas, S. Valverde, D. Pareto, J.C. Vilanova, Ll. Ramió-Torrentà, À. Rovira, and X. Lladó. "An SPM12 extension for multiple sclerosis lesion segmentation". SPIE Medical Imaging, San Diego (US), Vol. 9784 97842N-1/N-6 Feb 27- March 3, 2016. PDF
  13. [SERAM 2016] M. Cabezas, A. Oliver, X. Lladó, D. Pareto, and A. Rovira. "Analisis del uso de la imagen de sustraccion para detectar nuevas lesiones de T2 en pacientes de esclerosis multiple". 33 Congreso Nacional de la SERAM 2016, Bilbao, Basque Country, May 19-22, 2016. PDF
  14. [MS 2015] E. Roura, A. Oliver, M. Cabezas, S. Valverde, D. Pareto, J.C. Vilanova, Ll. Ramió-Torrentà, À. Rovira, and X. Lladó. "A toolbox for segmenting multiple sclerosis lesions using T1w and FLAIR images". Multiple Sclerosis. 21(S11), pp 678. Barcelona. October 2015. PDF
  15. [MS 2015] M. Cabezas, A. Oliver, X. Lladó, C. Auger, J. Sastre-Garriga, D. Pareto, X, Montalban, À. Rovira. "A pipeline for detecting new multiple sclerosis lesions on longitudinal brain magnetic resonance imaging". Multiple Sclerosis. 21(S11), pp 179-180.Barcelona. October 2015. PDF
  16. [MS 2015] M. Cabezas, J.F. Corral, A. Oliver, X. Lladó, C. Auger, J. Sastre-Garriga, M. Tintore, D. Pareto, X, Montalban, À. Rovira. "Evaluating the sensitivity of subtraction imaging for the detection of new T2 multiple sclerosis lesions when using visual analysis, semiautomatic and automatic approaches". Multiple Sclerosis. 21(S11), pp 175.Barcelona. October 2015. PDF
  17. [JEMGI 2015] S. Valverde, A.Oliver, J.Freixenet, M.Cabezas, O. Ganiler, Y. Diez, E. Roura, S. González, X.Lladó. "Passat, present i futur en la quantificació automàtica del teixit cerebral en pacients d'esclerosi múltiple". Ponència invitada a la 5 Jornada d'Esclerosis Múltiple de Girona celebrada a Girona, el 10/07/2015. Ponent: S. Valverde.
  18. [JEMGI 2014] A. Oliver, J. Freixenet, M. Cabezas, O. Ganiler, Y. Diez, E. Roura, S. Valverde, X.Lladó. "Neuroimatge en EM: de les noves tecnologies a la capçalera del pacient". Ponència invitada a la I4 Jornada d'Esclerosis Múltiple de Girona celebrada a Pals (Girona), el 4/07/2014. Ponent: A. Oliver.
  19. [IDIBGI 2014] S. Valverde, A. Oliver, J. Freixenet, M.Cabezas, O. Ganiler, Y. Diez, E. Roura, S. Valverde, X.Lladó. "Neuroimatge en Esclerosi Múltiple: Anàlisi Automàtic". Ponència invitada a la Jornada Científica de l'IDIBGI de Girona celebrada a Sant Feliu de Guíxols (Girona), el 11/07/2014. Ponent: S. Valverde. PDF
  20. [MS 2013] E. Roura, A. Oliver, M. Cabezas, J. Freixenet, X. Lladó, J.C. Vilanova, A. Rovira and Ll. Ramió-Torrentà. "Extracting the brain in axial MR images with an adaptive segmentation technique". Multiple Sclerosis. 19(S1), pp 417-418. Copenhagen, Denmark. 2-5 October 2013. PDF
  21. [MS 2013] S.Valverde, A. Oliver, M. Cabezas, Y. Díez, J. Freixenet, X. Lladó, J.C. Vilanova, A. Rovira and Ll. Ramió-Torrentà. "A quantitative study of the effects of White Matter MS Lesions on tissue segmentation methods". Multiple Sclerosis. 19(S1), pp 407-408. Copenhagen, Denmark. 2-5 October 2013. PDF
  22. [IbPRIA2013] M. Cabezas, A. Oliver, J. Freixenet and X. Lladó. "A supervised approach for multiple sclerosis lesion segmentation using context features and an outlier map". Iberian Conference on Pattern Recognition and Image Analysis. LNCS, To appear. Madeira, Portugal, 2013. PDF
  23. [ECTRIMS 2012] M. Cabezas, A. Oliver, X. Lladó, Y. Díez, J. Freixenet, J.C. Vilanova, A. Quiles, G. Laguillo, Ll. Ramió-Torrentà, D. Pareto, and A. Rovira. "A supervised approach to segment multiple sclerosis lesions using context-rich features and a boosting classifier". European Committee for Treatment and Research in Multiple Sclerosis conference. Multiple Sclerosis, 18(4S), pp 157. Lyon, France. October 2012. PDF
  24. [ECTRIMS 2012] Y. Díez, X. Lladó, A. Oliver, R. Martí, E. Roura, M. Cabezas, O. Ganiler, J. Freixenet, J.C. Vilanova, L. Valls, Ll. Ramió-Torrentà, D. Pareto, and A. Rovira. "Registration of serial brain MRI scans from multiple sclerosis patients. Analysis of 3D intensity-based methods". European Committee for Treatment and Research in Multiple Sclerosis conference. Multiple Sclerosis, 18(4S), pp 384-385. Lyon, France. October 2012. PDF
  25. [SPIE 2012] G. Pons, J. Martí, R. Martí, M. Cabezas, A. Di Battista and J.A. Noble. "Lesion Segmentation and Bias Correction in Breast Ultrasound B-mode Images Including Elastography Information". SPIE Conference on Medical Imaging, 8314, pp. 83141E1-1E6. San Diego, California, USA, February 2012. PDF
  26. [ECTRIMS 2011] X. Lladó, O. Ganiler, A. Oliver, M. Cabezas, J. Freixenet, J.C. Vilanova, L. Valls, Ll. Ramió-Torrentà, and A. Rovira. "Computer-assisted strategies to automated quantification of multiple sclerosis lesion evolution on brain magnetic resonance imaging". European Committee for Treatment and Research in Multiple Sclerosis conference. Multiple Sclerosis, 17(10S), pp 161-162. Amsterdam, Holland, 2011 PDF
  27. [ECTRIMS 2011] M. Cabezas, M. Bach-Cuadra, A. Oliver, X. Lladó, J. Freixenet, J.C. Vilanova, L. Valls, Ll. Ramió-Torrentà, E. Huerga, D. Pareto, and A. Rovira. "A pipeline approach with spatial information for segmenting multiple sclerosis lesions on brain magnetic resonance imaging". European Committee for Treatment and Research in Multiple Sclerosis conference. Multiple Sclerosis, 17(10S), pp 381. Amsterdam, Holland, 2011. PDF
  28. [ECTRIMS 2010] X. Lladó, M. Cabezas, O. Ganiler, A. Oliver, J. Freixenet, J.C. Vilanova, A. Quiles, Ll. Ramió-Torrenta, A. Rovira. "Strategies for Automated Segmentation of Multiple Sclerosis Lesions on Brain Magnetic Resonance Imaging". European Committee for Treatment and Research in Multiple Sclerosis conference. Multiple Sclerosis, 16(10), pp S256. Gothenburg, Sweden, 2010. PDF

Theses

  • [PhDThesis 2013] M. Cabezas. "Atlas-based segmentation of multiple sclerosis lesions in magnetic resonance imaging", PhD thesis. July 2013. PDF
  • [MscThesis 2010] M. Cabezas. "Atlas-based segmentation of brain MRI: Application to multiple sclerosis", Master thesis. September 2010. PDF

Visit MS-Seg 2016 challenge page

Contact me

Feel free to email me to provide some feedback, give me suggestions, ask me anything or to just say hello! As you can see, I try to keep my code up to date with my personal github page!

mariano.cabezas@sydney.edu.au