LesionBrain: An Online Tool for White Matter Lesion Segmentation

  • Pierrick CoupéEmail author
  • Thomas Tourdias
  • Pierre Linck
  • José E. Romero
  • José V. Manjón
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11075)


In this paper, we present a new tool for white matter lesion segmentation called lesionBrain. Our method is based on a 3-stage strategy including multimodal patch-based segmentation, patch-based regularization of probability map and patch-based error correction using an ensemble of shallow neural networks. Its robustness and accuracy have been evaluated on the MSSEG challenge 2016 datasets. During our validation, the performance obtained by lesionBrain was competitive compared to recent deep learning methods. Moreover, lesionBrain proposes automatic lesion categorization according to location. Finally, complementary information on gray matter atrophy is included in the generated report. LesionBrain follows a software as a service model in full open access.


White matter lesion segmentation Patch-based segmentation Service as a software 



This work benefited from the support of the project DeepVolBrain of the French National Research Agency (ANR). This study was achieved within the context of the Laboratory of Excellence TRAIL ANR-10-LABX-57 for the BigDataBrain project. Moreover, we thank the Investments for the future Program IdEx Bordeaux (ANR-10-IDEX- 03- 02, HL-MRI Project), Cluster of excellence CPU and the CNRS. This study has been also supported by the DPI2017-87743-R grant from the Spanish Ministerio de Economia, Industria y Competitividad.


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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Pierrick Coupé
    • 1
    • 2
    Email author
  • Thomas Tourdias
    • 3
    • 4
    • 5
  • Pierre Linck
    • 4
    • 5
  • José E. Romero
    • 6
  • José V. Manjón
    • 6
  1. 1.CNRS, LaBRI, UMR 5800, PICTURATalenceFrance
  2. 2.Univ. Bordeaux, LaBRI, UMR 5800, PICTURATalenceFrance
  3. 3.Neurocentre Magendie, INSERM U1215BordeauxFrance
  4. 4.Univ. BordeauxBordeauxFrance
  5. 5.CHU de Bordeaux, Services de Neurologie et NeuroradiologieBordeauxFrance
  6. 6.Instituto de Aplicaciones de las Tecnologías de la Información y de las Comunicaciones Avanzadas (ITACA)Universitat Politècnica de ValènciaValenciaSpain

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