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LESIONBRAIN : Software providing ICextraction, brain tissue clasification and delineation/classification of white matter hyperintense lesions using T1 and flair MR images

Domaine Santé et Bien-être

Technologies Technologies d'imagerie pour la santé
Exploitation numérique des données de santé


Software providing researchers and practitioners with automated quantitative analysis of MRI data. LesionBrain is able to extract lesions and classify them into subcategories in a very accurate way. The volume and category of brain lesions can represent important biomarkers for several neurological diseases (multiple sclerosis, Alzheimer's disease, lupus, etc.).

Innovative solution

lesionBrain is a pipeline to automatically segment white matter lesions from MRI data (T1 + FLAIR). It gets anonymized MRI brain volumes in NIFTI format and produces a pdf report with the volumes of the lesions and their locations. The average processing time of the whole pipeline is around 20 minutes.


  • Clinical trials

  • Companion diagnostics

  • Clinical routine


  • No need of learning complex software packages

  • No need having expensive computational infrastructures in your local site

  • Faster and more accurate than other solutions

  • LesionBrain works in a fully automatic manner and is able to provide brain structure volumes without any human interaction

  • Two reports (CSV and PDF) providing all the volumetry values calculated from the segmentations as well as asymmetry indexes


  • LesionBrain already processed more than 18000 MRI through volBrain platform.

How it works

White matter lesions were manually outlined by an expert radiologist using multimodal MRI data (T1w + FLAIR) to create a library of 43 cases. After the segmentation process, lesions are classified based on their location as periventricular, deep white, juxtacortical and infratentorial.



Once the process is finished, you will be notified by e-mail so you will be able to download a package including some image files and two reports (CSV and PDF) offering all the volumes estimated from the segmentations. The PDF includes patient information, lesion classes, volumes and their locations in MNI space. It also includes several snapshots from the different labeling steps as a quality control.



Developed by Pierrick COUPÉ (LaBRI - université de Bordeaux, CNRS, Bordeaux INP) & Jose Vicente MANJON HERRERA (Universitat Politècnica de València)

Propriété intellectuelle

Software registered with the Program Protection Agency APP



License to companies providing :

  • Global healthcare solutions
  • Diagnostic medical imaging solutions
  • Medical imaging equipment






Associated innovations

  • VolBrain A software to analyze MRI brain data. It provides a report including volume information on brain structures.
  • CERES : A software to automatically analyze the cerebellum in brain MRI to provide a report including volume information on different aspects of the cerebellum
  • pBrain : A software providing Parkinson’s disease related deep nucleus segmentation (Substantia Nigra locus niger), Red Nucleus and Subthalamic nucleus) using T2w MR images.
  • HIPS : A software providing hippocampus subfield segmentation based on two different delineation protocols using both monomodal (T1w) and multimodal (T1w and T2w) MR images.
  • AssemblyNet : A software providing segmentation of the intracranial cavity, brain tissues (WM, subcortical GM, cortical GM, CSF), cortical lobes, cortical and subcortical structures using a T1w MR image.



LesionBrain is available on :

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