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pBRAIN : Software providing parkinson’s disease related deep nucleus segmentation using T2w MR images

Domaine Santé et Bien-être

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


pBrain automatically analyzes and provides quantitative analyses of Parkinson related structures (Substantia Nigra (locus niger), Red Nucleus and Subthalamic nucleus).It can help to evaluate therapy and to guide neurosurgery.

Innovative solution

pBrain is a pipeline for automatic segmentation of Parkinson related structures (substantia nigra, red nucleus and subthalamic nucleus) from monomodal (T2) at high or standard resolution. It gets an anonymized MRI brain volume in NIFTI format and produces a pdf report with the volumes of different structures. The average processing time of the whole pipeline is around 10 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

  • pBrain 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

How it works

pBrain offers a novel pipeline to segment three deep brain structures related to Parkinson's disease (substantia nigra, subthalamic nucleus and red nucleus). The proposed method is based on the multi-atlas label fusion technology that works on standard and high-resolution T2-weighted images. The proposed method also includes as post-processing a new neural network-based error correction step to minimize systematic segmentation errors. To create pBrain example library, 15 high resolution (0.5 mm) T2 images were manually annotated by an expert in brain anatomy. This resulted in 6 labels for substantia nigra, red nucleus and subthalamic nucleus bilaterally (3 for each hemisphere).



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 (CSV and PDF) reports gathering all the volumetry values calculated from the segmentations. As you can see in the figure below the PDF includes patient information, subfield volumes and their asymmetries in MNI



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
  • HIPS:A software providing hippocampus subfield segmentation based on two different delineation protocols using both monomodal (T1w) and multimodal (T1w and T2w) MR images.
  • LesionBrain : A software providing IC extraction, brain tissue classification and delineation/ classification of white matter hyperintense lesions using T1w and FLAIR 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.



pBrain is available on :

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