Research contracts

Last modified on : January 2015

Large Brain Nets – Associate Team: January 2016 to December 2019

Principal Investigators: Demian Wassermann (ATHENA, Inria EPI) Vinod Menon (Stanford Medical School, USA)

The major goal of this project is to develop and validate sophisticated computational tools for identifying functional nodes at the whole-brain level and measuring structural and functional connectivity between them, using state-of-the-art human brain MR imaging techniques and open-source datasets such as Human Connectome Project data. Our proposed methods will reveal in unprecedented detail the structural and functional connectivity of the human brain. Furthermore, our innovative computational approach to brain connectomics will help create the building blocks for shaping the next generation of research on brain function and psychopathology.

ANR MOSIFAH – Duration: October 2013 to September 2017

Participants: Rachid Deriche, Maureen Clerc, Théodore Papadopoulo, Gonzalo Sanguinetti.
This ANR Numerical Models 2013 project is about multimodal and multiscale modelling and simulation of
the fiber architecture of the human heart. It started on October 2013 and involves three partners : Creatis Team,
INSA, Lyon (I. Magnin, Y. Zhu); TIMC-IMAG, CNRS, Grenoble (Y. Uson) and the ATHENA project team.
It consists in modelling and simulating the ex vivo and in vivo 3D fiber architectures at various scales using
multiphysical data from different imaging modalities working at different spatial resolutions. To this end, the
myocardium of the human heart will be imaged using respectively Polarized Light Imaging (PLI) and dMRI.
Appropriate diffusion models will be explored including second and fourth order DTI models as well as
HARDI models such as the single shell Q-Ball Imaging (QBI). These various types of images will be
processed within the right Riemannian mathematical framework to provide tensor as well as Ensemble Average
Propagator (EAP) and Orientation Distribution Function (ODF) fields. Virtual cardiac fiber structure (VCFS)
will then be modelled using myocardial fiber information derived from each of these imaging modalities.
Finally, diffusion behavior of water molecules in these VCFSs will be simulated by means of quantum spin
theory, which allows computing ex vivo and in vivo virtual diffusion magnetic resonance (MR) images at
various scales ranging from a few microns to a few millimeters. From the obtained virtual diffusion MR
images, multiscale and probabilistic atlas describing the 3D fiber architecture of the heart ex vivo and in vivo
will be constructed. Meanwhile, the simulation involving a large number of water molecules, grid computing
will be used to cope with huge computation resource requirement.
We expect to construct a complete database containing a very wide range of simulated (noise and artifact-free)
diffusion images that can be used as benchmarks or ground-truth for evaluating or validating diffusion image
processing algorithms and create new virtual fiber models allowing mimicking and better understanding the
heart muscle structures. Ultimately, the proposed research can open a completely novel way to approach the
whole field of heart diseases including the fundamental understanding of heart physiology and pathology, and
new diagnosis, monitoring and treatment of patients.

ANR VIBRATIONS – Duration: February 2014 to February 2018

Participants: Théodore Papadopoulo, Maureen Clerc, Rachid Deriche, Demian Wassermann.
This Translational ANR project has just been been accepted.
Computational modeling, under the form of a “virtual brain” is a powerful tool to investigate the impact of
different configurations of the sources on the measures, in a well-controlled environment.
The VIBRATIONS project proposes to simulate in a biologically realistic way MEG and EEG fields produced
by different configurations of brain sources, which will differ in terms of spatial and dynamic characteristics.
The research hypothesis is that computational and biophysical models can bring crucial information to
clinically interpret the signals measured by MEG and EEG. In particular, they can help to efficiently address
some complementary questions faced by epileptologists when analyzing electrophysiological data.
The project follows a three-fold strategy:

  • construct virtual brain models with both dynamic aspects (reproducing both hyperexcitability and hypersynchronisation alterations observed in the epileptic brain) and a realistic geometry based on
    actual tractography measures performed in patients
  • explore the parameter space though large-scale simulations of source configurations, using parallel computing implemented on a computer cluster.
  • confront the results of these simulations to simultaneous recordings of EEG, MEG and intracerebral
    EEG (stereotactic EEG, SEEG). The models will be tuned on SEEG signals, and tested versus the surface signals in order to validate the ability of the models to represent real MEG and EEG signals.

The project constitutes a translational effort from theoretical neuroscience and mathematics towards clinical
investigation. A first output of the project will be a database of simulations, which will permit in a given
situation to assess the number of configurations that could have given rise to the observed signals in EEG,
MEG and SEEG. A second – and major – output of the project will be to give the clinician access to a software
platform which will allow for testing possible configurations of hyperexcitable regions in a user-friendly way.
Moreover, representative examples will be made available to the community through a website, which will
permit its use in future studies aimed at confronting the results of different signal processing methods on the
same ‘ground truth’ data.

ADT BOLIS – Duration: December 2014 to December 2016

Participants: Théodore Papadopoulo, Juliette Leblond [APICS], Jean-Paul Marmorat [APICS].
ADT BOLIS aims to build a sofware platform dedicated to inverse source localisation, building upon the elements of software found in FindSources3D. The platform will be modular, ergonomic, accessible and interactive. It will offer a detailed visualisation of the processing steps and the results.

ADT OpenVIBE-X – Duration: October 2014 to October 2016

Participants: Théodore Papadopoulo, Maureen Clerc, Nathanaël Foy.
The OpenViBE-X ADT addresses the OpenViBE Brain Computer Interfaces (BCI) platform, in order to:
1. make BCI easier to apprehend by end-users
2. enrich the interaction with multimodal biosignals (eye gaze, heart-rate)
3. implement methods for auto-calibration and online adaptation of the classification
4. provide support, maintenance and dissemination for this software.
The OpenViBE platform is a central element to BCI research at Inria, and in the international community.

CIFRE PhD contract with Neurelec – Duration: December 2013 to December 2016

Participants: Maureen Clerc, Kai Dang, Théodore Papadopoulo, Jonathan Laudanski [Neurelec].
Title: Modeling and characterizing electrical conductivity for the placement of cochlear implants.
Neurostimulation consists in applying an electrical current close to a nerve to trigger its activation. This is
the principle of cochlear implants, which aim to stimulate the auditory nerve via an electrode coil inserted in
the cochlea. The interplay between the stimulating electrodes and the bioelectrical medium is modeled by a
partial differential equation whose main parameters are the electrical conductivity and geometry of the tissues.
This equation also links active sources and electric potential measurements by electroencephalography. The
objective of Kai Dang’s PhD thesis is to propose models for efficiently representing tissues and their electrical
conductivity within the auditory system (bone, cochlea, ganglia, auditory cortex). This will make it possible
to optimize the stimulating current, thanks to a better knowledge of the current diffusion due to the anatomical
conformation of the cochlea.

PACA PhD contract with Olea Medical – Duration: December 2013 to November 2016

Participants: Marco Pizzolato, Rachid Deriche.
Title: Diffusion & Perfusion MRI : From bench to bedside
The objectives of Marco Pizzolato’s PhD thesis are to develop innovative techniques in diffusion and perfusion
MRI in close collaboration with OLEA MEDICAL. A certain number of important issues related to dMRI and
pMRI signal processing and modeling have been identified by ATHENA and OLEA MEDICAL. These technical
issues will be tackled within the framework of this PhD thesis fully granted by the Region PACA and by OLEA

BESA GmbH – Duration: October 2014 to September 2017

Participants: Maureen Clerc, Théodore Papadopoulo, Juliette Leblond [APICS], Christos Papageorgakis.
We are collaborating with the BESA company (Brain Electromagnetic Source Analysis) on modeling head
tissue conductivity, and on forward and inverse problems of source localization. The PhD thesis of C.
Papageorgakis, 50% funded by BESA, started in October 2014.

ARSLA with Nice University Hospital – September 2013 to August 2015

Participants: Maureen Clerc, Théodore Papadopoulo, Loïc Mahé, Asya Metelkina, Violaine Guy [Nice
University Hospital], Claude Desnuelle [Nice University Hospital].
We are partners of Nice University Hospital in a project funded by “Association pour la Recherche sur la
Sclérose Latérale Amyotrophique” (ARSLA), thanks to which we are conducting a clinical feasibility study
on a Brain Computer Interface system called the P300 speller (see section New Results on Brain Computer


  • Brain Connectivities – Associate Team – Duration: January 2012 – December 2014
  • ANR NucleiPark – AAP MNP 2009 and France-Parkinson Association – Duration: September 2009 to December 2013
  • ANR Vimagine – AAP Blanc – Duration: September 2009 to June 2013
  • ANR CO-ADAPT – Duration: September 2009 to April 2014
  • ANR MULTIMODEL – Duration: December 2010 to May 2014
  • ADT Immersive BCI – Duration: December 2009 to December 2011
  • ADT MedINRIA-NT – December 2010 to December 2014

Back to top