Section: Partnerships and Cooperations

National Initiatives


BrainPedia project

Participants : Bertrand Thirion [Correspondant] , Gaël Varoquaux, Yannick Schwartz, Virgile Fritsch.

BrainPedia is an ANR JCJC (2011-2015) which addresses the following question: Neuroimaging produces huge amounts of complex data that are used to better understand the relations between brain structure and function. While the acquisition and analysis of this data is getting standardized in some aspects, the neuroimaging community is still largely missing appropriate tools to store and organize the knowledge related to the data. Taking advantage of common coordinate systems to represent the results of group studies, coordinate-based meta-analysis approaches associated with repositories of neuroimaging publications provide a crude solution to this problem, that does not yield reliable outputs and looses most of the data-related information. In this project, we propose to tackle the problem in a statistically rigorous framework, thus providing usable information to drive neuroscientific knowledge and questions.

IRMgroup project

Participants : Bertrand Thirion [Correspondant] , Alexandre Gramfort, Michael Eickenberg.

This is a joint project with Polytechnique/CMAP http://www.cmap.polytechnique.fr/ : Stéphanie Allassonnière and Stéphane Mallat (2010-2014).

Much of the visual cortex is organized into visual field maps, which means that nearby neurons have receptive fields at nearby locations in the image. The introduction of functional magnetic resonance imaging (fMRI) has made it possible to identify visual field maps in human cortex, the most important one being the medial occipital cortex (V1,V2,V3). It is also possible to relate directly the activity of simple cells to an fMRI activation pattern and Parietal developed some of the most effective methods. However, the simple cell model is not sufficient to account for high-level information on visual scenes, which requires the introduction of specific semantic features. While the brain regions related to semantic information processing are now well understood, little is known on the flow of visual information processing between the primary visual cortex and the specialized regions in the infero-temporal cortex. A central issue is to better understand the behavior of intermediate cortex layers.

Our proposition is to use our mathematical approach to formulate explicitly some generative model of information processing, such as those that characterize complex cells in the visual cortex, and then to identify the brain substrate of the corresponding processing units from fMRI data. While fMRI resolution is still too coarse for a very detailed mapping of detailed cortical functional organization, we conjecture that some of the functional mechanisms that characterize biological vision processes can be captured through fMRI; in parallel we will push the fMRI resolution to increase our chance to obtain a detailed mapping of visual cortical regions.

Niconnect project

Participants : Bertrand Thirion, Gaël Varoquaux [Correspondant] , Alexandre Abraham.

  • Context: The NiConnect project (2012-2016) arises from an increasing need of medical imaging tools to diagnose efficiently brain pathologies, such as neuro-degenerative and psychiatric diseases or lesions related to stroke. Brain imaging provides a non-invasive and widespread probe of various features of brain organization, that are then used to make an accurate diagnosis, assess brain rehabilitation, or make a prognostic on the chance of recovery of a patient. Among different measures extracted from brain imaging, functional connectivity is particularly attractive, as it readily probes the integrity of brain networks, considered as providing the most complete view on brain functional organization.

  • Challenges: To turn methods research into popular tool widely usable by non specialists, the NiConnect project puts specific emphasis on producing high-quality open-source software. NiConnect addresses the many data analysis tasks that extract relevant information from resting-state fMRI datasets. Specifically, the scientific difficulties are i) conducting proper validation of the models and tools, and ii) providing statistically controlled information to neuroscientists or medical doctors. More importantly, these procedures should be robust enough to perform analysis on limited quality data, as acquiring data on diseased populations is challenging and artifacts can hardly be controlled in clinical settings.

  • Outcome of the project: In the scope of computer science and statistics, NiConnect pushes forward algorithms and statistical models for brain functional connectivity. In particular, we are investigating structured and multi-task graphical models to learn high-dimensional multi-subject brain connectivity models, as well as spatially-informed sparse decompositions for segmenting structures from brain imaging. With regards to neuroimaging methods development, NiConnect provides systematic comparisons and evaluations of connectivity biomarkers and a software library embedding best-performing state-of-the-art approaches. Finally, with regards to medical applications, the NiConnect project also plays a support role in on going medical studies and clinical trials on neurodegenerative diseases.

  • Consortium

    • Parietal Inria research team: applied mathematics and computer science to model the brain from MRI

    • LIF INSERM research team: medical image data analysis and modeling for clinical applications

    • CATI center: medical image processing center for large scale brain imaging studies

    • Henri-Mondor hospital neurosurgery and neuroradiology: clinical teams conducting research on treatments for neurodegenerative diseases, in particular Huntington and Parkinson diseases

    • Logilab: consulting in scientific computing