- A quick presentation of brainVISA's authors...
Ile de France's imaging facilities : http://www.ifr49.org/
BrainVISA results from collaborative work of methodologists of IFR 49. The goal was to provide to potential users of the methodological results a unifying interface as user friendly as possible. This interface was also supposed to simplify exchange of softwares between the different laboratories of the Institute. This project has been initiated thanks to financial support from the french Research ministry (ACI télémédecine). The first prototype of BrainVISA has been developed by Yann Cointepas during years 2000/2001.
Since then, the core of brainVISA has been developed in SHFJ and now in Neurospin by the team of JF Mangin, LNAO (Y. Cointepas, D. Rivière, D. Papadopoulos-Orfanos) and engineers of the IFR 49 (Y. Cointepas, I. Denghien, D. Geffroy). Several toolboxes have already been developped for BrainVISA (https://brainvisa.info/toolboxes.html):
- The toolbox dedicated to T1 MRI and cortical sulci has been developed in SHFJ and now in Neurospin by the team of JF Mangin (D. Rivière, A. Cachia, E. Duchesnay) in collaboration with the Functional Neurosurgery Service of La Timone, Marseille (J. Régis), INSERM unit ERM 205, Orsay (A. Cachia, E. Duchesnay, M. Zilbovicius JL Martinot), and ESIL, Marseille (O. Coulon, C. Clouchoux).
- The toolbox dedicated to MR diffusion imaging has been developed by the team of JF Mangin (Y. Cointepas) in close collaboration with the team of D. LeBihan (C. Poupon)
- The toolbox dedicated to fMRI is developed at Neurospin/LNAO, INRIA Saclay/Parietal and partners (B. Thririon, P. Ciuciu, A Roche)
- Cortical Surface toolbox: analysis of the cortical surface geometry and of functional data projected on this surface (Operto, 2008)
- BrainRat toolbox: automated processing of histological and autoradiographic sections (A. Dubois, 2008).
- The toolbox dedicated to MEG/EEG is developed by the MEG center in La Pitié-Salpêtrière (D. Schwartz), the CNRS unit LENA in La Pitié-Salpêtrière (S. Baillet, L. Garnero), and the INSERM unit 678 (M. Pelegrini, H. Benali, J. Daunizeau, J. Mattout)
- The stereotaxy toolbox is developed in the CNRS unit LENA in La Pitié-Salpêtrière (E. Bardinet, M. Bhattacharjee)
For the time being, the only references to the BrainVISA framework are related to conference articles or abstracts:
- BrainVISA: a complete software platform for neuroimaging.
D. Geffroy, D. Rivière, I. Denghien, N. Souedet, S. Laguitton, and Y. Cointepas.
In Python in Neuroscience workshop, Paris, Aug. 2011.- The BrainVISA project: a shared software development infrastructure for biomedical imaging research.
Y. Cointepas, D. Geffroy, N. Souedet, I. Denghien, and D. Rivière.
In Proc. 16th HBM, 2010.- BrainVISA: an extensible software environment for sharing multimodal neuroimaging data and processing tools.
D. Rivière, D. Geffroy, I. Denghien, N. Souedet, and Y. Cointepas.
In Proc. 15th HBM, 2009.- BrainVISA: Software platform for visualization and analysis of multi-modality brain data.
Y. Cointepas, J.-F. Mangin, L. Garnero, J.-B. Poline and H. Benali.
In Proc. 7th HBM, Brighton, United Kingdom, pages S98, 2001Other references deal with BrainVISA toolboxes:
- Diffusion & Tracking toolbox:
A freely available Anatomist/BrainVISA package for analysis of diffusion MR images.
Y. Cointepas, C. Poupon, R. Maroy, D. Rivière, D. Le Bihan, and J.-F. Mangin.
In Proc. 9th HBM CD-Rom Neuroimage vol 19 (2), New York,June19--22 2003- T1 MRI toolbox:
A freely available Anatomist/BrainVISA package for structural morphometry of the cortical sulci.
D. Rivière, J. Régis, Y. Cointepas, D. Papadopoulos-Orfanos, A. Cachia, and J.-F. Mangin.
In Proc. 9th HBM, Neuroimage 19(2), pages 934, 2003- BrainRAT toolbox:
BrainRAT: Brain Reconstruction and Analysis Toolbox. A freely available toolbox for the 3D reconstruction of anatomo-functional brain sections in rodents.
A. Dubois, J. Dauguet, N. Souedet, A.-S. Hérard, D. Rivière, Y. Cointepas, G. Bonvento, P. Hantraye, V. Frouin, T. Delzescaux.
In Proc. 38th annual meeting of the Society for Neuroscience, Washington, USA, 2008.- fMRI toolbox:
A Comprehensive fMRI Processing Toolbox for BrainVISA.
L. Favre, A.-L. Fouque, T. Vincent, A. Tucholka, M. Keller, G. Operto, B. Thyreau, C. Clouchoux, L. Risser, A. Moreno, D. Geffroy, Y. Cointepas, O. Coulon, P. Ciuciu, B. Thirion, and A. Roche.
In Hum. Brain Mapp., 2009.- MEEG toolbox:
A MEG/EEG analysis toolbox for BrainVISA
D. P. Schwartz, K. N'Diaye, A. Bellio, J. Mattout, M. Pélégrini, Y. Cointepas, D. Rivière, and A. Ducorps.
In Hum. Brain Mapp., 2004A list of other publications related to BrainVISA can be found here on BrainVISA website.
The teams implied in the initial project:
- Line Garnero's team was in charge of issues related to the inverse problem of MEG and EEG;
Neurosciences Cognitives et Imagerie Cérébrale
UPR 640-CNRS LENA
47 boulevard de l'Hôpital
75651 Paris Cedex 13
France
WWW: http://web.ccr.jussieu.fr/cnrs-upr640-lena
- Habib Benali's team was in charge of image processing issues related to la Pitié-Salpêtrière site;
INSERM U494
CHU Pitié-Salpêtrière
91 boulevard de l'Hôpital
75634 Pa ris Cedex 13
France
WWW: http://www.imed.jussieu.fr
- Jean-Baptiste Poline's team was in charge of the issues related to functional image analysis, and has brought the experience of SPM software design (http://www.fil.ion.ucl.ac.uk/spm);
UNAF
Service Hospitalier Frédéric Joliot
Département de Recherche Medicale, CEA
4 place du Gal Leclerc
91401 Orsay Cedex
France
WWW: http://www-dsv.cea.fr/content/cea/d_dep/d_drm/d_shfj/d_unaf/
- Jean-François Mangin's team was in charge of the issues related to anatomical image analysis, and has brought Anatomist visualization software;
UNAF
Service Hospitalier Frédéric Joliot
Département de Recherche Medicale, CEA
4 place du général Leclerc
91401 Orsay Cedex
France
WWW: http://www-dsv.cea.fr/content/cea/d_dep/d_drm/d_shfj/d_unaf/
- Finally, clinicians of la Salpêtrière Hospital have brought their knowledge of the actual clinical world...
Stéphane Lehéricy has brought the point of view of a radiologist with a rich experience of functional MRI: research protocoles performed with a high field magnet in SHFJ and simpler protocoles routinely performed in a clinical context;
Service de Neuroradiologie Fischgold
Bâtiment Babinski
Hôpital de la Salpêtrière
47 Bd de l'Hôpital
75013 Paris cedex 13
France
Hugues Duffau has brought the point of view of a neurosurgeon willing to add brain mapping experiments into surgical planning. One of the goal was the use of per-operative stimulations in a guided surgery framework (Surgiscope) to assess the reliability of functional imaging results.
Service de Neurochirurgie 1
Hôpital de la Salpêtrière
47-83 boulevard de l'hôpital
75013 Paris
France