Software at Parietal

MedINRIA

The MedINRIA software (initiated by Pierre Fillard) is a potential common platform to transfer towards clinics the methodological advances made at INRIA.
Since the recruitment of Pierre Fillard at Parietal, efforts are deployed to finalize the next generation of MedINRIA. With the help of Olivier Clatz and Julien Wintz (both at Asclepios), and with the support of INRIA (with the ADT MedINRIA), we expect to release a beta version early next year. Technological transfer will follow, starting with the advances initially implemented in the former version of MedINRIA (image registration and diffusion MRI processing), completed by new progress in function MRI developed by Parietal.
 

NiPy

 Nipy is a development framework in python for the neuroimaging community (publicly available at http://nipy.org), developed mainly at Berkeley, Stanford, MIT and Neurospin. It is open to any contributors and aims at developing code and tools sharing.

Some parts of the library are completely developed by Parietal and LNAO (CEA, DSV, Neurospin). It  is devoted to algorithmic solutions for various issues in neuroimaging data analysis.  All the nipy project is freely available, under BSD licence.

The last coding sprint took place at Berkeley this year (March 21st-29th 2009).

The first release is expected in December 2009.

Mayavi

Mayavi is the most used scientific 3D visualization python software. It has been developed by Prabhu Ramachandran (IIT Bombay) and Gaël Varoquaux (Parietal, INRIA Saclay). Mayavi can be used as a visualization tool, through interactive command line or as a library. It is distributed under Linux through Ubuntu, Debian, Fedora and Mandriva, as well as in PythonXY and EPD Python scientific distributions. Mayavi is used by several software platforms, such as PDE solvers (fipy, sfepy), molecule visualization tools (pyrx.scripps.edu) and brain connectivity analysis tools (connectomeViewer).

Scikit-learn

scikit learn is a python scikit  for machine learning. It is an open source (BSD-licensed) library that exposes many standard algorithms for supervised and unsupervised classification. It is shared by the python scientific community. The scikit is now contributed by Parietal, with the full-time involvement of Fabian Pedregosa.

fMRI toolbox in Brainvisa

Parietal is involved in the development of a functional neuroimaging analysis toolbox in Brainvisa: this project includes the implementation of standard toolkit for the analysis of fMRI data, which is an important building block of Neurospin software platform, but it is an interface for the diffusion of the methods developed in our team, in particular those developed in nipy.
It benefits from the general infrastructure of Brainvisa, that has been set since 2001 by the LNAO laboratory (CEA, DSV, Neurospin) and several other teams from IFR 49.

OpenMEEG

Parietal is involved in the development of OpenMEEG via Alexandre Gramfort who is a core developer of this project. OpenMEEG is a C++ project that provides tools for solving forward problems for Magneto- and Electro-encephalography (MEG and EEG).

OpenMEEG is hosted on the INRIA GForge.