SOFTWARE

Electroencephalography (EEG)

Cartool

Cartool is the EEG analysis software developped at the Functional Brain Mapping Lab (FBMLab), by members of the CIBM Clinical and Translational Neuroimaging (HUG-UNIGE) section, in Geneva, Switzerland. This project was initiated in 1996, and is still actively developped up to these days. It has been entirely programmed by Denis Brunet in C++, and doesn’t rely on any other dependency to run.

STEN

STEN (Statistical Toolbox for Electrical Neuroimaging) is an open source software toolbox based on Python and R that can be used to compute statistics on several measures of electro- and magnetoencephalographic (EEG and MEG) signals. 

Magnetic Resonance Imaging (MRI)

BrainVoyager

BrainVoyager contains everything you need for the advanced analysis and visualization of structural and functional magnetic resonance imaging (MRI) data and for EEG / MEG distributed source imaging. The powerful C++ software runs natively on all major computer platforms, including Windows, Linux and macOS, and provides an integrated Python interpreter.

By using the MRI 7T machine, you have access to the BrainVoyager software.

Mango

Mango is a versatile DICOM viewer for medical research images. It provides analysis tools and a user interface to navigate image volumes.

Mango is used at the CIBM CHUV for the MRI 3T machine.

ParaVision

The ParaVision® software package has been designed for users of Bruker’s BioSpec® , PharmaScan® , ICONTM and micro imaging product lines to perform MRI/MRS data acquisition and reconstruction. In addition, the ParaVision modules can be used to analyze, visualize and manage the data generated on Bruker MRI/MRS systems. The software is optimized for pre-clinical investigations, including in vivo investigations on small animals, and for other biomedical and pharmaceutical research based on analytical and imaging magnetic resonance technologies. In addition to life science applications a broad range of investigations in the domain of material science is supported by ParaVision MRI/MRS data measurement methods and data processing tools

LCModel

The LCModel package is for the automatic quantitation of in vivo proton MR spectra [1]. LCMgui is a graphical user interface for running LCModel with more convenience and less knowledge of this manual. LCMgui is provided without charge for use with LCModel only.

Signal Processing (SP)

GlobalBioIm Library

GlobalBioIm Library is a unifying Matlab library for imaging inverse problem developped by members of the CIBM Mathematical Imaging EPFL section.

When being confronted with a new inverse problem, the common experience is that one has to reimplement (if not reinvent) the wheel (=forward model + optimization algorithm), which is very time consuming and also acts as a deterrent for engaging in new developments. This Matlab library GlobalBioIm aims at simplifying this process by decomposing the workflow onto smaller modules, including many reusable ones since several aspects such as regularization and the injection of prior knowledge are rather generic. It also capitalizes on the strong commonalities between the various image formation models that can be exploited to obtain fast, streamlined implementations.

MIALSRTK

The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ image processing tools necessary to perform motion-robust super-resolution fetal MRI reconstruction. This toolkit, supported by the Swiss National Science Foundation (grant SNSF-141283), includes all algorithms and methods for brain extraction, intensity standardization, motion estimation and super-resolution developed during my PhD. It uses the CMake build system and depends on the open-source image processing Insight ToolKit (ITK) library, the command line parser TCLAP library and OpenMP for multi-threading.

DIPY

DIPY is an imaging library in Python. It contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion, and structural imaging.