Software

Brain network toolbox

Logo_alto_100 A list of MATLAB routines for characterizing brain network topology though graph theoretical indices can be found at the website of the FreeBorN consortium, which promotes the interaction and visibility of the research teams studying brain connectivity and network theory.

Contacts: fabrizio [dot] devicofallani [at] gmail [dot] com and mario [dot] chavez [at] upmc [dot] fr

Reference: https://sites.google.com/site/fr2eborn/download

 

Clinica

ClinicaClinica is a software platform for multimodal brain image analysis in clinical research studies. It makes it easy to apply advanced analysis tools to large scale clinical studies. For that purpose, it integrates a comprehensive set of processing tools for the main neuroimaging modalities: currently MRI (anatomical, functional, diffusion) and PET, in the future, EEG/MEG.
For each modality, Clinica allows to easily extract various types of features (regional measures, parametric maps, surfaces, curves, networks). Such features are then subsequently used as input of machine learning, statistical modeling, morphometry or network analysis methods. Clinica also provides an integrated data management specification to store raw and processing data. Overall, Clinica helps to: i) apply advanced analysis tools to clinical research studies, ii) easily share data and results, iii) make research more reproducible.

Contacts: olivier [dot] colliot [at] inria [dot] fr

Some papers using Clinica:

 

  1. T. Jacquemont, et al. Amyloidosis and neurodegeneration result in distinct structural connectivity patterns in mild cognitive impairment. Neurobiology of Aging, Elsevier, 2017.
  2. A. Bertrand, et al. Early Cognitive, Structural, and Microstructural Changes in Presymptomatic C9orf72 Carriers Younger Than 40 Years. JAMA Neurol, 2017.

 

Deformetrica

Deformetrica_logo_altoDeformetrica is a software for the statistical analysis of 2D and 3D shape data. It essentially computes deformations of the 2D or 3D ambient space, which, in turn, warp any object embedded in this space, whether this object is a curve, a surface, a structured or unstructured set of points, or any combination of them.

Contacts: stanley [dot] durrleman [at] inria [dot] fr

Reference: S. Durrleman et al. Morphometry of anatomical shape complexes with dense deformations and sparse parameters. NeuroImage. 101(1): 35-49, 2014.