Restricted access applications

Constellation: Connectivity-based Parcellation

Cortex parcellation based on structural connectivity information. It performs group-wise parcellations, either on a “group-only” basis (one group result), or provides individual results, from a group analysis. The whole cortex is parcelled by patches.

This toolbox, developed in NeuroSpin / UNATI lab, will be released “soon” when it is completely ready.

Constellation toolbox brainvisa help pages

Connectomist 2: Diffusion MRI and connectivity

Diffusion imaging processing, tractography and bundles analysis.

Connectomist-2 is developed by The UNIRS lab of NeuroSpin (Cyril Poupon), in a different software framework, but is also using Anatomist for all visualization needs. It features dMRI preprocessings (outliers detection, distortion correction), local diffusion models processing, tractography, and fibers bundles post-processing (bundles measurements, clustering...).

DISCO: constraints-based diffeomorphic registration

Diffeomorphic structural-based cortical registration: 3D registration using sulcal constraints.

DISCO toolbox brainvisa help pages

DISCO is developed both by the MeCA research group in Marseille, the hbp_logo Human Brain Project and the cati_logo CATI project labs

HighRes cortex: lamintion of the cortex

Analysis of the laminar structure of the cortex in high resolution MRI

For now it is a development library and tools, available on a public sources repository:

Nuclear imaging toolbox

A toolbox for BrainVISA developed by the cati_logo CATI project labs

Baby toolbox

Semi-automatic segmentation toolbox for T2-weighted neonatal MRI images. This toolbox has been developed in Neurospin in the Developing Brain team. It is derived from Morphologist with adaptations to take into account the T2-weighted image contrast, the partially myelinated nature of baby brains, thus involving some steps of manual corrections, alterning automatic and interactive parts.

The toolbox is used internally and has no public release up to now.

Primate segmentation toolbox

A segmentation toolbox dedicated to primate brain images is currently developed in MirCen, BioPicsel team. It is based on the Morphologist pipeline steps, with alternative or adapted steps, dedicated to primate (mainly macaque) brains, and to T2 contrasts.

SACHA: Hippocampus segmentation and morphometry


Automatic segmentation of hippocampus and amygdalia. Developed by the Aramis team, ICM, Paris.

WHASA: White matter hyper-intensities segmentation

Developed by the Aramis team, ICM, Paris.