In Summary

Brain Connectivity and Behaviour toolkit (Foulon et al. 2018 ) is a free and open-source software package based on open source libraries which aims to provide the scientific community with the several tools to indirectly assess brain disconnections. Subscribe to the mailing list to receive updates.

BCB toolkit includes:

Tractotron (standalone version): For a given lesion, Tractotron provides a probability (but not the severity) of disconnection for almost all known tracts.

Disconnectome maps (standalone version): For a given lesion, disconnectome map provides a map  indicating a probability to be disconnected for every voxel of the MNI152

Normalisation (standalone version) based on ANTs scripts, normalisation is adapted to use a mask to register patients with lesions to the MNI152. This is a long and very strong registration based on diffeomorphic algorithms.

Cortical Thickness (standalone version) based on ANTs scripts. Cortical Thickness will produce a map indicating the thickness of the cortex.

AnaCOM2 (requires R language) AnaCOM2 aims at establishing structure–function relationships by comparing neuropsychological scores between patients and healthy controls.

Funcon-Preprocessing (requires FSL) Removing of the head motion and other artifacts on fMRI raw data.

Funcon-Connectivity (requires FSL) Calculation of the functional connectivity on fMRI data from seeds regions to a target area.

If you are on OSX:

To launch the BCBtoolkit, double-click on the script : BCBToolKit.command

Note for Catalina users

you might have come across difficulties for running BCBtoolkit as well as many other softwares.

We found an easy fix.

+ Open your terminal and run the following command: sudo spctl --master-disable

You will need to provide your administrator password.

If you are on Linux:

To launch the BCBtoolkit, double-click on the script : (Or launch it in terminal if .sh scripts are not directly executable by double-click on your OS)

You can access to the entire file tree of the BCBtoolkit in tree.txt and a summary here:


the root of the toolkit with readme, license and information files etc ...


the launching script

├── sources.jar

the compiled java executable

├── Sources

the folder containing the uncompiled java sources

├── Tools

│   ├── binaries

│   │   ├── ANTs

the ANTs software

│   │   ├── bin

binaries used for the standalone modules

│   │   ├── data

data imported from the FSL library, templates, gray matter masks etc ...

│   │   └── ICA-AROMA-master

the ICA-AROMA software

│   ├── extraFiles

configuration file, templates, priors etc ...

│   │   ├── Hypertron

healthy control tractographies used for disconnectome maps

│   ├── libraries

required libraries for binaries from fsl

│   ├── scripts

sources of the bash and R scripts of the BCBtoolkit

├── Tracts

atlas of white matter tracts from Rojkova et al., BSF 2015