Our tools


TractoFlow is our recommended processing pipeline, starting from raw DWI up to the generation of whole brain tractograms. It is robust, efficient and fully reproducible, leveraging the Nextflow pipeline engine and container systems such as Singularity or Docker.


Scilpy is a lightweight Diffusion Imaging processing library developed for the needs of members and collaborators of the SCIL. It mainly contains wrappers for DIPY functionalities, as well as tools not already integrated into Dipy.


The SCIL distributes a few containers that can be used to run the TractoFlow pipeline, as well as easily interact with various diffusion MRI focused tools. See the containers list for downloads.


The SCIL has contributed to, and highly recommends, MI-Brain as a visualization and interaction tool for Diffusion MRI and neuroimaging datasets.


The Tractometer is our online evaluation system for tractography. It has been used in various challenges. Code of the ISMRM 2015 tractography challenge can be seen here.