SCIL tools

SCIL flows

Most of the SCIL pipelines are based on Nextflow pipeline engine and container systems such as Singularity or Docker and we based their name around the suffix flow.


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.


Rbx_flow (RecobundlesX) pipeline extracts bundles from a whole brain tractogram.


Tractometry_flow pipeline allows you to extract tractometry information by combining subjects’s fiber bundles and any metric in diffusion space.


ConnectoFlow is a state-of-the-art structural connectivity (connectomics) pipeline.


Bst_flow pipeline allows you to enhance fODFs to run bundle specific tractography.


freewater_flow pipeline computes FW-corrected DTI metrics.


Noddi_flow pipeline runs the NODDI priors estimation and NODDI modelling pipeline.

SCIL tools


Dmriqc_flow is our pipeline for diffusion MRI quality check. Using different profiles you’ll be able to QC any output from most scil flows mentioned above.


Combine_flows is a collection of bash scripts that glues or connects all our flows together. These scripts mostly create a valid input strucuture for a flow, based on the output structure of another flow.


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.


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

SCIL projects


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.