scilus / tractoflow

TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity

TractoFlow pipeline

The TractoFlow pipeline is a fully automated and reproducible dMRI processing pipeline. TractoFlow takes raw DWI, b-values, b-vectors, T1 weighted image (and a reversed phase encoded b=0 if available) to process DTI, fODF metrics and a whole brain tractogram.

Documentation:

TractoFlow documentation is available here:

https://tractoflow-documentation.readthedocs.io

This documentation presents how to install and launch TractoFlow on a local computer and a High Performance Computer.

If you are a user and NOT A DEVELOPER, we HIGHLY RECOMMEND following the instructions on the documentation website.

Support:

For questions or help on TractoFlow, please create a topic on Neurostars with the tractoflow tag.

Before posting, please check the topics already created.

Singularity

If you are on Linux, we recommend using the Singularity container to run TractoFlow

Prebuild Singularity images are available here:

https://scil.usherbrooke.ca/pages/containers/

FOR DEVELOPERS: The containers repository is available here: containers-scilus

Docker

If you are on MacOS or Windows, we recommend using the Docker container to run TractoFlow

Prebuilt Docker images are available here:

https://hub.docker.com/r/scilus/scilus

FOR DEVELOPERS: The containers repository is available here: containers-scilus

Steps

Diffusion processes

• preliminary DWI brain extraction (FSL)
• denoise DWI (Mrtrix3)
• gibbs correction (Mrtrix3)
• topup (FSL)
• eddy (FSL)
• extract B0 (Scilpy)
• dwi brain extraction (FSL)
• N4 DWI (ANTs)
• crop DWI (Scilpy)
• upsample DWI (Scilpy)
• upsample B0 (Scilpy)
• extract SH fitted to DWI (Scilpy)

T1 processes

• denoise T1 (Scilpy)
• N4 T1 (ANTs)
• resample T1 (Scilpy)
• T1 brain extraction (ANTs)
• crop T1 (Scilpy)
• registration on diffusion (ANTs)
• tissue segmentation (FSL)

Metrics processes

• extract DTI shells (configurable in nextflow.config) (Scilpy)
• dti metrics (Scilpy)
• extract fODF shells (configurable in nextflow.config) (Scilpy)
• compute fiber response function (Scilpy)
• mean fiber response function (Scilpy)
• fODF and fODF-derived metrics (Scilpy)
• particle filter tractography maps (Scilpy)
• seeding mask (Scilpy)
• particle filter tracking (Scilpy)

Usage

See USAGE or run nextflow run main.nf --help

References

To refer to TractoFlow, please see References section on TractoFlow documentation