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.
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.
For questions or help on TractoFlow, please create a topic on Neurostars with the tractoflow
tag.
Before posting, please check the topics already created.
If you are on Linux, we recommend using the Singularity container to run TractoFlow
Prebuild Singularity images are available here:
http://scil.usherbrooke.ca/en/containers_list/
FOR DEVELOPERS: The Singularity repository is available here: singularity-TractoFlow
If you are on MacOS or Windows, we recommend using the Docker container to run TractoFlow
Prebuilt Docker images are available here:
http://scil.usherbrooke.ca/en/containers_list/
Diffusion processes
- preliminary DWI brain extraction (FSL)
- denoise DWI (Mrtrix3)
- topup (FSL)
- eddy (FSL)
- extract B0 (Scilpy)
- dwi brain extraction (FSL)
- N4 DWI (ANTs)
- crop DWI (Scilpy)
- upsample DWI (Scilpy)
- upsample B0 (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)
See USAGE or run nextflow run main.nf --help
To refer to TractoFlow, please see References
section on TractoFlow documentation